Identifying new therapeutic agents

A method of screening a test compound, which, when complexed to a presenter protein, binds to a target protein, the method comprising:

• (a) providing the Test Compound;
• (b) contacting the Test Compound with (i) a presenter protein, and (ii) a target protein that is not mTOR or calcineurin, under conditions suitable for formation of a binary complex comprising the Test Compound and the presenter protein;
• and
• (c) determining whether the Test Compound, when complexed to the presenter protein, binds the target protein with at least a two-fold increase in affinity relative to the affinity of the Test Compound for the target protein in the absence of the presenter protein,
• wherein the Test Compound has the formula:
• wherein
• each L is independently a bond or a bivalent substituted or unsubstituted portion of the Test Compound;
• the TIS is a Target Interacting Site that contacts one or more corresponding interacting sites on the target protein;
• and
• the PIS is a Presenter Interacting Site that contacts one or more corresponding interacting sites on the presenter protein, and wherein the PIS comprises the formula selected from the formulas consisting of (A), (B) and (C):
• wherein:
• J is hydrogen or (C1-C2) alkyl;
• K is (C1-C4)-straight or branched alkyl, benzyl or cyclohexylmethyl;
• or
• wherein J and K may be taken together to form a 5-7 membered heterocyclic ring which may contain an O, S, SO or SO2 substituent therein;
• the stereochemistry at carbon position 1 is R or S;
• X is selected from —NH—, —N(alkyl)-, —O—, —C(O)—, —CHOH—, —CH═, or —CH2—;
• Y is selected from —C(O)NH—, —C(O)N(alkyl)-, —C(O)O—, —C(O)C(O)—, —C(O)CHOH—, —C(O)CH═, —C(O)CH2—, and —S(O)2;
• and
• represents a single or a double bond;
• and the points of attachment to the rest of the compound are through a terminus of each L;
• wherein:
• each X is independently selected from —NH—, —N(alkyl)-, —O—, —C(O)—, —CHOH—, or —CH2—;
• and
• the points of attachment to the rest of the compound is by a covalent bond to a terminus of each L;
• and
• wherein:
• each X is independently selected from —NH—, —N(alkyl)-, —O—, —C(O)—, —CHOH—, or —CH2—,
• R1 is selected from (C1-C6)-alkyl, (C1-C6)-alkenyl, (C1-C6)-alkynyl, aryl, (C3-C7)-carbocyclyl, —(C1-C4 alkylene)-aryl, and —(C1-C4 alkylene)-(C3-C7) carbocyclyl;
• each R2 is independently selected from halo, —C≡N, C1-C4 alkyl, ═O, C3-C7 cycloalkyl, C1-C4 alkyl, —OH, —O—(C1-C4 alkyl)-, —SH, —S—(C1-C4 alkyl), —(C1-C4 alkyl)-N(Rb)(Rb), —N(Rb)(Rb), —O—(C1-C4 alkyl)-N(Rb)(Rb), —(C1-C4 alkyl)-O—(C1-C4 alkyl)-N(Rb)(Rb), —C(O)—N(Rb)(Rb), —(C1-C4 alkyl)-C(O)—N(Rb)(Rb), —O-(heteroaryl), —O-(heterocycle), —O-phenyl, -heteroaryl, -heterocycle, and -phenyl, wherein:
• each Rb is independently selected from hydrogen, and —C1-C4 alkyl;
• or two Rb are taken together with the nitrogen atom to which they are bound to form a 4- to 8-membered saturated heterocycle optionally comprising one additional heteroatom selected from N, S, S(═O), S(═O)2, and O,
• any alkyl substituent is optionally further substituted with one or more of —OH, —O—(C1-C4 alkyl), halo, —NH2, —NH(C1-C4 alkyl), or —N(C1-C4 alkyl)2;
• and
• any carbon atom on a phenyl, cycloalkyl, heteroaryl or heterocycle substituent is optionally further substituted with one or more of —(C1-C4 alkyl), —(C1-C4 fluoroalkyl), —OH, —O—(C1-C4 alkyl), —O—(C1-C4 fluoroalkyl), halo, —NH2, —NH(C1-C4 alkyl), or —N(C1-C4 alkyl)2;
• m is 0, 1, 2 or 3;
• and
• the points of attachment to the rest of the compound is by a covalent bond to a terminus of each L;
• wherein each L is independently selected from a bond and a linear chain of up to 10 atoms, independently selected from carbon, nitrogen, oxygen, sulfur or phosphorous atoms, wherein each atom in the chain is optionally substituted with one or more substituents independently selected from alkyl, alkenyl, alkynyl, aryl, heteroaryl, chloro, iodo, bromo, fluoro, hydroxy, alkoxy, aryloxy, carboxy, amino, alkylamino, dialkylamino, acylamino, carboxamido, cyano, oxo, thio, alkylthio, arylthio, acylthio, alkylsulfonate, arylsulfonate, phosphoryl, and sulfonyl, and wherein any two atoms in the chain may be taken together with the substituents bound thereto to form a ring, wherein the ring may be further substituted and/or fused to one or more optionally substituted carbocyclic, heterocyclic, aryl or heteroaryl rings;
• wherein when the PIS has formula (A) or (C), the presenter protein is a member of the FKBP family, and when the PIS has formula (B), the presenter protein is a member of the cyclophilin family, and
• wherein the Test Compound is between 10 and 40 ring atoms and wherein each of the ring atoms is selected from the group consisting of oxygen, nitrogen, carbon, sulfur, and phosphorus.