Synthesis and composition of rapafucin libraries

Abstract

A Rapafucin library containing compounds of the general structure, (A) and (E), and a synthesis of these compounds are provided.

Description

BACKGROUND OF THE INVENTION

Field of the Invention

The invention relates generally to hybrid cyclic molecules, and more specifically to hybrid cyclic libraries based on the immunophilin ligand family of natural products FK506 and rapamycycin.

Background Information

The macrocyclic natural products FK506 and rapamycin are approved immunosuppressive drugs with important biological activities. Both have been shown to inhibit T cell activation, albeit with distinct mechanisms. In addition, rapamycin has been shown to have strong anti-proliferative activity. FK506 and rapamycin share an extraordinary mode of action; they act by recruiting an abundant and ubiquitously expressed cellular protein, the prolyl cis-trans isomerase FKBP, and the binary complexes subsequently bind to and allosterically inhibit their target proteins calcineurin and mTOR, respectively. Structurally, FK506 and rapamycin share a similar FKBP-binding domain but differ in their effector domains. In FK506 and rapamycin, nature has taught us that switching the effector domain of FK506 to that in rapamycin, it is possible to change the targets from calcineurin to mTOR. The generation of a rapafucin library of macrocytes that contain FK506 and rapamycin binding domains should have great potential as new leads for developing drugs to be used for treating diseases.

With the completion of the sequencing and annotation of the human genome, a complete catalog of all human proteins encoded in the genome is now available. The functions of a majority of these proteins, however, remain unknown. One way to elucidate the functions of these proteins is to find small molecule ligands that specifically bind to the proteins of interest and perturb their biochemical and cellular functions. Thus, a major challenge for chemical biologists today is to discover new small molecule probes for new proteins to facilitate the elucidation of their functions. The recent advance in the development of protein chips has mitered an exciting new opportunity to simultaneously screen chemical libraries against nearly the entire human proteome. A single chip, in the form of a glass slide, is sufficient to display an entire proteome in duplicate arrays. Recently, a protein chip with 17,000 human proteins displayed on a single slide has been produced. A major advantage of using human protein chips for screening is that the entire displayed proteome can be interrogated at once in a small volume of assay buffer (<3 mL). Screening of human protein chips, however, is not yet feasible with most, if not all, existing chemical libraries due to the lack of a universal readout for detecting the binding of a ligand to a protein on these chips. While it is possible to add artificial tags to individual compounds in a synthetic library, often the added tags themselves interfere with the activity of ligands. Thus, there remains a need for new compounds and methods for screening chemical libraries against the human proteome.

SUMMARY OF THE INVENTION

One embodiment of the present invention is to provide a compound of the following structure:

R₁ and R₃ can independently be any of the following compounds:

R₂ and R₄ can independently be any of the following compounds:

Another embodiment of the present invention is to provide a compound of the following structure:

R₁, R₂, R₃ and R₄ are selected from the same groupings of compounds listed above.

Another embodiment of the present invention is to provide a compound that includes A15-34-2, A15-39-1, A15-39-2, A15-39-4, A15-39-6, A15-39-8, A15-39-15, A15-40-2, A15-40-4, A15-40-15, E15-32-2, E15-33-1, E15-33-2, E15-34-1, E15-34-2, E15-39-1, E15-39-2, E15-39-5, E15-40-2, E15-40-4, E15-S-19, E15-S-21, and E15-S-22.

Another embodiment of the present invention is to provide synthetic methods as outlined in the “Detailed Description of the Invention” for producing a Rapafucin library.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Number of compounds in library.

DETAILED DESCRIPTION OF THE INVENTION

Example 1

R₁ and R₃ in Scheme 1 are amino acids selected from the following group of amino acids:

R₂ and R₄ in Scheme 1 are amino acids selected from the following group of amino acids:

The synthesis of the amide mFKBD in Scheme 1 is as follows:

The synthesis of the ether mFKBD in Scheme 1 is as follows:

The general formula for a Rapafucin with an amide mFKBD is represented by “A”.

The general formula for a Rapafucin with an ether mFKBD is represented by “E”.

Specific Examples of “A” and “E” as well as their properties are listed in Table 1.

TABLE 1
Name	Sequence	Hillslope	IC50(nM)	Name	Sequence	Hillslope	IC50(nM)
A15-39-1	Gly-dmPhe-	−0.9753	27.95	E15-40-2	Ala-dmPhe-	−1.212	34.15
	Pro-mVal				Pro-mlle
A15-39-2	Ala-dmPhe-	−1.164	23.73	E15-40-4	Nva-dmPhe-	−1.195	173.1
	Pro-mVal				Pro-mlle
A15-39-4	Nva-dmPhe-	−1.112	18	E15-32-2	Ala-dmPhe-	−1.134	66.71
	Pro-mVal				Pro-mAla
A15-39-6	Leu-dmPhe-	−1.105	54.14	E15-33-1	Gly-dmPhe-	−1.007	13.91
	Pro-mVal				Pro-mNIe
A15-39-8	Phe-dmPhe-	−1.191	54.99	E15-33-2	Ala-dmPhe-	−1.017	9.76
	Pro-mVal				Pro-mNIe
A15-39-15	Phg-dmPhe-	−0.8952	16.51	E15-34-1	Gly-dmPhe-	−1.494	28.54
	Pro-mVal				Pro-mLeu
E15-39-1	Gly-dmPhe-	−1.024	48.88	E15-34-2	Ala-dmPhe-	−0.741	10.53
	Pro-mVal				Pro-mLeu
E15-39-2	Ala-dmPhe-	−1.125	33.54	A15-34-2 **	Ala-dmPhe-	−0.3876	31.45
	Pro-mVal				Pro-mLeu
E15-39-5	HoSMe-	−0.8614	59.46	E15-S-19	Gly-dmPhe-	−1.363	42.27
	dmPhe-Pro-				Pro-mNva
	mVal
A15-40-2	Ala-dmPhe-	−0.6276	34.4	E15-S-21	Gly-dmPhe-	−1.314	154.9
	Pro-mlle				Pro-dmAla
A15-40-4	Nva-dmPhe-	−0.87	12.19	E15-S-22	Gly-dmPhe-	−1.236	261.9
	Pro-mlle				Pro-Ach
A15-40-15	Phg-dmPhe-	−0.9138	100.1
	Pro-mlle

Approximately, 45,000 compounds were obtained as part of the Rapafucin library (FIG. 1).

Although the invention has been described with reference to the above example, it will be understood that modifications and variations are encompassed within the spirit and scope of the invention. Accordingly, the invention is limited only by the following claims.

REFERENCES

The following reference is relied upon and incorporated herein in its entirety.

• 1. US 2014/0073581.

Claims

1. A compound of Formula I:

2. The compound of claim 1, wherein X2 is O and L1 is —CH2—C(O)—.

3. The compound of claim 1, wherein X2 is NR6C(O) and L1 is —(CH2)2C(O)—.

4. The compound according to claim 1, with the following formula

5. The compound according to claim 1, with the following formula