# US 11,299,513 B2 · Cyclative release of peptidic compounds

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- Number: US 11,299,513 B2
- Document ID: US11299513B2
- Status: Granted
- Kind: B2
- Application number: 16/633,969
- Filed: 2018-07-27
- Published: 2020-07-02
- Granted: 2022-04-12
- Earliest claimed: 2017-07-28
- Assignees: Circle Pharma, Inc.
- Applicants: Circle Pharma, Inc.
- Inventors: Mahesh Ramaseshan; Andrew Bockus
- Web page: https://patentgrep.com/patent/US11299513B2

## CPC

- C07K 1/042: {characterised by the nature of the carrier}
- C07K 1/107: by chemical modification of precursor peptides
- C07K 7/64: Cyclic peptides containing only normal peptide links
- C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00)

## Abstract

The present disclosure provides efficient and reliable methods for preparing cyclized peptidic compounds. Advantageously, the currently described methods allow for on-resin cyclization using a limited number of processing steps, while increasing the chemical diversity available for the cyclized peptidic compounds produced.

## Claims

### Claim 1

A method for preparing a cyclized peptidic compound of Formula
the method comprising
forming a cyclization reaction mixture comprising a thiophilic catalyst, a non-nucleophilic base, and a compound of Formula II:
under conditions suitable to form the cyclized peptidic compound of Formula I, wherein
is a solid-phase support;
R1a is selected from the group consisting of H, NH2, C1-8 alkyl, and C3-8 cycloalkyl;
L1 is selected from the group consisting of a bond, N—H, and —O—,
provided that when R1a is NH2, then L1 is a bond; and
provided that when L1 is —O—, then R1a is H, C1-8 alkyl, or C3-8 cycloalkyl;
R1 is selected from the group consisting of H, NH2, C1-8 alkyl, and C3-8 cycloalkyl,
provided than when R1 is NH2, then L1 is a bond;
R2 is H;
L2 is selected from the group consisting of C2-8 alkylene, C3-8 cycloalkylene, 3- to 8-membered heterocycloalkylene, C6-10 arylene, and 5- to 10-membered heteroarylene, each of which is optionally substituted with from 1 to 4 substituents selected from the group consisting of C1-4 alkyl, cyano, —C(O)Ra, —C(O)ORa, —SRa, —C1-4alkyl-SRa, and oxo, wherein the heterocycoalkylene and heteroarylene each have from 1 to 3 heteroatom ring members each independently selected from the group consisting of N, O and S; and
Ra is selected from the group consisting of H and C1-8 alkyl.

### Claim 2 (depends on 1)

The method of claim 1, wherein the thiophilic catalyst is a metal thiophilic catalyst.

### Claim 3 (depends on 2)

The method of claim 2, wherein the metal thiophilic catalyst is selected from the group consisting of copper, nickel, mercury, silver, ruthenium, osmium, and strontium.

### Claim 4 (depends on 3)

The method of claim 3, wherein the metal thiophilic catalyst is silver.

### Claim 5 (depends on 1)

The method of claim 1, wherein the non-nucleophilic base is an amine non-nucleophilic base.

### Claim 6 (depends on 5)

The method of claim 5, wherein the amine non-nucleophilic base is selected from the group consisting of trimethylamine, triethylamine, diisopropylethylamine (DIPEA), 1,8-diazabicycloundec-7-ene (DBU), 2,6-di-tert-butylpyridine, and quinuclidine.

### Claim 7 (depends on 6)

The method of claim 6, wherein the amine non-nucleophilic base is DIPEA.

### Claim 8 (depends on 1)

The method of claim 1, wherein R1 is H.

### Claim 9 (depends on 1)

The method of claim 1, wherein R1 is NH2.

### Claim 10 (depends on 1)

The method of claim 1, wherein L1 is a bond.

### Claim 11 (depends on 1)

The method of claim 1, wherein R1a is H.

### Claim 12 (depends on 1)

The method of claim 1, wherein the Peptidic Unit has the structure:
wherein,
m is an integer from 2 to 10;
each X is independently selected from the group consisting of C3-8 cycloalkylene, X1—C3-8 cycloalkylene, heterocycloalkylene, X1-heterocycloalkylene, C6-10 arylene, —X1—C6-10 arylene, heteroarylene, —X1-heteroarylene,
wherein each heterocycoalkylene comprises from 3 to 8 ring members having 1 to 3 heteroatom ring members, each independently selected from N, O and S, and each heteroarylene comprises from 5 to 10 ring members having 1 to 3 heteroatom ring members, each independently selected from the group consisting of N, O and S,
wherein
each Y is independently selected from the group consisting of CH2, NR5, O, S, S(O), and S(O)2;
each n is an integer from 1 to 8;
each R3 is independently selected from the group consisting of H, halogen, cyano, C1-8 alkyl, C2-8 alkenyl, C2-8 alkynyl, C1-8 haloalkyl, —ORd, —X1—ORd, —SRb, —X1—SRb, —NRbRd, —X1—NRbRd, (O)Rb—X1—C(O)Rb, —C(O)ORb, —X1—C(O)ORb, —C(O)NRbRc, —X1—C(O)NRbRc, —OC(O)NRbRc, —X1—OC(O)NRbRc, —NRbC(O)Rc, —X1—NRbRc (O)Rc, —NRbC(O)2Rc, —X1—NRbC(O)2Rc, —NRbC(O)NRbRc, —X1—NRbC(O)NRbRc, —S(O)2NRbRc, —X1—S(O)2NRaRb, —NRbC(NH)NRbRc, —X1—NRb (NH)NRbRc, C3-8 cycloalkyl, X1—C3-8 cycloalkyl, C6-10 aryl, —X1—C6-10aryl, heterocycloalkyl, —X1-heterocycloalkyl, heteroaryl, and —X1-heteroaryl,
wherein the C3-8 cycloalkyl, C6-10 aryl, heterocycloalkyl, and heteroaryl moieties are optionally substituted with 1 to 4 substituents each independently selected from the group consisting of C1-4 alkyl, halogen, cyano, —ORb, —X1—ORb, —SRb, —X1—SRb, —NRbRd, and —X1—NRbRd,
each heterocycloalkyl comprises from 3 to 8 ring members having 1 to 3 heteroatom ring members each independently selected from the group consisting of N, O and S, and
each heteroaryl comprises 5 to 10 ring members having 1 to 3 heteroatom ring members each independently selected from the group consisting of N, O and S;
R4 is selected from the group consisting of H, C1-8 alkyl, —ORd, —NRbRd, —[C(H)(R3)]1-6 NRbRd, —X1—C(O)Rb, C(O)Rb, NH—C(O)Rb, C(O)ORb, —X1—C(O)ORb, —C(O)NRbRc, and C3-8 cycloalkyl;
each R5 is independently selected from the group consisting of H and C1-8 alkyl;
alternatively, R3 and R5 within the same X unit are combined with the atoms to which they are attached to form a 5- to 6-membered heterocycloalkyl ring having from 1 to 3 additional heteroatoms each independently selected from the group consisting of N, O and S, the 5- to 6-membered heterocycloalkyl ring is optionally further substituted with from 1 to 3 substituents independently selected from the group consisting of halogen, cyano, C1-8 alkyl, C2-8 alkenyl, C2-8 alkynyl, C1-8 haloalkyl, —ORb, —X1—ORb, —SRb, —X1—SRb, —NRbRd, —X1—NRbRd, C(O)Rb, —X1—C(O)Rb, —C(O)ORb, —X1—C(O)ORb, —C(O)NRbRc, —X1—C(O)NRbRc, —NRbC(O)Rc, —X1—NRbC(O)Rc, —NRbC(O)2Rc, —X1—NRbC(O)2Rc, —S(O)2NRbRc, or —X1—S(O)2NRaRb;
R6a and R6b are each independently selected from the group consisting of H and halogen;
R9 and R10 are each independently selected from the group consisting of H, C1-8 alkyl, and OH;
each X1 is independently C1-6alkylene;
each Rb and Rc is independently selected from the group consisting of H, C1-8 alkyl, and C1-8 haloalkyl; and
each Rd is independently selected from the group consisting of H, C1-8alkyl, C1-8 haloalkyl, and NH2.

### Claim 13 (depends on 12)

The method of claim 12, wherein each X has the structure selected from the group consisting of:

### Claim 14 (depends on 12)

The method of claim 12, wherein each X has the structure selected from the group consisting of:

### Claim 15 (depends on 12)

The method of claim 12, wherein the peptidic unit includes at least one natural amino acid.

### Claim 16 (depends on 1)

The method of claim 1, wherein L2 has a structure:
wherein,
q is an integer from 1 to 3; and
R7a, R7b and each R8a, and R8b are independently selected from the group consisting of H, C1-4alkyl, cyano, —C(O)Ra, —C(O)ORa, —C1-4alkyl-SRa, —SRa, and oxo;
alternatively, R7b and R8a are combined with the atoms to which they are attached to form a member selected from the group consisting of C3-8 cycloalkyl, C6-10 aryl, 3- to 8-membered heterocycloalkyl, and 5- to 10-membered heteroaryl,
wherein the heterocycloalkyl and heteroaryl groups each have from 1 to 3 heteroatom ring members each independently selected from the group consisting of N, O and S.

### Claim 17 (depends on 16)

The method of claim 16, wherein q is 1.

### Claim 18 (depends on 16)

The method of claim 16, wherein R7a, R7b and each R8a, and R8b are independently selected from the group consisting of H, C1-4alkyl, and —SRa.

### Claim 19 (depends on 16)

The method of claim 16, wherein R7a, R7b, and each R8a, and R8b are H.

### Claim 20 (depends on 1)

The method of claim 1, wherein the compound of Formula II has the structure of Formula IIa:

### Claim 21 (depends on 1)

The method of claim 1, wherein the compound of Formula I has the structure of Formula Ia:

### Claim 22 (depends on 1)

The method of claim 1, further comprising
forming a transfer reaction mixture comprising the compound of Formula III:
and a first acid under conditions suitable to form an intermediate of Formula IV:
wherein the intermediate of Formula IV undergoes an N- to S-acyl transfer reaction to form a compound of Formula IIb:
and
forming a deprotection reaction mixture comprising the compound of Formula IIb and a second acid under conditions suitable to form the compound of Formula II,
wherein
PG1 is a mercapto protecting group;
R1c is selected from the group consisting of NH—PG2, H, C1-8 alkyl, and C3-8 cycloalkyl;
provided that when R1c is NH2, then L1 is a bond; and
provided that when L1 is —O—, then R1c is H, C1-8 alkyl, or C3-8 cycloalkyl;
R2c is selected from the group consisting of PG2 and H,
provided that when R2c is H, then R1c is NH—PG2, and
provided that when R2c is PG2, then R1c is H, C1-8 alkyl, or C3-8 cycloalkyl; and
PG2 is an amine protecting group.

### Claim 23 (depends on 1)

The method of claim 1, further comprising forming a transfer/deprotection reaction mixture comprising the compound of Formula III:
and an acid under conditions suitable to form an intermediate of Formula IVa:
wherein the intermediate of Formula IVa undergoes an N- to S-acyl transfer reaction to form a compound of Formula II:
wherein
PG1 is a mercapto protecting group;
R1c is selected from the group consisting of NH—PG2, H, C1-8 alkyl, and C3-8 cycloalkyl;
provided that when R1c is NH2, then L1 is a bond; or
provided that when L1 is —O—, then R1c is H, C1-8 alkyl, or C3-8 cycloalkyl;
R2c is selected from the group consisting of PG2 and H,
provided that when R2c is H, then R1c is NH—PG2, or
provided that when R2c is PG2, then R1c is H, C1-8 alkyl, or C3-8 cycloalkyl; and
PG2 is an amine protecting group.

### Claim 24 (depends on 22)

The method of claim 22, further comprising:
forming a coupling reaction mixture comprising the compound of Formula V:
and a compound of Formula VI:
under Mitsunobu reaction conditions to form the compound of Formula III.

### Claim 25 (depends on 1)

The method of claim 1, wherein the compound of Formula I has the structure of Formula Ia:
the method comprising
i) forming a coupling reaction mixture comprising a compound of Formula Va:
and triisopropylsilyl (TIP S)-protected mercaptoethanol under Mitsunobu reaction conditions to form a compound of Formula IIIa:
ii) forming a transfer reaction mixture comprising the compound of Formula Ma, acetic acid, and tetra-N-butylammonium fluoride (TBAF) under conditions suitable to form an intermediate of Formula IVb:
wherein the intermediate of Formula IVb undergoes an N- to S-acyl transfer reaction to form a compound of Formula IIc:
iii) forming a deprotection reaction mixture comprising the compound of Formula IIc and trifluoroacetic acid (TFA) to form a compound of Formula IIa:
iv) forming a cyclization reaction mixture comprising silver, N,N-diisopropylethylamine (DIPEA), and the compound of Formula IIa under conditions suitable to form the cyclized peptidic compound of Formula Ia.

### Claim 26

A method for preparing a cyclized peptidic compound comprising
forming a reaction mixture comprising a metal thiophilic catalyst, a non-nucleophilic base and a linear peptidic compound covalently linked to a solid-phase support via a linker, under conditions suitable to form the cyclized peptidic compound and cleave the cyclized peptidic compound from the solid-phase support,
wherein the linear peptidic compound is covalently linked to the linker via a thioester moiety, and wherein the linker is covalently linked to the solid-phase support via a sulfonamide moiety, such that cyclization and cleavage of the linear peptidic compound cleaves the thioester moiety to form an amide.