WO2011150500A1 - Cyclic amino acid molecules containing aziridine amino acids and methods of preparing same - Google Patents

Abstract

Cyclic amino acid molecules containing aziridine amino acids are provided, as well as methods of preparing same. Linear peptides containing aziridine amino acids and methods of preparing same are also provided.

Description

CYCLIC AMINO ACID MOLECULES CONTAINING AZIRIDINE AMINO ACIDS

AND METHODS OF PREPARING SAME

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No. 61 /349,864, filed May 30, 2010, the contents of which are hereby incorporated by reference in its entirety.

FIELD

The present invention relates to cyclic amino acid molecules and methods of preparing same, and in particular cyclic amino acid molecules containing aziridine amino acids and methods of preparing same. BACKGROUND

1 2

Peptides control a vast range of intra- and intercellular processes. ' In contrast to linear peptides, cyclic variants are more resistant to both exo- and endoproteases,^3'4 which explains the potential of this class of molecules as therapeutics and as molecular probes in chemical biology.⁵'⁶'⁷ Peptide macrocycles have shown remarkable capacity for functional fine-tuning. Once the amino acid sequence involved in target binding is known, high levels of specificity can be attained by adjusting the peptide conformation. For example, Cilengitide, a cyclic pentapeptide containing an RGD fragment, inhibits angiogenesis by targeting (¾,/¾ receptors on the surfaces of cancer cells.⁸ A simple change from a penta- to a hexapeptide macrocycle equipped with the RGD fragment switches the selectivity from the α_ν/¾ receptor towards the aubft receptor.

Amino acid residues, the main constituents of peptide macrocycles, participate in "native" interactions with protein targets.⁹ Interrogation of protein-protein interactions using these cyclic molecules is arguably their most attractive application.¹⁰ Cyclic peptides are widely used as molecular scaffolds that mimic and stabilize secondary peptide structures such as oc- helices, β-turns, γ-turns, and β-sheets, which gives rise to a multitude of closely related, low energy peptide conformers. The resulting molecules can effectively represent different regions of protein loops and grooves, accurately recreating inter-surface binding elements. ⁿ '¹²'^{1 3} Cyclic peptides can be difficult to prepare using traditional synthetic methods. This is because the ground state E geometry of the amide bond makes it challenging to attain the ring-like conformation conducive to cyclization. We have been interested in developing general strategies for constraining linear peptides into their macrocyclic forms. Recently, we resorted to amphoteric aziridine aldehydes

Nucleophilic

and Ugi four-component condensation to achieve this goal.¹⁴'¹⁵'¹⁶ While this method is effective, there remains a need for further synthetic methods for the preparation of cyclic amino acid molecules.

SUMMARY OF THE INVENTION

In one aspect, there is provided a process for preparing a cyclic peptide, the process comprising: reacting a compound of formula (I):

wherein

n = 0 or 1 ,

Ri , R₂, R , R4 and R5 are independently selected from H; lower alkyl; aryl; heteroaryl; alkenyl; heterocycle; esters of the formula -C(0)OR^* wherein R^* is selected from alkyl and aryl; amides of the formula -C(0)NR^**R^***, wherein R^** and R^*** are independently selected from alkyl and aryl; -CH₂C(0)R, wherein R is selected from lower alkyl, aryl, -loweralkyl- aryl, or -NR_aR_b, where R_a and R_b are independently selected from H, lower alkyl, aryl or - loweralkyl-aryl; -C(0)R_c, wherein R_c is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-ORd, wherein Rj is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents,

PG] is an allyl-based protecting group,

the (amino acid molecule 1 ) is an amino acid, a linear peptide or a salt of the foregoing, wherein N' is the nitrogen at the amino temiinus end of the (amino acid molecule 1 ) and C is the carbon at the carboxy terminus end of the (amino acid molecule 1 );

R' is an amino acid side chain of the amino temiinus amino acid;

R^z is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R and R' combine to form a cycloalkyl ring, preferably a cyclopentyl ring; with a compound of formula (II):

wherein

PG₂ is an allyl-based protecting group,

R^A is an amino acid side chain;

R^ZA is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^ZA and R^A combine to form a cycloalkyl ring, preferably a cyclopentyl ring; to form a compound of formula (III):

wherein PG₂, R^ZA, R^A, R, -R₅, n, N\ R^z, R', (amino acid molecule 1 ), C\ and PGj are as defined above; deprotecting the allyl-based protecting groups PGi and PG₂ to form a compound of formula (IV):

wherein R^ZA, R^A, R,-R₅, n, N', R^z, R', (amino acid molecule 1), and C are as defined above,

or a salt thereof; and cyclizing the compound of formula (IV) to form a cyclic peptide of formula (V):

wherein R^ZA, R^A, R1-R5, n, N\ R^z, R', (amino acid molecule 1 ), and C are as defined above.

In another aspect, there is provided a compound of formula (III):

Ri R, R₅ molecule 1 (III)

z, R', (amino acid molecule 1), and C are as defined above,

In still yet another aspect, there is provided a compound of formula (IV):

wherein R , R^A, R₁ -R5, n, N\ R^z, R', (amino acid molecule 1), and C are defined above,

or a salt thereof.

In another aspect, there is provided a process for preparing a cyclic peptide, the process comprising: reacting a compound of formula (VI):

wherein

n = 0 or 1,

Ri, R₂, R3, R and R₅ are independently selected from H; lower alkyl; aryl; heteroaryl; alkenyl; heterocycle; esters of the formula -C(0)OR^* wherein R^* is selected from alkyl and aryl; amides of the formula -C(0)NR R , wherein R and R are independently selected from alkyl and aryl; -CH₂C(0)R, wherein R is selected from lower alkyl, aryl, -loweralkyl- aryl, or -NR_aRb, where R_a and R_b are independently selected from H, lower alkyl, aryl or - loweralkyl-aryl; -C(0)R_c, wherein R_c is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-OR^, wherein R^ is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents, and

PG] is an allyl-based protecting group; with a compound of formula (VII):

mo ecu e / (VII) wherein

PG₂ is an allyl-based protecting group,

the (amino acid molecule 2) is an amino acid, a linear peptide or a salt of the foregoing, wherein N" is the nitrogen at the amino terminus end of the (amino acid molecule 2) and C" is the carbon at the carboxy terminus end of the (amino acid molecule 2);

R^A is an amino acid side chain of the amino terminus amino acid; R^ZA is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or Pv^ZA and R^A combine to form a cycloalkyl ring, preferably a cyclopentyl ring; to form a compound of formula (VIII):

wherein PG₂, R^ZA, R^A, N", (amino acid molecule 2), C", Ri -R₅, n, and PG, are as defined above; deprotecting the allyl-based protecting groups PGi and PG₂ to form a compound of formula (IX):

wherein R^ZA, R^A, N", (amino acid molecule 2), C", R₁-R₅, and n are as defined above, or a salt thereof; and cyclizing the compound of formula (IX) to form a cyclic peptide of formula (X):

wherein R , R^A, N", (amino acid molecule 2), C", R₁-R₅, and n are as defined above, provided that the (amino acid molecule 2) is not a dipeptide or a salt thereof.

In another aspect, there is rovided a compound of formula (VIII)

wherein R^ZA R^A N" amino acid molecule 2), C", R₁ -R₅, and n are as defined above,

In yet another aspect, there is provided a compound of formula (IX):

wherein R , R , N", (amino acid molecule 2), C" , R1 -R5, and n are as defined above,

or a salt thereof.

In still yet another aspect, there is provided a compound of formula (XIV):

amino acid

molecule

wherein

n = 0 or 1 ,

Ri , R₂, R3, R4 and R5 are independently selected from H; lower alkyl; aryl; heteroaryl; alkeriyl; heterocycle; esters of the formula -C(0)OR* wherein R* is selected from alkyl and aryl; amides of the formula -C(0)NR**R***, wherein R** and R*** are independently selected from alkyl and aryl; -CH₂C(0)R, wherein R is selected from lower alkyl, aryl, -loweralkyl- aryl, or -NR_aRb, where R_a and Rb are independently selected from H, lower alkyl, aryl or - loweralkyl-aryl; -C(0)Rc, wherein R is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-ORd, wherein R_d is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents,

the (amino acid molecule) is an amino acid, a linear peptide or a salt of the foregoing, wherein N' is the nitrogen at the amino terminus end of the (amino acid molecule) and C is the carbon at the carboxy terminus end of the (amino acid molecule);

R' is an amino acid side chain of the amino terminus amino acid; R^z is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^z and R' combine to form a cycloalkyl ring, preferably a cyclopentyl ring. BRIEF DESCRIPTION OF THE FIGURES:

Embodiments of the invention may best be understood by referring to the following description and accompanying drawings. In the description and drawings, like numerals refer to like structures or processes. In the drawings:

FIG. 1 shows suitable allyl-based protecting groups for use in the processes described herein, wherein the C-terminal ester protecting group (PGi) for the aziridine (Azy)-amino acid- containing linear peptides is drawn on the left, while its corresponding carbamate on the right would be used to protect the N-terminus (PG₂).

1

FIG. 2 shows the H NMR spectrum for compound (2).

1 1 3

FIG. 3 shows the (A) H and (B) C NMR spectra for compound (3). FIG. 4 shows the (Α)Ή and (B)'³C NMR spectra for compound (4).

1 1 3

FIG. 5 shows the (A) H and (B) C NMR spectra for compound (6).

1 1 3

FIG. 6 shows the (A) H and (B) C NMR spectra for compound (7).

1 1 3

FIG. 7 shows the (A) H and (B) C NMR spectra for compound (3a).

1

FIG. 8 shows the H NMR spectaim for compound (4a). FIG. 9 shows the (Α)Ή and (B)'³C NMR spectra for compound (5a).

DETAILED DESCRIPTION

There is described herein a general method to incorporate the unnatural and highly reactive amino acid, aziridine-2-carboxylic acid (Azy) into the backbone of homodetic cyclic peptides. These constrained macrocycles may be synthesized in solution. The Azy-amino W acid is first incorporated into the backbone of a linear peptide, and after deprotection of the N- and C-termini the molecule can be cyclized in an end-to-end fashion with a coupling reagent.

Unless defined otherwise, all technical and scientific terms and any acronyms used herein have the same meanings as commonly understood by one of ordinary skill in the art in the field of the invention.

As used herein, the term "amino acid molecule" is meant to include single amino acids and also peptides.

As used herein, the term "amino acid" refers to molecules containing an amine group, a carboxylic acid group and a side chain that varies. Amino acid is meant to include not only the twenty amino acids commonly found in proteins but also non-standard amino acids and unnatural amino acid derivatives known to those of skill in the art, and therefore includes, but is not limited to, alpha, beta and gamma amino acids. Peptides are polymers of at least two amino acids and may include standard, non-standard, and unnatural amino acids. The term "suitable substituent" as used in the context of the present invention is meant to include independently H; hydroxyl; cyano; alkyl, such as lower alkyl, such as methyl, ethyl, propyl, n-butyl, t-butyl, hexyl and the like; alkoxy, such as lower alkoxy such as methoxy, ethoxy, and the like; aryloxy, such as phenoxy and the like; vinyl; alkenyl, such as hexenyl and the like; alkynyl; formyl; haloalkyl, such as lower haloalkyl which includes CF₃, CC1₃ and the like; halide; aryl, such as phenyl and napthyl; heteroaryl, such as thienyl and furanyl and the like; amide such as C(0)NR_aR_b, where R_a and R are independently selected from lower alkyl, aryl or benzyl, and the like; acyl, such as C(0)-C₆H5, and the like; ester such as - C(0)OCH₃ the like; ethers and thioethers, such as O-Bn and the like; thioalkoxy; phosphino; and - NR_aRb, where R_a and R_b are independently selected from lower alkyl, aryl or benzyl, and the like. It is to be understood that a suitable substituent as used in the context of the present invention is meant to denote a substituent that does not interfere with the formation of the desired product by the processes of the present invention.

As used in the context of the present invention, the term "lower alkyl" as used herein either alone or in combination with another substituent means acyclic, straight or branched chain alkyl substituent containing from one to six carbons and includes for example, methyl, ethyl, 1 -methyl ethyl, 1-methylpropyl, 2-methylpropyl, and the like. A similar use of the term is to be understood for "lower alkoxy", "lower thioalkyl", "lower alkenyl" and the like in respect of the number of carbon atoms. For example, "lower alkoxy" as used herein includes methoxy, ethoxy, i-butoxy. The term "alkyl" encompasses lower alkyl, and also includes alkyl groups having more than six carbon atoms, such as, for example, acyclic, straight or branched chain alkyl substituents having seven to ten carbon atoms.

The term "aryl" as used herein, either alone or in combination with another substituent, means an aromatic monocyclic system or an aromatic polycyclic system. For example, the term "aryl" includes a phenyl or a napthyl ring, and may also include larger aromatic polycyclic systems, such as fluorescent (eg. anthracene) or radioactive labels and their derivatives.

The term "heteroaryl" as used herein, either alone or in combination with another substituent means a 5, 6, or 7-membered unsaturated heterocycle containing from one to 4 heteroatoms selected from nitrogen, oxygen, and sulphur and which form an aromatic system. The term "heteroaryl" also includes a polycyclic aromatic system comprising a 5, 6, or 7-membered unsaturated heterocycle containing from one to 4 heteroatoms selected from nitrogen, oxygen, and sulphur.

The term "cycloalkyl" as used herein, either alone or in combination with another substituent, means a cycloalkyl substituent that includes for example, but is not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl and cycloheptyl.

The term "cycloalkyl-alkyl-" as used herein means an alkyl radical to which a cycloalkyl radical is directly linked; and includes, but is not limited to, cyclopropylmethyl, cyclobutylmethyl, cyclopentylmethyl, 1 -cyclopentylethyl, 2-cyclopentylethyl, cyclohexylmethyl, 1 -cyclohexyl ethyl and 2-cyclohexylethyl. A similar use of the "alkyl" or "lower alkyl" terms is to be understood for aryl-alkyl-, aryl-loweralkyl- (eg. benzyl), -lower alkyl-alkenyl (eg. allyl), heteroaryl-alkyl-, and the like as used herein. For example, the term "aryl-alkyl-" means an alkyl radical, to which an aryl is bonded. Examples of aryl-alkyl- include, but are not limited to, benzyl (phenylmethyl), 1-phenylethyl, 2-phenylethyl and phenylpropyl. As used herein, the term "heterocycle", either alone or in combination with another radical, means a monovalent radical derived by removal of a hydrogen from a three- to seven-membered saturated or unsaturated (including aromatic) heterocycle containing from one to four heteroatoms selected from nitrogen, oxygen and sulfur. Examples of such heterocycles include, but are not limited to, aziridine, epoxide, azetidine, pyrrolidine, tetra- hydrofuran, thiazolidine, pyrrole, thiophene, hydantoin, diazepine, imidazole, isoxazole, thiazole, tetrazole, piperidine, piperazine, homopiperidine, homopiperazine, 1,4-dioxane, 4-morpholine, 4-thiomorpholine, pyridine, pyridine-N-oxide or pyrimidine, and the like.

The term "alkenyl", as used herein, either alone or in combination with another radical, is intended to mean an unsaturated, acyclic straight chain radical containing two or more carbon atoms, at least two of which are bonded to each other by a double bond. Examples of such radicals include, but are not limited to, ethenyl (vinyl), 1-propenyl, 2-propenyl, and l -butenyl.

The term "alkynyl", as used herein is intended to mean an unsaturated, acyclic straight chain radical containing two or more carbon atoms, at least two of which are bonded to each other by a triple bond. Examples of such radicals include, but are not limited to, ethynyl, 1 -propynyl, 2-propynyl, and 1-butynyl.

The term "alkoxy" as used herein, either alone or in combination with another radical, means the radical -0-(C]._n)alkyl wherein alkyl is as defined above containing 1 or more carbon atoms, and includes for example methoxy, ethoxy, propoxy, 1-methylethoxy, butoxy and 1 ,1 -dimethylethoxy. Where n is 1 to 6, the term "lower alkoxy" applies, as noted above, whereas the term "alkoxy" encompasses "lower alkoxy" as well as alkoxy groups where n is greater than 6 (for example, n = 7 to 10). The term "aryloxy" as used herein alone or in combination with another radical means -O-aryl, wherein aryl is defined as noted above. A peptide is a polymer of two or more amino acids. In one embodiment, the amino acids are linked exclusively via peptide bonds. In another embodiment, the peptide may be a depsipeptide.

Cyclic amino acid molecules and methods of preparing the same are described in PCT Application No. PCT/CA2010/000408, filed March 16, 2010 (published as WO/2010/105363 on September 23, 2010) to Andrei K. Yudin et al., the contents of which are hereby incorporated by reference in its entirety. The aziridine aldehyde precursors to the cyclic peptide molecules referenced above are described in PCT Application No. PCT/CA2007/001882, filed October 22, 2007 (published as WO/2008/046232 on April 24, 2008) to Andrei K. Yudin et al., the contents of which are hereby incorporated by reference in its entirety.

In one embodiment, there is provided a process for preparing a cyclic peptide, the process comprising: reacting a compound of formula (I):

wherein

n = 0 or 1 ,

Ri , P2, R₃, R4 and R₅ are independently selected from H; lower alkyl; aryl; heteroaryl; alkenyl; heterocycle; esters of the formula -C(0)OR^* wherein R^* is selected from alkyl and aryl; amides of the formula -C(0)NR R , wherein R and R are independently selected from alkyl and aryl; -CH₂C(0)R, wherein R is selected from lower alkyl, aryl, -loweralkyl- aryl, or -NR_aRb, where R_a and R are independently selected from H, lower alkyl, aryl or - loweralkyl-aryl; -C(0)Rc, wherein Rc is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-ORd, wherein R_d is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents,

PGi is an allyl-based protecting group,

the (amino acid molecule 1 ) is an amino acid, a linear peptide or a salt of the foregoing, wherein N' is the nitrogen at the amino terminus end of the (amino acid molecule 1 ) and C is the carbon at the carboxy terminus end of the (amino acid molecule 1 );

R' is an amino acid side chain of the amino terminus amino acid;

R⁷ is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^z and R' combine to form a cycloalkyl ring, preferably a cyclopentyl ring; with a compound of formula (II):

wherein

PG₂ is an allyl-based protecting group,

R^A is an amino acid side chain;

R ^A is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^ZA and R^A combine to form a cycloalkyl ring, preferably a cyclopentyl ring; to form a compound of formula (III):

wherein PG₂, R^z'\ R^A, RpR_?, n, N\ R^z, R', (amino acid molecule 1), C\ and PGi are as defined above; deprotecting the allyl-based protecting groups PGi and PG₂ to form a compound of formula (IV):

Ri ² R4 ₅ I molecule li ^0H (IV) wherein R^ZA, R^A, R₁ -R5, n, N' , R^z, R', (amino acid molecule 1), and C are as defined above,

or a salt thereof; and cyclizing the compound of formula (IV) to form a cyclic peptide of formula (V):

wherein R^ZA, R^A, R₁ -R5, n, N', R^z, R', (amino acid molecule 1), and C are as defined above.

In another embodiment, the compound of formula (I) is prepared by a process comprising: reacting a compound of formula (XI):

molecule 1 (XI) wherein

PGi , (amino acid molecule 1), N' , C, R', and R^z are as defined above,

or a salt thereof: with a compound of formula (XII):

wherein PG_N is a protecting group, preferably a trityl group, and

n, and R_\ - R₅ are as defined above; to form a compound of formula (XIII):

wherein PG_N, n, R_\- R₅, PGi, (amino acid molecule 1), N' , C\ R', and R^z are as defined above, and subsequently deprotecting the protecting group PGN to form the compound of formula (I).

Those of skill in the art will recognize that other protecting groups, such as dimethoxy trityl (DMT), could also be used for the aziridine nitrogen atom.

In another embodiment, the process comprises reacting the compound of formula (I) and the compound of formula (II) with PyBOP and DIPEA. Those of skill in the art will understand that other agents may be used in place of PyBOP, including but not limited to HBTU, TBTU, HCTU, HATU, TATU, BOP, AOP, PyAOP, BOP-C1, DPPA, EDC, DIC, DCC, FDPP, DMTMM, CDI, DEPBT, COMU, TNTU, TOTU, TPTU, PyBrOP, iso-butyl chloroformate, HAPipU, or HAPyU. Likewise, those of skill in the art will understand that NMM, 2,4,6- collidine, 2,6-lutidine, triethylamine, pyridine, or sodium bicarbonate, for example, may be used in place of DIPEA. Preferably, PyBOP and DIPEA are used.

In still yet another embodiment, the reaction between the compound of formula (I) and the compound of formula (II) is conducted in a non-nucleophilic reaction medium. Those of skill in the art will recognize that a range of non-protic solvents can be used, including but not limited to CHC1₃, CH₂C1₂, DMF, DMSO, NMP, DMA, MeCN, Ethyl acetate, diethyl ether, THF, dioxane, and benzene. Preferably, CHC1₃ is used.

In another embodiment, R^z is H. In another embodiment, R^ZA is H.

In yet another embodiment, the (amino acid molecule 1) is a linear peptide. In another embodiment, the linear peptide is between 2 and 29 amino acids in length. In still yet another embodiment, the linear peptide is a dipeptide. In another embodiment, the dipeptide is Phe- Gly. In still yet another embodiment, the (amino acid molecule 1) is a D or L amino acid selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine. In other embodiments, the (amino acid molecule 1) is an alpha-amino acid, a beta-amino acid, or a gamma-amino acid.

In another embodiment, the compound of formula (II) is a D or L amino acid having the protecting group PG₂ at the N-terminus, wherein the D or L amino acid is selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine. In other embodiments, the compound of formula (II) is an alpha-amino acid, a beta-amino acid, or a gamma-amino acid, all of which have the protecting group PG₂ at the N-terminus. In another embodiment, the compound of formula (II) is leucine having the protecting group PG₂ at the N-terminus. In another embodiment, there is provided a process for preparing a cyclic peptide, the process comprising: reacting a compound of formula (VI):

wherein

n = 0 or 1 ,

Ri , R₂, R₃, R4 and R5 are independently selected from H; lower alkyl; aryl; heteroaryl; alkenyl; heterocycle; esters of the formula C(0)OR^* wherein R^* is selected from alkyl and aryl; amides of the formula -C(0)NR^**R^***, wherein R^** and R^*** are independently selected from alkyl and aryl; -CH₂C(0)R, wherein R is selected from lower alkyl, aryl, -loweralkyl- aryl, or -NR_aR_b, where R_a and R_b are independently selected from H, lower alkyl, aryl or - loweralkyl-aryl; -C(0)R_<;, wherein P is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-ORd, wherein ¾ is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents, and

PGi is an allyl-based protecting group; with a compound of formula (VII):

molecule 2/ (VII) wherein

PG₂ is an allyl-based protecting group,

the (amino acid molecule 2) is an amino acid, a linear peptide or a salt of the foregoing, wherein N" is the nitrogen at the amino terminus end of the (amino acid molecule 2) and C" is the carbon at the carboxy terminus end of the (amino acid molecule 2);

R^A is an amino acid side chain of the amino terminus amino acid;

R^ZA is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^ZA and R^A combine to form a cycloalkyl ring, preferably a cyclopentyl ring; to form a compound of formula (VIII):

wherein PG₂, R^ZA, R^A, N", (amino acid molecule 2), C", R₁ -R5, n, and PGi are as defined above; deprotecting the allyl-based protecting groups PGi and PG₂ to form a compound of formula (IX):

wherein R , R , N", (amino acid molecule 2), C", R1 -R5, and n are as defined above, or a salt thereof; and cyclizing the compound of formula (IX) to form a cyclic peptide of formula (X):

wherein R^ZA, R^A, N", (amino acid molecule 2), C", R1 -R5, and defined above, provided that the (amino acid molecule 2) is not a dipeptide or a salt thereof.

In another embodiment, the process comprises reacting the compound of formula (VI) and the compound of formula (VII) with PyBOP and DIPEA. Those of skill in the art will understand that other agents may be used in place of PyBOP, including but not limited to HBTU, TBTU, HCTU, HATU, TATU, BOP, AOP, PyAOP, BOP-C1, DPPA, EDC, DIC, DCC, FDPP, DMTMM, CDI, DEPBT, COMU, TNTU, TOTU, TPTU, PyBrOP, iso-butyl chloroformate, HAPipU, or HAPyU. Likewise, those of skill in the art will understand that NMM, 2,4,6-collidine, 2,6-lutidine, triethylamine, pyridine, or sodium bicarbonate, for example, may be used in place of DIPEA. Preferably, PyBOP and DIPEA are used.

In another embodiment, the reaction between the compound of formula (VI) and the compound of formula (VII) is conducted in a non-nucleophilic reaction medium. Those of skill in the art will recognize that a range of non-protic solvents can be used, including but not limited to CHC1₃, CH₂C1₂, DMF, DMSO, NMP, DMA, MeCN, Ethyl acetate, diethyl ether, THF, dioxane, and benzene. Preferably, CHCI₃ is used.

In one embodiment, R^ZA is H.

In another embodiment, the (amino acid molecule 2) is a linear peptide. In yet another embodiment, the linear peptide is between 3 and 30 amino acids in length. In still yet another embodiment, the linear peptide is a tripeptide.

In another embodiment, the (amino acid molecule 2) is a D or L amino acid selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine. In other embodiments, the (amino acid molecule 2) is an alpha-amino acid, a beta-amino acid, or a gamma-amino acid.

In one embodiment, there is provided a process for preparing a cyclic peptide, the process comprising: reacting a compound of formula (I):

(I) wherein

n = 0 or 1 ,

Pvi , R₂, R₃, R4 and R₅ are independently selected from H; lower alkyl; aryl; heteroaryl; alkenyl; heterocycle; esters of the formula -C(0)OR* wherein R* is selected from alkyl and aryl; amides of the formula -C(0)NR**R***, wherein R** and R*** are independently selected from alkyl and aryl; -CH₂C(0)R, wherein R is selected from lower alkyl, aryl, -loweralkyl- aryl, or -NR_aR_b, where R_u and R_b are independently selected from H, lower alkyl, aryl or - loweralkyl-aryl; -C(0)Rc, wherein R is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-OR^, wherein R^ is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents,

PG] is an allyl-based protecting group, the (amino acid molecule 1) is an amino acid, a linear peptide or a salt of the foregoing, wherein N' is the nitrogen at the amino terminus end of the (amino acid molecule 1 ) and C is the carbon at the carboxy terminus end of the (amino acid molecule 1);

R' is an amino acid side chain of the amino terminus amino acid;

R^z is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHC¾CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^z and R' combine to form a cycloalkyl ring, preferably a cyclopentyl ring; with a compound of formula (VII):

wherein

PG₂ is an allyl-based protecting group,

the (amino acid molecule 2) is an amino acid, a linear peptide or a salt of the foregoing, wherein N" is the nitrogen at the amino terminus end of the (amino acid molecule 2) and C" is the carbon at the carboxy terminus end of the (amino acid molecule 2);

R^A is an amino acid side chain of the amino terminus amino acid;

R^ZA is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^/A and R^A combine to form a cycloalkyl ring, preferably a cyclopentyl ring; to form a compound of formula (XV):

wherein PG₂, R^ZA, R^A, N", (amino acid molecule 2), C", R1 -R5, n, N\ R^z, R', (amino acid molecule 1), C\ and PGi are as defined above; deprotecting the allyl-based protecting groups PGi and PG₂ to form a compound of formula (XVI):

wherein R^ZA, R^A, N", (amino acid molecule 2), C", R1 -R5, n, N', R^z, R', (amino acid molecule 1 ), and C are as defined above, or a salt thereof; and cyclizing the compound of formula (XVI) to form a cyclic peptide of formula (XVII):

wherein R^ZA, R^A, N", (amino acid molecule 2), C", R1 -R5, n, N', R^z, R', (amino acid molecule 1), and C are as defined above, provided that the (amino acid molecule 2) is not a dipeptide or a salt thereof.

In another embodiment, the process comprises reacting the compound of formula (I) and the compound of formula (VII) with PyBOP and DIPEA. Those of skill in the art will understand that other agents may be used in place of PyBOP, including but not limited to HBTU, TBTU, HCTU, HATU, TATU, BOP, AOP, PyAOP, BOP-C1, DPPA, EDC, DIC, DCC, FDPP, DMTMM, CDI, DEPBT, COMU, TNTU, TOTU, TPTU, PyBrOP, iso-butyl chloroformate, HAPipU, or HAPyU. Likewise, those of skill in the art will understand that NMM, 2,4,6- collidine, 2,6-lutidine, triethylamine, pyridine, or sodium bicarbonate, for example, may be used in place of DIPEA. Preferably, PyBOP and DIPEA are used.

In still yet another embodiment, the reaction between the compound of formula (I) and the compound of formula (VII) is conducted in a non-nucleophilic reaction medium. Those of skill in the art will recognize that a range of non-protic solvents can be used, including but not limited to CHC1₃, CH₂C1₂, DMF, DMSO, NMP, DMA, MeCN, Ethyl acetate, diethyl ether, THF, dioxane, and benzene. Preferably, CHCI3 is used.

In another embodiment, R^z is H. In another embodiment, R^ZA is H.

In yet another embodiment, the (amino acid molecule 1) and/or (amino acid molecule 2) is a linear peptide. In another embodiment, the sum of the amino acids in (amino acid molecule

1 ) and (amino acid molecule 2) is between 2 and 30, provided that the (amino acid molecule

2) is not a dipeptide.

In still yet another embodiment, the (amino acid molecule 1) and/or (amino acid molecule 2) is a D or L amino acid selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine. In other embodiments, the (amino acid molecule 1 ) and/or (amino acid molecule 2) is an alpha-amino acid, a beta-amino acid, or a gamma-amino acid.

The following embodiments relate to all of the above-referenced processes: · In one embodiment, n=0. In another embodiment, at least one of R1 -R3 is H. In yet another embodiment, at least two of R1 -R3 is H.

• In another embodiment, Ri is lower alkyl, preferably methyl.

• In yet another embodiment, Ri , R₂ and R3 are H.

• In still yet another embodiment,

• In a further embodiment, PG₂ is

• In still yet another embodiment, the allyl-based protecting groups PGi and PG₂ are simultaneously deprotected using Pd° in the presence of a weakly nucleophilic scavenger. Weakly nucleophilic scavengers may include but are not limited to N,N- dimethyl barbituric acid and dimedone. Preferably, the weakly nucleophilic scavenger is NN-dimethyl barbituric acid. In other embodiments, the Pd° is in the form of Pd(PPh₃)₄ or Pd₂(dba)₃. Preferably, the Pd° is in the form of Pd(PPh₃)₄. In another embodiment, the deprotecting step is conducted in a non-nucleophilic reaction medium, preferably CH₂C1₂.

• In another embodiment, the cyclizing step is effected using HATU and DIPEA.

Those of skill in the art will understand that other agents may be used in place of HATU, including but not limited to TBTU, HCTU, HBTU, TATU, BOP, PyBOP, AOP, PyAOP, BOP-Cl, DPPA, EDC, DIC, DCC, FDPP, DMTMM, CDI, DEPBT, COMU, TNTU, TOTU, TPTU, PyBrOP, iso-butyl chloroformate, HAPipU, or HAPyU. Likewise, those of skill in the art will understand that NMM, 2,4,6- collidine, 2,6-lutidine, triethylamine, pyridine, or sodium bicarbonate, for example, may be used in place of DIPEA. Preferably, HATU and DIPEA are used in the processes outlined herein.

• In one embodiment, the cyclizing step is conducted in a non-nucleophilic reaction medium. In one embodiment, the non-nucleophilic reaction medium is selected from NMP, DMA, DMSO, or DMF. Preferably, the non-nucleophilic reaction medium is DMF.

• In another embodiment, the process is conducted at room temperature. In yet another embodiment, there is provided a compound of formula (III):

wherein R^ZA, R^A, R1 -R5, n, N\ R^z, R', (amino acid molecule 1), and C are as defined above,

PG, is V and PG₂ is O

In still yet another embodiment, there is provided a compound of formula (IV):

molecule 1 (IV) wherein R^/A, R^A, R₁ -R5, n, N', R , R', (amino acid molecule 1 ), and C are as defined above,

or a salt thereof.

In another embodiment, there is provided a compound of formula (VIII):

wherein R^ZA, R^A, N" , (amino acid molecule 2), C", R, -R₅, and n are as defined above, PG, is \ , and PG₂ is

In yet another embodiment, there is provided a compound of formula (IX):

wherein R^ZA, R^A, N", (amino acid molecule 2), C", R₁ -R5, and n are as defined above,

or a salt thereof. In yet another embodiment, there is provided a compound of formula (XV):

wherein R^ZA, R^A, N", (amino acid molecule 2), C", Ri-R₅, n, N\ R^z, R', (amino acid molecule 1 ), and C are as defined above,

is V and PG₂ is O

In still yet another embodiment, there is provided a compound of formula (XVI):

wherein R^ZA, R^A, N", (amino acid molecule 2), C", R R₅, n, N\ R^z, R', (amino acid molecule 1), and C are as defined above,

or a salt thereof.

In still yet another embodiment, there is provided a compound of formula (XVII):

wherein R^ZA, R^A, N", (amino acid molecule 2), C", R)-R₅, n, ', R^z, R',

(amino acid molecule 1 ), and C are as defined above. In still yet another embodiment, there is provided a compound of formula (XIV):

amino acid

molecule '

wherein

n = 0 or 1 ,

Ri , R₂, R3, R4 and R5 are independently selected from H; lower alkyl; aryl; heteroaryl; alkenyl; heterocycle; esters of the formula -C(0)OR* wherein R* is selected from alkyl and aryl; amides of the formula -C(0)NR R , wherein R and R are independently selected from alkyl and aryl; -CH₂C(0)R, wherein R is selected from lower alkyl, aryl, -loweralkyl- aryl, or -NR_aRb, where R_a and R_b are independently selected from H, lower alkyl, aryl or - loweralkyl-aryl; -C(0)Rc, wherein Rc is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-ORd, wherein R^ is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents,

the (amino acid molecule) is an amino acid, a linear peptide or a salt of the foregoing, wherein N' is the nitrogen at the amino terminus end of the (amino acid molecule) and C is the carbon at the carboxy terminus end of the (amino acid molecule);

R' is an amino acid side chain of the amino terminus amino acid;

R^z is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^z and R' combine to form a cycloalkyl ring, preferably a cyclopentyl ring.

In one embodiment, n=0. In another embodiment, at least one of R1 -R3 is H. In still yet another embodiment, at least two of R1 -R3 is H. In another embodiment, Ri is lower alkyl, preferably methyl. In another embodiment, Ri , R₂ and R3 are H. In yet another embodiment, R^z is H. In still yet another embodiment, the (amino acid molecule) is a linear peptide. In another embodiment, the linear peptide is between 2 and 30 amino acids in length.

In another embodiment, the (amino acid molecule) is a D or L amino acid selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine. In other embodiments, the (amino acid molecule) is an alpha-amino acid, a beta-amino acid, or a gamma-amino acid.

Those of skill in the art will recognize that the compound of formula (XIV) encompasses the compounds of formulae (V), (X), and (XVII) shown above.

A variety of allyl-based protecting groups may be used in the processes described herein. Suitable allyl-based protecting groups include but are not limited to those shown in Figure 1 , wherein the C-terminal ester protecting group (PGi ) is drawn on the left, while its

corresponding carbamate on the right would be used to protect the N-terminus (PG₂).

One would understand that cyclization, in some cases, may require and would include protecting certain peptide or amino acid side chains in manner known to a person skilled in the art. For example, any nucleophilic side chains such as in lysine or cysteine should be protected to avoid regioselectivity issues.

As illustrated in Scheme 1 , the Azy-amino acid may be incorporated at the second position relative to the N-terminus of a peptide. When Azy is incorporated at the third position, however, the resulting linear peptide may decompose upon exposure to base via a trans- acylation of the aziridine amide bond with the N-terminus of the peptide to form the corresponding diketopiperazinone. The incorporation of the Azy-amino acid at the C- terminus of a linear peptide is also possible, provided that the linear peptide is not a tripeptide. Scheme 1 : Possible positions to install Azy amino acid into a tetrapeptide

Those of skill in the art will appreciate that typical procedures for protection-deprotection of functional groups often employ some form of acid/base chemistry or the use of nucleophiles. Acylated aziridines are highly reactive towards a wide range of nucleophiles and can readily participate in trans-acylation or ring-opening reactions. Attempts to synthesize peptides containing an Azy amino acid wherein n=0 and R^R^R^H using conventional Boc or Fmoc-based peptide synthesis were not successful. Benzyl-based protecting groups also did not work, as the acylated aziridine was found to be unstable to hydrogenative conditions. Therefore, an appropriate protecting group strategy had to be established in order to incorporate Azy-amino acids into the backbone of homodetic cyclic peptides.

After exhaustive efforts focused on testing the compatibility of various protecting groups with acylated aziridines, it was hypothesized that an Azy-containing linear peptide doubly protected with an alloc group and allyl ester at the N- and C-terminus, respectively, could be deprotected mildly with Pd° in the presence of a weakly nucleophilic scavenger. N, N- dimethyl barbituric acid was shown to be a very effective scavenger and did not react with acylated aziridines, even after prolonged exposure (24 hours).

A general scheme for the synthesis of representative cyclic tetrapeptides containing Azy- amino acids is shown below (Scheme 2; R = H, CH₃). Scheme 2: Synthetic scheme for the synthesis of representative cyclic peptides

The N-Alloc protected peptide or amino acid may be prepared using standard peptide chemistry that is well known in the art. It should also be noted that Azy-containing peptides in which both ends are deprotected (such as Compound (6) as shown in Scheme 2) are stable and easy to isolate via a simple filtration.

Regarding the compound:

17 the R = C¾ derivative has been prepared and fully characterized by Galonic et al. and the same procedure was used to prepare this compound (see Examples section). The R = H derivative has been reported by Moroder and co-workers. Azy-amino acids having different patterns of substitution may be prepared according to methods known to those of skill in the art.

The procedures for cyclization are preferably conducted at room temperature. The peptide and a base are added (in separate syringes in solutions of DMF) to a solution of the coupling reagent. These are preferably added via a syringe pump at a speed of 2.5mL/hr. While Scheme 2 illustrates the incorporation of Azy-amino acids into the backbone of homodetic cyclic peptides, it is also believed that the processes described herein will be compatible with depsipeptides.

It is also possible to incorporate the Azy-amino acid at the C-terminus of a linear peptide, as shown in Scheme 3. This synthetic approach is expected to be problematic for linear tripeptides having Azy-amino acid at the C-terminus.

Scheme 3: Synthesis of C-terminal aziridine-positioned peptides - prophetic example

v.

Agam, the N-Alloc protected peptide or amino acid may be prepared using standard peptide chemistry that is well known in the art. When R^{, =}H or C¾, the N-H aziridine 2-carboxylic acid allyl ester can be prepared as shown in Scheme 4 from the commercially available N- trityl protected serine or threonine according to methods known to those of skill in the art.

The first two reactions have been described by Liu et al. (Liu, H., Pattabiraman, V.R.,

Vederas, J.C. Org. Lett. 2007, 9, 421 1 -4214) and the last reaction (trityl deprotection) has been described by Vedejs et al. (Vedejs, E., Kiapers, A., Warner, D.L., Weiss, A.H. J. Org.

Chem. 2001 , 66, 7542-7546).

Scheme 4: Synthesis of N-H aziridine 2-carboxylic acid allyl ester derivatives

O TFA (4 equiv.)

Rl Et₃SiH (4 equiv.)

O'

CH₂CI₂, 0°C, 30min.

N

H then DIPEA (5 equiv.) The following examples are illustrative of various aspects of the invention, and do not limit the broad aspects of the invention as disclosed herein.

EXAMPLES

Abbreviations and Acronyms

TLC = thin layer chromatography HATU = 2-(7-Aza-lH-benzotriazole-l - 25 yl)-l ,l ,3,3-tetramethyluronium hexa¬

NMR = nuclear magnetic resonance

fluorophosphate

spectroscopy

DIPEA = N,N-diisopropylethylamine

ESI = electrospray ionization

DMF = N,7V-dimethylformamide

RP-HPLC = Reverse-phase high

performance liquid chromatography Trityl = triphenylmethyl

TMS = tetramethylsilane 30 CH₂CI₂ = Dichloromethane Boc = /er/-butyloxycarbonyl THF = tetrahydrofuran

CHC1₃ = Chloroform EtaSiH = triethylsilane

PyBOP = benzotriazol-l-yl- NEt₃ = triethylamine

oxytripyrrolidinophosphonium

MsCl = methanesulfonyl chloride hexafluorophosphate

35 TFA = trifluoroacetic acid

Alloc = allyloxycarbonyl

DCHA = dicyclohexylamine

Pd(PPh₃)₄ = Tetrakis(triphenyl- phosphine)palladium CD₃OD = Methanol d₄

DMSO = dimethylsulfoxide rt = room temperature Azy = aziridine-2-carboxylic acid PyAOP = 2-(7-Aza-l H-benzotriazole-l - yloxy)tripyrrolidinophosphonium hexaRf = retention factor fluorophosphate

Fmoc = 9H-fluoren-9-yl-methoxycarbonyl BOP-C1 = Bis(2-oxo-3-oxazo- lidinyl)phosphonic chloride

DMT = dimethoxytrityl

DPPA = Diphenylphosphoryl azide HBTU = 2-(lH-Benzotriazole-l -yl)- 1 ,1 ,3,3-tetramethyluronium EDC = l -Ethyl-3-(3-dimethyl-amino- hexafluorophosphate propyl)carbodiimide hydrochloride

TBTU = 2-(lH-Benzotriazole-l-yl)- DIC = N,N'-Diisopropylcarbodiimide 1 , 1 ,3,3-tetramethyluronium

tetrafluoroborate DCC = N,N'-Dicyclohexylcarbodiimide

HCTU = 2-(6-Chloro-lH-benzotriazole-l - FDPP = Pentafluorophenyl diphenyl- yl)- 1.1 ,3,3-tetramethylaminium hexaphosphinate

fluorophosphate

DMTMM = 4-(4,6-Dimethoxy-l ,3,5-

TATU = 2-(7-Aza-l H-benzotriazole- l -yl)- triazin-2-yl)-4-methylmorpholinium 1 ,1 ,3.3-tetramethyluronium chloride

tetrafluoroborate

CDI = Ι, -Carbonyldiimidazole

BOP = Benzotriazole-l-yl-oxy-tris- (dimethylamino)-phosphonium hexaDEPBT = 3-(Diethylphosphoryloxy)- fluorophosphate 1 ,2,3-benzotriazin-4(3H)-one

AOP = 2-(7-Aza-lH-benzotriazole- 1 -yl) COMU = (l -Cyano-2-ethoxy-2- tris(dimethylamino)phosphonium hexa oxoethylidenaminooxy)dimethylamino- fluorophosphate mo holino-carbenium

hexafluorophosphate TNTU = 2-(5-Norborene-2,3- HAPipU = 2-(7-aza-lH-benzotriazole-l- dicarboximido)- 1 ,1,3,3- yl)-l ,l ,3,3-bis(pentamethylene)uronium tetramethyluronium tetrafluoroborate hexafluorophosphate

TOTU = O-[(Ethoxycarbonyl)- 15 HAPyU = 1 -(1-pyrrolidinyl-l H- 1 ,2,3- cyanomethylenaminoj-1 ,1 ,3,3- triazolo [4,5 -b] pyridine- 1 -ylmethylene) tetramethyluronium tetrafluoroborate pyrrolidinium hexafluorophosphate TV- oxide

TPTU = O-(l,2-dihydro-2-oxo-pyridyl)-

1 ,1 ,3,3-tetramethyluronium NMM = TV-methylmorpholine

tetrafluoroborate

20 NMP = N-methylpyrollidinone

PyBrOP = Bromo-tris-pyrrolidino- phosphonium hexafluorophosphate DMA = N, TV-Dimethyl acetamide

Materials and Methods

General Information : Reagents were purchased from Sigma- Aldrich and used as received. Chromatography: Flash column chromatography was carried out using Silicycle 230-400 mesh silica gel. Thin-layer chromatography (TLC) was performed on Macherey Nagel pre- coated glass backed TLC plates (SIL G/UV254, 0.25 mm) and visualized using a UV lamp (254 nm) and iodine stain. RP-HPLC was performed on a Waters Prep LC 4000 system with Waters 2487 dual X absorbance detector with CI 8 semi-preparative column. Nuclear magnetic resonance spectra: Ή and ¹³C NMR spectra were recorded on Varian Mercury 400 or 500 MHz spectrometers. Ή NMR spectra were referenced to TMS (0 ppm), CD₃OD (3.30 ppm) and ¹³C NMR spectra were referenced to CDC13 (77.2 ppm) and CD₃OD (49.0 ppm). Cyclic peptides aggregate at concentrations higher than 0.5-3 mM. Peak multiplicities are designated by the following abbreviations: s, singlet; bs, broad singlet; d, doublet; t, triplet; q, quartet; m, multiplet; ds, doublet of singlets; dd, doublet of doublets; ddd, doublet of doublet of doublets; bt, broad triplet; td, triplet of doublets; tdd, triplet of doublets of doublets. Mass Spectrometry: High-resolution mass spectra were obtained on a VG 70-250S (double focusing) mass spectrometer at 70 eV on a QStar XL (AB Sciex, Concord, ON, Canada) mass spectrometer with electrospray ionization (ESI) source, MS/MS and accurate mass capabilities. Low resolution mass spectra (ESI) were obtained at 60 eV, 70 eV and 100 eV. Experimental Data

(S)-allyl 2-(2-((tert-butoxycarbonyl)amino)-3-phenylpropanamido)acetate (1)

To a flame-dried lOOmL round bottom flask was added 9.17g (32mmol) of V-Boc- phenylalanine, 8.55g (32mmol) of glycine ally! ester tosylate and 16.8g (32mmol) of PyBOP, which were then suspended in 40mL of anhydrous CHCI₃ under an atmosphere of nitrogen with stirring. The solution was then cooled in an ice bath and to this was added 16.7mL (96mmol) of N,N-diisopropylethylamine dropwise. Once the addition was complete, the ice bath was removed and the solution was stirred at 23°C for 2 hours. The chloroform was then removed /; vacuo and the resulting residue was dissolved in 400mL of ethyl acetate. The solution was then washed subsequently with 200mL of 10% aqueous citric acid, 200mL of saturated aqueous sodium bicarbonate, 200mL of water and 200mL of saturated aqueous sodium chloride. The organic layer was then dried with sodium sulfate, filtered and concentrated in vacuo. The residue was purified by silica-gel flash chromatography (43% ethyl acetate in hexanes to 75% ethyl acetate in hexanes) to afford the dipeptide 1 (1 1.3 lg, 97.5%) as a white, crystalline solid. R = 0.58 (75% ethyl acetate in hexanes). Spectral information of 1 was identical to that which has been previously reported.¹⁹ (S)-l-((2-(allyloxy)-2-oxoethyl)amino)-l-oxo-3-phenylpropan-2-aminium 2,2,2- trifluoroacetate (2)

11.08g (30.6mmol) of dipeptide 1 was added to a flame dried 250mL round bottom flask and dissolved in 40mL of anhydrous dichloromethane under an atmosphere of nitrogen with stirring. The solution was cooled to -10°C in a saturated aqueous sodium chloride ice bath and to this was added 30mL (389mmol) of trifluoroacetic acid dropwise. The solution was stirred at this temperature for 2 hours, at which point TLC indicated complete consumption of the dipeptide 1. The flask was then warmed to 23"C and concentrated in vacuo (with co- evaporation of toluene to remove excess trifluoroacetic acid) to give the deprotected dipeptide 2 (10.60g, 92%) as an off-white oil that slowly precipitates over a period of several days. The product was used with further purification. 1H NMR (400 MHZ, DMSO-i/₆): δ = 9.01 (t, J = 5.8 Hz, 1H), 8.20 (br s, 3H), 7.38 - 7.23 (m, 5H), 5.92 (ddt, J= 17.3, 10.6, 5.4 Hz, 1 H), 5.34 (dd, J = 17.3, 1.7 Hz, 1H), 5.23 (dd, J = 10.5, 1.6 Hz, 1H), 4.61 (dt, J= 5.4, 1.5 Hz, 2H), 4.09 (br s, 1 H), 4.00 (dd, J = 5.8, 3.2 Hz, 2H), 3.13 (dd, J = 14.1 , 5.4 Hz, 1H), 2.96 (dd, J = 14.1, 7.9 Hz, 1 H); MS (ESI) [MH]⁺ calcd. 263.3, found 263.2

allyl 2-((S)-2-((2S,3S)-3-methyl-l-tritylaziridine-2-carboxamido)-3- phenylpropanamido)acetate (3)

To a flame-dried lOOmL round bottom flask was added 5.66g (17.2mmol) of (2S,3S)-3- methyl-l-tritylaziridine-2-carboxylic acid,¹⁷ 6.40g (17.0mmol) of dipeptide 2 and 8.94g (17.2mmol) of PyBOP, which were then suspended in 40mL of anhydrous CHC1₃ under an atmosphere of nitrogen with stirring. The solution was then cooled in an ice bath and to this was added 8.90mL (51.Ommol) of NN-diisopropylethylamine dropwise. Once the addition was complete, the ice bath was removed and the solution was stirred at 23°C for 13 hours. The chloroform was then removed in vacuo and the resulting residue was dissolved in 400mL of ethyl acetate. The solution was then washed subsequently with 200mL of 10% aqueous citric acid, 200mL of saturated aqueous sodium bicarbonate, 200mL of water and 200mL of saturated aqueous sodium chloride. The organic layer was then dried with sodium sulfate, filtered and concentrated in vacuo. The residue was purified by silica-gel flash

chromatography (1 : 1 ethyl acetate in hexanes) to afford the tripeptide 3 (9.04g, 90.4%) as a white foam. = 0.53 (1 : 1 ethyl acetate in hexanes); H¹ NMR (400 MHz, CDC1₃): δ = 7.37- 7.19 (m, 21H), 6.48 (br s, 1H), 5.95-5.85 (m, 1 H), 5.34 (dd, J= 17.2, 2.9 Hz, 1H), 5.26 (dd, J = 10.4 Hz, 2.5 Hz, 1H), 4.74 (dd, J = 13.9, 6.7 Hz, 1H), 4.63 (d, J = 5.8, 2H), 4.04 (dd, J = 18.1 , 5.5 Hz, 1H), 3.96 (dd, J = 18.1 , 5.5 Hz, 1 H), 3.30 (dd, J= 14.1, 7.2 Hz, 1H), 3.19 (dd, J= 14.1 , 6.6 Hz, 1H), 2.03 (d, J= 7.0 Hz, 1 H), 1.46 (m, 1H), 0.96 (d, J = 5.7 Hz, 3H); ¹³C NMR (100 MHz, CDCI₃): δ = 171.1 , 169.8, 168.9, 143.3, 131.6, 129.5, 129.0, 127.8, 127.4, 127.1 , 1 18.9, 75.3, 66.0, 53.8, 41.4, 38.5, 37.7, 34.8, 12.8; MS (ESI) [MH]⁺ calcd. 588.7 found, 588.7.

allyl 2-((S)-2-((2S,3S)-3-methylaziridine-2-carboxamido)-3-phenylpropanamido)acetate

(4)

4.28g (7.29mmol) of tripeptide 3 was added to a flame-dried 250mL round bottom flask and dissolved in 140mL of anhydrous dichloromethane under an atmosphere of nitrogen. 4.7mL (29mmol) of triethylsilane was then added and the solution was cooled to -10°C in a saturated aqueous sodium chloride ice bath. Once cooled, 2.24mL (29mmol) of trifluoroacetic acid was added and the solution was stirred at this temperature for 30 minutes, at which point TLC indicate complete consumption of the tripeptide 3. 6.35mL (36mmol) of N,N- diisopropylethylamine was then added dropwise at this temperature and the solution was allowed to warm to 23°C over 20 minutes. The reaction was then concentrated in vacuo and the resulting residue was purified by silica-gel flash chromatography (chloroform to 1 1% methanol in chloroform) to afford the deprotected tripeptide 4 (2.61 g, quant.) as a pale- yellow oil. R/= 0.41 (1 1 % methanol in chloroform); ^lH NMR (400 MHz, CDC1₃): δ = 7.32 - 7.16 (m, 5H), 7.04 (br s, 1H), 6.82 (br s, 1H), 5.95-5.85 (m, 1H), 5.33 (dddd, J= 17.1 , 2.8, 1 .5, 0.6 Hz, 1H), 5.26 (dddd, J = 10.4, 2.5, 1.2, 0.7 Hz, 1H), 4.71 (dd, J = 14.7, 8.1 Hz, 1H), 4.63 (d, J= 5.8 Hz, 2H), 4.06 (dd, J= 18.2, 5.3 Hz, 1H), 3.97 (dd, J = 18.2, 5.3 Hz, 1H), 3.20 (dd, J = 14.0, 6.2 Hz, 1H), 3.08 - 2.91 (m, 1H), 2.68 (br s, 1H), 2.29 (br s, 1H), 1.04 (br s, 1 H), 0.66 (d, J = 5.5 Hz, 3H); ¹³C NMR (100 MHz, CDCI₃): δ = 171 .5, 170.0, 169.1 , 136.5, 131 .4, 129.0, 128.4, 126.7, 1 18.6, 65.6, 53.6, 41.1, 37.5, 36.1 , 31.7, 12.8; MS (ESI) [MH]⁺ calcd. 346.2 found 346.2.

allyl 2-((S)-2-((2S,3S)-l-((S)-2-(((allyloxy)carbonyl)amino)-4-methylpentanoyl)-3- methylaziridine-2-carboxamido)-3-phenylpropanamido)acetate (5)

0.793g (2mmol) of N-Alloc-leucine dicyclohexylammonium (DCHA) salt was added to a lOOmL round bottom flask and suspended in 20mL of ethyl acetate with stirring. To this was added 10% aqueous phosphoric acid until all of the DCHA salt dissolved and two clear phases appear (approx. 3mL). The solution was transferred to a separatory funnel and the aqueous layer was removed. The organic layer was then subsequently washed once with 5mL of 10%) aqueous phosphoric acid and three times with 5mL of water. The organic phase was dried over sodium sulfate, filtered and concentrated in vacuo to give /V-Alloc-leucine (0.384g, 1.78mmol) as a colourless oil. This amino acid was then dissolved in lOmL of anhydrous chloroform and transferred to a flame-dried lOOmL round bottom flask containing 0.537g ( 1.55mmol) of tripeptide 4 and 0.968mg (1.86mmol) of PyBOP dissolved in 15mL of anhydrous chloroform. To this solution was added 0.8 lmL (4.65mmol) of N,N- diisopropylehtylamine dropwise and the system was stirred at 23°C for 13 hours under an atmosphere of nitrogen. The chloroform was then removed in vacuo and the residue dissolved in l OOmL of ethyl acetate. The solution was then subsequently washed with 50mL of 10% aqueous citric acid, 50mL of water and 50mL of saturated aqueous sodium chloride. The organic layer was then dried over sodium sulfate, filtered and concentrated in vacuo. The resulting residue was then purified by silica-gel flash chromatography (1 : 1 ethyl acetate to hexanes to 8:2 ethyl acetate to hexanes) to give the protected tetrapeptide 5 (0.699g, 83%) as an off-white film. R_f = 0.58 (1 : 1 ethyl acetate to hexanes); Ή NMR (400 MHz, CDC1₃): δ = 7.34 - 7.14 (m, 5H), 6.85 (t, J= 8.5 Hz, 1 H), 6.72 (d, J = 25.0 Hz, 1H), 5.99 - 5.81 (m, 2H), 5.44 (dd, J- 16.7, 8.1 Hz, 1H), 5.44 (dd, J = 16.7, 8.1 Hz, 2H), 5.37 - 5.18 (m, 4H), 4.76 (dd, J= 14.8, 8.3 Hz, 1 H), 4.63 (dd, J= 5.8, 1.2 Hz, 2H), 4.59 - 4.48 (m, 2H), 4.24 (td, J = 9.0, 5.0 Hz, 1H), 4.12 (dt, J = 17.8, 5.2 Hz, 1H), 3.94 (dd, J= 18.2, 5.1 Hz, 1H), 3.21 (dd, J = 14.2, 6.0 Hz, 1 H), 3.16 (d, J = 6.8 Hz, 1 H), 3.05 (dd, J= 14.3, 8.7 Hz, 1H), 2.86 (dt, J= 1 1.9, 5.8 Hz, 1 H), 1.79 - 1.54 (m, 3H), 0.98 (dd, J= 1 1.9, 6.1 Hz, 6H), 0.83 (d, J= 5.7 Hz, 3H); ¹ C NMR (100 MHz, CDC1₃): δ = 185.2, 171.1, 169.4, 166.8, 156.2, 136.6, 132.5, 131.5, 129.2, 128.7, 127.0, 1 18.9, 1 18.2, 66.0, 60.4, 54.5, 54.0, 41.6, 41.5, 41.3, 38.2, 37.3, 24.9, 23.0, 21.8, 21.0, 14.2, 12.5; MS (ESI) [MH]⁺ calcd. 543.3, found 543.2

2- ((S)-2-((2S,3S)-l-((S)-2-amino-4-methyJpentanoyI)-3-methylaziridine-2-carboxamido)-

3- phenylpropanamido)acetic acid (6)

0.679g (1.25mmol) of tetrapeptide 5 and 0.072g (0.063mmol) of Pd(PPh₃)₄ were added to a lOOmL flame-dried round bottom flask and dissolved in 25mL of anhydrous dichloromethane under an atmosphere of nitrogen.0.390g (2.50mmol) of N,N-dimefhylbarbituric acid was dissolved separately in 2mL of dichloromethane and added dropwise to the reaction system. After stirring for 1 hour, the deprotected tetrapeptide had precipitated out and the solution was filtered. The precipitate was washed with several milliliters of dichloromethane and dried in vacuo to yield the desired product 6 (0.516g, quant.) as an orange solid. The product was used with further purification. 1H NMR (400 MHz, DMSO-d₆): δ = 8.21 (d, J= 5.3 Hz, 1H), 8.18 (d, J= 8.8 Hz, 1H), 7.28 - 7.16 (m, 5H), 4.62 - 4.53 (m, 1H), 3.70 (d, J = 5.3 Hz, 2H), 3.47 (dd, J = 8.6, 5.2 Hz, 1H), 3.13 - 2.95 (m, 2H), 2.91 - 2.78 (m, 2H), 1.87-1.77 (m, 1H), 1.54 (ddd, J= 13.4, 8.2, 5.3 Hz, 1H), 1.43 - 1.34 (m, 1H), 0.90 (dd, J = 1 1.5, 6.6 Hz, 6H), 0.82 (d, J= 5.5 Hz, 3H); ^I C NMR (100 MHz, DMSO-i¾: δ = 183.3, 171.6, 170.9, 166.2, 138.1 , 129.5, 128.5, 126.8, 54.5, 52.8, 42.8, 42.0, 41.0, 37.8, 37.3, 24.2, 22.9, 22.2, 12.3; MS (ESI) [MH]⁺ calcd. 419.5, found 419.2

(3S,9S,12S,13S)-9-benzyl-3-isobutyl-13-methyl-l ,4,7,10- tetraazabicyclo[l 0.1.0] tridecane-2,5,8,11 -tetraone (7)

0.063g (0.165mmol) of HATU was added to a flame-dried l OOmL round bottom flask and dissolved in 30mL of anhydrous N,N-dimethylformamide under an atmosphere of nitrogen. 0.063g (0.15mmol) of tetrapeptide 6 was dissolved separately in 7.5mL of anhydrous N,N- dimethylformamide in a scintillation vial (complete dissolution was effected with the aid of sonication). In a separate scintillation vial a solution of 0.052mL (0.30mmol) of N,N- diisopropylethylamine in 7.5mL of anhydrous N,N-dimethylformamide was prepared. These two solutions were taken up separately into syringes and simultaneously added to the reaction solution with HATU at the same rate with the aid of a syringe pump (flow rate: 0.03mLmin^" ). After the solutions have been completely added, the N, N-dimethylformamide was removed by blowing over a brisk stream of nitrogen gas. The cyclic peptide 7 was purified by RP- HPLC by gradient elution with water/acetonitrile (5% to 95% acetonitrile over 60 min.) mixture buffered with 0.1 % formic acid on a C- 18 semi-preparative column. Retention time = 24 min. After lyophilization, cyclic peptide 7 was isolated (0.022g, 37%) as a white fluffy solid. ^lH NMR (400 MHz, DMSO- ₆): δ = 8.22 (br s, 1H), 7.82 (br s, 1H), 7.63 (t, J= 7.5 Hz, 1H), 7.28 - 6.89 (m, 5H), 4.87 (br s, 1H), 4.43 (br s, 1H), 3.56 (dd, J= 18.2, 8.6 Hz, 1H), 3.46 (br d, J= 13.4 Hz, 1 H), 3.19 - 3.07 (m, 1H), 2.81 (br s, 1H), 2.67 - 2.50 (m, 2H), 1.76 1 .61 (m, 1H), 1.58 - 1.40 (m, 2H), 0.84 (d, J= 6.5 Hz, 3H), 0.81 (d, J = 4.8 Hz, 3H), 0.74 (d, J - 6.4 Hz, 3H); ¹³C NMR (100 MHz, DMSO-d₆): δ = 183.8, 173.0, 169.5, 165.4, 137.9,

129.6, 127.7, 125.9, 53.8, 51.1, 50.2, 45.7, 40.9, 37.2, 36.9, 24.0, 23.4, 20.7, 13.0; MS (ESI) [MH]⁺ calcd. 401.5, found 401.2 and 423.2 [M+Na]⁺ ally! 2-((S)-3-phenyl-2-((S)-l-tritylaziridine-2-carboxamido)propanamido)acetate (3a)

The synthetic procedure was similar to that used to produce compound (3), except that the R = H protected aziridine carboxylic acid derivative was used.¹⁸ The desired product was purified by silica-gel flash chromatography (3:7 to 1 : 1 ethyl acetate in hexanes) and isolated as a white foam (61% yield). R = 0.32 (2:3 ethyl acetate in hexanes); H¹ NMR (400 MHz, CDCI₃): δ = 7.36-7.18 (m, 21H), 6.71 (s, 1 H), 5.90 (ddt, J - 16.2, 10.5, 5.8 Hz, 1H), 5.33 (dd, J= 17.2, 1.4 Hz, 1H), 5.25 (dd, J= 10.4, 1.2 Hz, 1H), 4.71 (dd, J= 14.5, 7.6 Hz, 1H), 4.63 (d, J= 5.8 Hz, 2H), 4.12 - 3.97 (m, 2H), 3.25 (dd, J = 14.3, 6.6 Hz, 1H), 3.19 (dd, J = 14.2, 7.9 Hz, 1H), 1.95 (dd, J- 6.5, 2.6 Hz, 1H), 1.46 (d, J= 2.2 Hz, 1H), 1.29 (d, J= 6.8 Hz, 1H); ¹³C NMR (100 MHz, CDC1₃): δ = 171.24, 171.16, 169.02, 143.05, 136.44, 131.54, 129.33, 129.24, 128.72, 127.71 , 127.08, 1 18.76, 74.42, 65.84, 53.15, 41.29, 37.51, 33.66, 29.66; MS (ESI) [MH]⁺ calcd. 574.7 found, 574.7. allyl 2-((S)-2-((S)-aziridine-2-carboxamido)-3-phenylpropanamido)acetate (4a)

The synthetic procedure was similar to that used to produce compound (4). The desired product was purified by silica-gel flash chromatography (chloroform to 0% methanol in chloroform) and isolated as a white solid (77% yield). R = 0.37 (10% methanol in chloroform); H¹ NM (400 MHz, CDC1₃): δ = 7.37 - 7.12 (m, 5H), 6.90 (d, J= 7.8 Hz, 1H), 6.68 (bs, 1H), 6.58 (bs, 1H), 6.15 (bs, 1H), 5.90 (m, 1H), 5.33 (d, J= 17.2 Hz, 1H), 5.27 (d, J = 10.4 Hz, 1H), 4.73 (dd, J= 14.1 , 7.3 Hz, 1 H), 4.67 - 4.55 (m, 2H), 4.13 - 3.89 (m, 3H), 3.26 - 3.04 (m, 2H), 2.93 (dd, J= 14.2, 9.0 Hz, 1H), 2.68 - 2.58 (m, 1H), 2.34 - 2.25 (m,

1H), 2.34 - 2.25 (m, 2H), 1.74 (dd, J= 7.6, 5.5 Hz, 1H), 1.62 (d, J= 2.3 Hz, 1H), 1.19 - 1.08 (m, 2H), 0.78 (dd, J= 17.1 , 8.5 Hz, 1H); MS (ESI) [MH]⁺ = calcd. 332.4 found 332.4

allyl 2-((S)-2-((S)-l-((S)-2-(((allyloxy)carbonyl)amino)-4-methylpentanoyl)aziridine-2- carboxamido)-3-phenylpropanamido)acetate (5a)

The synthetic procedure was similar to that used to produce compound (5). The desired product was purified by silica-gel flash chromatography ( 1 : 1 to 4: 1 ethyl acetate in hexanes) and isolated as a white foam (83% yield). R = 0.44 (3:2 ethyl acetate in hexanes); H¹ NMR

(400 MHz, CDCI₃): δ = 7.34 - 7.13 (m, 5H), 6.92 (bs, 2H), 5.98 - 5.74 (m, 3H), 5.40 - 5.15

(m, 4H), 4.81 (d, J = 7.7 Hz, 1 H), 4.63 (s, 2H), 4.60 - 4.41 (m, 2H), 4.31 - 4.22 (m, 1H), 4.22 - 4.10 (m, 1 H), 3.88 (d, J = 18.0 Hz, 1H), 3.22 (dd, J = 12.7, 5.0 Hz, 1 H), 3.08 (d, J= 3.0 Hz, 1H), 2.99 (dd, J = 13.8, 8.3 Hz, 1H), 2.60 (d, J = 5.6 Hz, 1H), 1.94 (d, J = 5.7 Hz, 1H), 1.83 - 1.53 (m, 4H), 1.00 - 0.93 (m, 6H); ¹³C N R (100 MHz, CDC1₃): δ = 184.87, 171.06, 169.55, 167.37, 155.97, 136.30, 132.40, 131.34, 129.21 , 128.39, 126.84, 1 18.77, 118.05, 65.89, 54.65, 53.33, 41.35, 41.10, 37.75, 36.07, 30.42, 24.71 , 22.93, 21.48; MS (ESI) [MH]⁺ = calcd. 529.6 found 529.6

Compounds (6a) and (7a) are prepared according to methods described for compounds (6) and (7), respectively.

Although preferred embodiments of the invention have been described herein, it will be understood by those skilled in the art that variations may be made thereto without departing from the spirit of the invention or the scope of the appended claims. All references mentioned herein are incorporated by reference in their entirety.

References:

(1 ) Nomura, D.K., Dix, M.M. & Cravatt, B.F. Nat. Rev. Cancer 10, 630-638 (2010).

(2) Bromley, E.H.C., Channon, K., Moutevelis, E. & Woolfson, D.N. ACS Chem.

Biol. 3, 38-50 (2008).

(3) Fletcher, J.M., Morton, C.J., Zwar, R.A., Murray, S.S., O'Leary, P.D. & Hughes, R.A. J. Biol. Chem. 283, 33375-3383 (2008).

(4) Tyndall, J.D.A., Nail, T. & Fairlie, D.P. Chem. Rev. 105, 973-999 (2005).

(5) Frye S.V. Nat. Chem. Biol. 6, 159-161 (2010).

(6) Kwon, Y-U., Reddy, M.M. & Kodadek, T. Chem. Commun. 44, 5704-5706

(2008).

(7) Agarwal, T., Roy, S., Chakraborty, T.K. & Maiti, S. Biochemistry 49, 8388-8397 (2010).

(8) Haubner, R., Schmitt, W., Holzemann, G., Goodman, S.L., Jonczk, A. & Kessler, H. J. Am. Chem. Soc. 118, 7881 -7891 (1996). (9) London, N., Movshovitz-Attias, D. & Schueler-Furman O. Structure 18, 188-199 (2010).

(10) Driggers, E.M., Hale, S.P., Lee, J. & Terrett, N.K. Nat. Rev. Drug Discov. 7, 608- 624 (2008).

(1 1 ) Wells J.A. & McClendon C.L. Nature 450, 1001 -1009 (2007).

(12) Schafmeister, C.E., Po, J. & Verdine G.L. J. Am. Chem. Soc. 122, 5891-5892 (2000).

(13) Stewart, M.L., Fire, E., Keating, A.E. & Walensky, L.D. Nat. Chem. Biol. 6, 595- 601(2010).

(14) Hili, R., Rai, V. & Yudin, A.K. J. Am. Chem. Soc. 132, 2889-2891 (2010);

WO/2010/105363 (published September 23, 2010).

(15) Jebrail, M.J.; Ng, A. H. C; Rai, V.; Yudin, A. K.; Wheeler, A. R. Angew. Chem.

Int. Ed. 2010, 49, 8625.

(16) Rotstein, B.; Rai, V.; Hili, R.; Yudin, A. K. "Synthesis of Cyclic Peptides Using Amphoteric Amino Aldehydes," Nature Prot. 2010, 5, 1813

(17) Galonic, D. P.; Ide, N. D.; van der Donk, W. A.; Gin, D. Y. J. Am. Chem. Soc.

2005, 127, 735.

(18) Moroder et al. Tet. Lett. 1994, 15,1717.

(19) Kazmaier, U. J. Org. Chem. 1994, 59, 6667.

Additional references may also be found within the text of the Detailed Description.

Claims

CLAIMS:

1 . A process for preparing a cyclic peptide, the process comprising: reacting a compound of formula (I):

(I) wherein

n = 0 or 1 ,

Ri , R₂, R₃, R4 and R5 are independently selected from H; lower alkyl; aryl;

heteroaryl; alkenyl; heterocycle; esters of the formula -C(0)OR^* wherein R^* is selected from alkyl and aryl; amides of the formula -C(0)NR^**R^***, wherein R^** and R^*** are independently selected from alkyl and aryl; -CH₂C(0)R, wherein R is selected from lower alkyl, aryl, -loweralkyl-aryl, or -NR_aR_b, where R_a and R_b are independently selected from H, lower alkyl, aryl or -loweralkyl-aryl; -C(0)R_c, wherein R^ is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-OR_d, wherein R_<i is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents,

PGi is an allyl-based protecting group,

the (amino acid molecule 1 ) is an amino acid, a linear peptide or a salt of the foregoing, wherein N' is the nitrogen at the amino terminus end of the (amino acid molecule 1) and C is the carbon at the carboxy terminus end of the (amino acid molecule 1);

R' is an amino acid side chain of the amino terminus amino acid;

R^z is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^z and R' combine to form a cycloalkyl ring, preferably a cyclopentyl ring; with a compound of formula (II):

wherein

PG₂ is an allyl-based protecting group,

R^A is an amino acid side chain;

R^ZA is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^ZA and R^A combine to form a cycloalkyl ring, preferably a cyclopentyl ring; to form a compound of formula (III) :

wherein PG₂, R^ZA, R^A, R₁-R5, n, N\ R^z, R', (amino acid molecule 1 ), C\ and PGi are as defined above; deprotecting the allyl-based protecting groups PGi and PG₂ to form a compound of formula (IV) :

wherein R^ZA, R^A, R,-R₅, n, N', R^z, R\ (amino acid molecule 1 ), and C are as defined above,

or a salt thereof; and cyclizing the compound of formula (IV) to form a cyclic peptide of formula (V) :

wherein R , R^A, R,-R₅, n, N\ R^z, R', (amino acid molecule 1), and C are as defined above.

2. The process of claim 1 , wherein the compound of formula (I) is prepared by a process comprising: reacting a compound of formula (XI):

wherein

PGi , (amino acid molecule 1), N' , C, R\ and R^z are as defined in claim 1 , or a salt thereof; with a compound of formula (XII):

^{R1 R2} R4 Ra (xii) wherein PGN is a protecting group, preferably a trityl group, and

n, and Ri- R₅ are as defined in claim 1 ; to form a compound of formula (XIII):

wherein PGN, n, Ri - R₅, PG ] , (amino acid molecule 1 ), N' , C\ R', and R are as defined above, and subsequently deprotecting the protecting group PG to form the compound of formula (I).

3. The process of claim 1 or claim 2, wherein the process comprises reacting the compound of formula (I) and the compound of formula (II) with PyBOP and DIPEA.

4. The process of any one of claims 1 -3, wherein the reaction between the compound of formula (I) and the compound of formula (II) is conducted in a non- nucleophilic reaction medium, preferably CHC1₃.

5. The process of any one of claims 1 -4, wherein R^z and/or R^ZA is H.

6. The process of any one of claims 1 -5, wherein the (amino acid molecule 1 ) is a linear peptide. 7. The process of claim 6, wherein the linear peptide is between 2 and 29 amino acids in length.

8. The process of claim 7, wherein the linear peptide is a dipeptide.

9. The process of claim 8, wherein the dipeptide is Phe-Gly.

1 0. The process of any one of claims 1 -4, wherein the (amino acid molecule 1 ) is a D or L amino acid selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine.

1 1. The process of any one of claims 1-4, wherein the (amino acid molecule 1) is an alpha-amino acid.

12. The process of any one of claims 1-4, wherein the (amino acid molecule 1) is a beta-amino acid. 13. The process of any one of claims 1-4, wherein the (amino acid molecule 1) is a gamma-amino acid.

14. The process of any one of claims 1-13, wherein the compound of formula (II) is a D or L amino acid having the protecting group PG₂ at the N-terminus, wherein the D or L amino acid is selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine.

15. The process of any one of claims 1-13, wherein the compound of formula (II) is an alpha-amino acid having the protecting group PG₂ at the N-terminus. 16. The process of any one of claims 1-13, wherein the compound of formula (II) is a beta-amino acid having the protecting group PG₂ at the N-terminus.

1 7. The process of any one of claims 1-13, wherein the compound of formula (II) is a gamma-amino acid having the protecting group PG₂ at the N-terminus.

18. The process of any one of claims 1-13, wherein the compound of formula (II) is leucine having the protecting group PG₂ at the N-terminus.

19. A process for preparing a cyclic peptide, the process comprising: reacting a compound of formula (VI):

wherein

n = 0 or 1 , Ri , R₂, R₃, R4 and R₅ are independently selected from H; lower alkyl; aryl;

heteroaryl; alkenyl; heterocycle; esters of the formula -C(0)OR wherein R is selected from alkyl and aryl; amides of the formula -C(0)NR R , wherein R and R are independently selected from alkyl and aryl; -CH₂C(0)R, wherein R is selected from lower alkyl, aryl, -loweralkyl-aryl, or -NR_aRb, where R_a and Rb are independently selected from H, lower alkyl, aryl or -loweralkyl-aryl; -C(0)Rc, wherein Rc is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-OR_<j, wherein j is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents, and

PG] is an allyl-based protecting group; with a compound of formula (VII):

wherein

PG₂ is an allyl-based protecting group,

the (amino acid molecule 2) is an amino acid, a linear peptide or a salt of the foregoing, wherein N" is the nitrogen at the amino terminus end of the (amino acid molecule 2) and C" is the carbon at the carboxy terminus end of the (amino acid molecule 2);

R is an amino acid side chain of the amino terminus amino acid;

R is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^ZA and R^A combine to form a cycloalkyl ring, preferably a cyclopentyl ring; to form a compound of formula (VIII):

wherein PG₂, R , R^A, N", (amino acid molecule 2), C", R,-R₅, n, and PGi as defined above; deprotecting the allyl-based protecting groups PGi and PG₂ to form a compound of formula (IX):

wherein R^ZA, R^A, N", (amino acid molecule 2), C", R1 -R5, and n are as defined above, or a salt thereof; and cyclizing the compound of formula (IX) to form a cyclic peptide of formula (X):

wherein R ^A, R^A, N", (amino acid molecule 2), C", R1 -R5, and n are as defined above, provided that the (amino acid molecule 2) is not a dipeptide or a salt thereof. 20. The process of claim 19, wherein the process comprises reacting the compound of formula (VI) and the compound of formula (VII) with PyBOP and DIPEA.

21. The process of claim 19 or claim 20, wherein the reaction between the compound of formula (VI) and the compound of formula (VII) is conducted in a non-nucleophilic reaction medium, preferably CHCI3.

22. The process of any one of claims 19-21 , wherein R^ZA is H. 23. The process of any one of claims 19-22, wherein the (amino acid molecule 2) is a linear peptide.

24. The process of claim 23, wherein the linear peptide is between 3 and 30 amino acids in length.

25. The process of claim 24, wherein the linear peptide is a tripeptide. 26. The process of any one of claims 19-21 , wherein the (amino acid molecule 2) is a D or L amino acid selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine. 27. The process of any one of claims 19-21 , wherein the (amino acid molecule 2) is an alpha-amino acid.

28. The process of any one of claims 19-21 , wherein the (amino acid molecule 2) is a beta-amino acid.

29. The process of any one of claims 19-21 , wherein the (amino acid molecule 2) is a gamma-amino acid.

30. The process of any one of claims 1 -29, wherein n=0.

31 . The process of claim 30, wherein at least one of R1 -R3 is H.

32. The process of claim 31 , wherein at least two of R1 -R.3 is H.

33. The process of any one of claims 1 to 32, wherein R_\ is lower alkyl, preferably methyl.

34. The process of any one of claims 1 to 32, wherein Ri , R₂ and R₃ are H. 35 The process of any one of claims 1 to 34, wherein PGi is

36. The process of any one of claims 1 to 35, wherein PG₂ is

37. The process of any one of claims 1 to 36, wherein the allyl-based protecting groups PGi and PG₂ are simultaneously deprotected using Pd° in the presence of a weakly nucleophilic scavenger.

38. The process of claim 37, wherein the weakly nucleophilic scavenger is N,N- dimethyl barbituric acid.

39. The process of claim 37 or claim 38, wherein the Pd° is in the form of Pd(PPh₃)₄.

40. The process of any one of claims 1 -39, wherein the deprotecting step is conducted in a non-nucleophilic reaction medium, preferably CH2CI2.

41. The process of any one of claims 1 to 40, wherein the cyclizing step is effected using HATU and D1PEA.

42. The process of any one of claims 1 to 41 , wherein the cyclizing step is conducted in a non-nucleophilic reaction medium, preferably DMF. 43. The process of any one of claims 1-42, wherein the process is conducted at room temperature.

44. A compound of formula (III):

wherein R^ZA, R^A, R1 -R5, n, N', R^z, R\ (amino acid molecule 1), and C are as defined claim 1 ,

compound of formula (IV):

wherein R^7A, R^A, R1 -R5, n, N', R^z, R', (amino acid molecule 1 ), and C are as defined in claim 1 ,

or a salt thereof.

46. The compound of claim 44 or claim 45, wherein n=0.

47. The compound of any one of claims 44-46, wherein at least one of R1-R3 is H.

48. The compound of claim 47, wherein at least two of R1 -R3 is H.

49. The compound of any one of claims 44-48, wherein R] is lower alkyl, preferably methyl.

50. The compound of any one of claims 44-48, wherein R|, R₂ and R3 are H.

51. The compound of any one of claims 44-50, wherein R^/A and/or R^z is H.

52. The compound of any one of claims 44-51 , wherein the (amino acid molecule 1) is a linear peptide. 53. The compound of claim 52, wherein the linear peptide is between 2 and 29 amino acids in length.

54. The compound of any one of claims 44-50, wherein the (amino acid molecule 1 ) is a D or L amino acid selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine.

55. The compound of any one of claims 44-50, wherein the (amino acid molecule 1 ) is an alpha- amino acid.

56. The compound of any one of claims 44-50, wherein the (amino acid molecule 1 ) is a beta-amino acid.

57. The compound of any one of claims 44-50, wherein the (amino acid molecule 1) is a gamma-amino acid. 58. A compound of formula (VIII):

wherein R^ZA, R^A, N", (amino acid molecule 2), C", R1 -R5, and n are as defined in claim

A compound of formula (IX)

wherein R^ZA, R^A, N", (amino acid molecule 2), C", R1-R.5, and n are as defined in claim 19, or a salt thereof. 60. The compound of claim 58 or claim 59, wherein n=0.

61. The compound of any one of claims 58-60, wherein at least one of R1 -R3 is H.

62. The compound of claim 61 , wherein at least two of R1 -R3 is H.

63. The compound of any one of claims 58-62, wherein R_\ is lower alkyl, preferably methyl.

64. The compound of any one of claims 58-62, wherein R_\ , R₂ and R₃ are H.

65. The compound of any one of claims 58-64, wherein R^ZA is H.

66. The compound of any one of claims 58-65, wherein the (amino acid molecule 2) is a linear peptide. 67. The compound of claim 66, wherein the linear peptide is between 2 and 30 amino acids in length.

68. The compound of any one of claims 58-64, wherein the (amino acid molecule 2) is a D or L amino acid selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine.

69. The compound of any one of claims 58-64, wherein the (amino acid molecule 2) is an alpha-amino acid.

70. The compound of any one of claims 58-64, wherein the (amino acid molecule 2) is a beta-amino acid.

71. The compound of any one of claims 58-64, wherein the (amino acid molecule 2) is a gamma-amino acid.

72. A compound of formula (XIV):

amino acid

/ molecule \

wherein

n = 0 or 1 , Ri, R₂, R3, R4 and R₅ are independently selected from H; lower alkyl; aryl;

heteroaryl; alkenyl; heterocycle; esters of the formula -C(0)OR wherein R is selected from alkyl and aryl; amides of the formula -C(0)NR^**R^***, wherein R^** and R^*** are independently selected from alkyl and aryl; -CH₂C(0)R, wherein R is selected from lower alkyl, aryl, -loweralkyl-aryl, or -NR_aR_b, where R_a and R are independently selected from H, lower alkyl, aryl or -loweralkyl-aryl; -C(0)Rc, wherein R; is selected from lower alkyl, aryl or -lower alkyl-aryl; or -lower alkyl-ORd, wherein _d is a suitable protecting group or OH group; all of which are optionally substituted at one or more substitutable positions with one or more suitable substituents,

the (amino acid molecule) is an amino acid, a linear peptide or a salt of the foregoing, wherein N' is the nitrogen at the amino terminus end of the (amino acid molecule) and C is the carbon at the carboxy terminus end of the (amino acid molecule);

R' is an amino acid side chain of the amino terminus amino acid;

R^z is selected from H, NHBn, NHCH₂CH₂S0₂Ph, NHCH₂CH₂CN, or lower alkyl, preferably methyl, optionally substituted at one or more substitutable positions with one or more suitable substituents;

or R^z and R' combine to form a cycloalkyl ring, preferably a cyclopentyl ring.

73. The compound of claim 72, wherein n=0.

74. The compound of claim 72 or 73, wherein at least one of R₁ -R₃ is H.

75. The compound of claim 74, wherein at least two of R₁ -R₃ is H.

76. The compound of any one of claims 72-75, wherein Ri is lower alkyl, preferably methyl.

77. The compound of any one of claims 72-75, wherein Ri , R₂ and R₃ are H.

78. The compound of any one of claims 72-77, wherein R^z is H.

79. The compound of any one of claims 72-78, wherein the (amino acid molecule) is a linear peptide.

80. The compound of claim 79, wherein the linear peptide is between 2 and 30 amino acids in length.

81. The compound of any one of claims 72-77, wherein the (amino acid molecule) is a D or L amino acid selected from the group consisting of: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, selenocysteine, serine, tyrosine, threonine, tryptophan and valine.

82. The compound of any one of claims 72-77, wherein the (amino acid molecule) is an alpha-amino acid.

83. The compound of any one of claims 72-77, wherein the (amino acid molecule) is a beta- amino acid. 84. The compound of any one of claims 72-77, wherein the (amino acid molecule) is a gamma-amino acid.