Methods for designing specific inhibitors for Pin1 proline isomerase and Pin1-related molecules
AssigneePintex Pharmaceuticals, Inc.
InventorsJanusz Sowadski, Robert K. Suto
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Abstract
This invention relates to methods for designing specific inhbitors of Pin1/parvulin family of peptidyl-prolyl cis-trans isomerases, particularly Pin1 and Pin1-related proteins, through the use of the structure coordinates and atomic details elucidated from the crystal structures of a mutant of Pin1, R14A, and co-complexes of R14A with various inhibitors. The invention further relates to inhibitors of Pin1 and Pin1-related proteins that are useful for therapeutic treatement of various disorders, and methods of using Pin1 inhibitors in pharmaceutical compositions. The invention further relates to the crystal structures of Pin1R14A alone, and of Pin1R14A in co-complex with molecules that bind to Pin1.
Claims40
A method of designing specific inhibitors of a Pin1 polypeptide, comprising the steps of:
- (a) determining the three-dimensional structures of crystallized Pin1 polypeptides in complex with small molecules;
- (b) employing the three-dimensional structures from step (a) to form an interaction template;
- (c) employing sequence and structural alignments to identify conserved amino acids among proline isomerases and distinguishing those amino acids that are specific to Pin1 to define a specificity template;
- (d) using the interaction template and the specificity template in conjunction with molecular modeling to design inhibitors specific to Pin1 or Pin1-like proline isomerases;
- and
- (e) determining the affinity and specificity of the inhibitors to Pin1.
A method for designing or selecting an inhibitor of a Pin1 polypeptide, comprising the steps of:
- a) using a three dimensional structure of a crystallized Pin1 polypeptide having a substitution, deletion or insertion of one or more amino acids of the sequence set forth in SEQ ID NO:1 to form a Pin1 interaction template;
- and
- b) employing the Pin1 interaction template to design or select the Pin1 inhibitor.
A Pin1 polypeptide in the crystallized form having a substitution, insertion or deletion of one or more amino acids of the amino acid sequence set forth in SEQ ID NO:1, wherein the active site of the Pin1 polypeptide is accessible to solvent and available for interaction with an inhibitor in a crystallized form.
A method for designing an inhibitor of a second peptidyl/prolyl isomerase comprising the steps of:
- (a) providing a first peptidyl/prolyl isomerase having a known three-dimensional structure;
- (b) identifying amino acids in the active site of said first peptidyl/prolyl isomerase that form close contacts with a compound know to bind to said active site;
- (c) employing protein alignment means to identify in a second peptidyl/prolyl isomerase one or more amino acids that align with, but differ in identity from, said close contact amino acids in said first peptidyl/prolyl isomerase;
- (d) altering an amino acid in the active site of said second peptidyl/prolyl isomerase identified in step (c) to produce a mutant second peptidyl/prolyl isomerase;
- (e) determining that said compound binds with at least 10-fold greater affinity to said mutant second peptidyl/prolyl isomerase than to said second peptidyl/prolyl isomerase, and
- (f) using molecular modeling means to determine how to modify said compound to design an inhibitor of said second peptidyl/prolyl isomerase, wherein said inhibitor binds to said second peptidyl/prolyl isomerase with at least 10-fold greater affinity than said compound binds to said peptidyl/prolyl isomerase, respectively.
Dependencies are inferred from the claim text.