PIN1 peptidyl-prolyl isomerase polypeptides, their crystal structures, and use thereof for drug design

A method of assaying a compound for its PIN1 modulating ability comprising:

• (a) adding a test compound to a polypeptide comprising a PIN1 peptidyl-prolyl isomerase, wherein said polypeptide does not contain a WW domain;
• (b) measuring said polypeptide's peptidyl-prolyl isomerase activity;
• and
• (c) determining if the activity of the polypeptide is modulated by said test compound.

A method of using a three-dimensional structure of a complex comprising a PIN1 peptidyl-prolyl isomerase polypeptide devoid of the WW domain and compound I, as defined by the structure coordinates of Table III or a portion thereof, in a drug discovery strategy comprising:

• (a) selecting a potential drug using computer-aided drug design with the three-dimensional structure determined from one or more sets of atomic coordinates in Table III, wherein said selecting is performed in conjunction with computer modeling;
• (b) contacting said potential drug with a polypeptide containing a functional PIN1 peptidyl-prolyl isomerase;
• and
• (c) detecting the binding of said potential drug with said polypeptide.

A method of using a three-dimensional structure of a complex comprising a PIN1 peptidyl-prolyl isomerase polypeptide devoid of the WW domain and compound I and as defined by the structure coordinates of Table III, or a portion thereof, in a drug discovery strategy comprising:

• (a) selecting a potential drug using computer-aided drug design with the three-dimensional structure determined from one or more sets of structure coordinates in Table III, wherein said selecting is performed in conjunction with computer modeling;
• (b) contacting said potential drug with a polypeptide containing a functional PIN1 peptidyl-prolyl isomerase;
• and
• (c) determining if said potential drug modulates the peptidyl-prolyl isomerase activity of a polypeptide containing a PIN1 peptidyl-prolyl isomerase.

A method for identifying a modulator of a molecule comprising a PIN1 PPIase substrate-binding domain comprising the steps of:

• (a) using a set of structure coordinates comprising structure coordinates of PIN1 PPIase amino acids His59, Leu61, Lys63, Ser67, Arg68, Arg69, Cys113, Leu122, Met130, Gln131, Phe134, Glu135, Thr152, Ser154, and His157, according to Table III to generate a three-dimensional structure of a molecule comprising a PIN1 PPIase or PPIase-like substrate-binding pocket;
• (b) employing said three-dimensional structure to design or select said modulator;
• (c) synthesizing or obtaining said modulator;
• and
• (d) contacting said modulator with said molecule to determine the ability of said modulator to interact with said molecule.

A method for evaluating the ability of a compound to associate with a molecule or molecular complex comprising a PIN1 PPIase substrate-binding pocket, said method comprising the steps of:

• (a) constructing a computer model of said binding pocket defined by a set of structure coordinates comprising structure coordinates of PIN1 PPIase amino acids His59, Leu61, Lys63, Ser67, Arg68, Arg69, Cys113, Leu122, Met130, Gln131, Phe134, Glu135, Thr152, Ser154, and His157 according to Table III;
• (b) selecting a compound to be evaluated by a method selected from the group consisting of (i) assembling molecular fragments into said compound, (ii) selecting a compound from a small molecule database, (iii) de novo ligand design of said compound, and (iv) modifying a known modulator, or a portion thereof, of a peptidyl-prolyl isomerase;
• (c) employing computational means to perform a fitting program operation between computer models of said compound to be evaluated and said binding pocket in order to provide an energy-minimized configuration of said compound in the binding pocket;
• and
• (d) evaluating the results of said fitting operation to quantify the association between said compound and the binding pocket model, thereby evaluating the ability of said compound to associate with said binding pocket.

A method for identifying a modulator of a molecule comprising a PIN1 PPIase substrate-binding site, comprising the steps of:

• (a) constructing a computer model of said binding pocket defined by a set of structure coordinates comprising structure coordinates of PIN1 PPIase substrate-binding site amino acids His59, Leu61, Lys63, Ser67, Arg68, Arg69, Cys113, Leu122, Met130, Gln131, Phe134, Glu135, Thr152, Ser154, and His157 according to Table III;
• (b) selecting a compound to be evaluated as a potential modulator by a method selected from the group consisting of (i) assembling molecular fragments into said compound, (ii) selecting a compound from a small molecule database, (iii) de novo ligand design of said compound, and (iv) modifying a known inhibitor, or a portion thereof, of a protein kinase;
• (c) employing computational means to perform a fitting program operation between computer models of said compound to be evaluated and said binding pocket in order to provide an energy-minimized configuration of said compound in the binding pocket;
• (d) evaluating the results of said fitting operation to quantify the association between said compound and the binding pocket model, thereby evaluating the ability of said compound to associate with said binding pocket;
• (e) synthesizing said compound;
• and
• (f) contacting said compound with said molecule to determine the ability of said compound to modulate the peptidyl-isomerase activity of said molecule.

A method for screening compounds for PIN1 PPIase modulating activity comprising the steps of:

• (a) providing an assay buffer containing a Pintide-PIN1 PPIase polypeptide complex;
• (b) adding a test compound;
• and
• (c) measuring the disruption of the Pintide-PIN1 PPIase complex.