NEMO coiled coil mimics and methods of using same

Patent metadata

Field	Value
Publication number	US-11891422-B2
Application number	US-201916684082-A
Country	US
Kind code	B2
Filing date	Nov 14, 2019
Priority date	Nov 16, 2018
Publication date	Feb 6, 2024
Grant date	Feb 6, 2024

Abstract

This invention relates to macrostructures (and pharmaceutical formulations containing them) that include a parallel coiled-coil structure, wherein the parallel coiled-coil comprises a first coil of Formula I and a second coil of Formula II:

T 1 -f 0 -g 0 -a 1 -b 1 -c 1 -d 1 -e 1 -f 1 -g 1 -a 2 -b 2 -c 2 -d 2 -e 2 -f 2 -g 2 -a 3 -b 3 -c 3 -d 3 -e 3 -T 2   (I)

T 3 -g′ 0 -a′ 1 -b′ 1 -c′ 1 -d′ 1 -e′ 1 -f′ 1 -g′ 1 -a′ 2 -b′ 2 -c′ 2 -d′ 2 -e′ 2 -f′ 2 -g′ 2 -a′ 3 -b′ 3 -c′ 3 -d′ 3 -e′ 3 -f′ 3 -T 4   (II),

as described in the present application. Methods of using these macrostructures are also disclosed.

First claim

What is claimed:

1. A macrostructure comprising a parallel coiled-coil, wherein the parallel coiled-coil comprises:
a first coil of Formula I and a second coil of Formula II:
T 1 -f 0 -g 0 -a 1 -b 1 -c 1 -d 1 -e 1 -f 1 -g 1 -a 2 -b 2 -c 2 -d 2 -e 2 -f 2 -g 2 -a 3 -b 3 -c 3 -d 3 -e 3 -T 2   (Formula I) (SEQ ID NO: 1)

T 3 -g′ 0 -a′ 1 -b′ 1 -c′ 1 -d′ 1 -e′ 1 -f′ 1 -g′ 1 -a′ 2 -b′ 2 -c′ 2 -d′ 2 -e′ 2 -f′ 2 -g′ 2 -a′ 3 -b′ 3 -c′ 3 -d′ 3 -e′ 3 -f′ 3 -T 4   (Formula II) (SEQ ID NO: 2),

wherein:
each a 1-3 , b 1-3 , c 1-3 , d 1-3 , e 1-3 , f 0-2 , g 0-2 , a′ 1-3 , b′ 1-3 , c′ 1-3 , d′ 1-3 , e′ 1-3 , f′ 1-3 , and g′ 0-2 is independently absent or a residue selected from the group consisting of modified or unmodified amino acid residues and analogues thereof,
one or more of the following residue pairs are covalently bound by a linker: g 0 -e′ 1 , g 1 -e′ 2 , g 2 -e′ 3 , d 1 -d′ 1 , d 2 -d′ 2 , d 3 -d′ 3 , a 1 -a′ 1 , a 2 a′ 2 , a 3 -a 3 , e 1 -g′ 0 , e 2 -g′ 1 , and e 3 -g′ 2 ;
each T 1 and T 3 is independently a point of attachment from a terminal nitrogen to one or more moieties, wherein each moiety is independently H, -PG 1 , —C(O)R, —C(O)NR 2 , —C(O)NH2, —R, —C(O)OR, an amino acid or analogue thereof, a peptide, a targeting moiety, or a tag, where PG 1 is an amine protecting group and each R is independently hydrogen, an alkyl, an alkenyl, an alkynyl, a cycloalkyl, an aryl, a heteroaryl, a heterocyclyl, an arylalkyl, a peptide, a targeting moiety, or a tag; and
each T 2 and T 4 is independently a point of attachment from a terminal carbonyl to H, —OPG 2 , —NPG 2 , —OR, —OH, —NR 2 , —NH 2 , —N(R)C(O)C 1-6 alkyl, —N(H)C(O)C 1-6 alkyl, an amino acid or analogue thereof, a peptide, a targeting moiety, or a tag, where PG 2 is a carboxylic acid protecting group and each R is independently hydrogen, an alkyl, an alkenyl, an alkynyl, a cycloalkyl, an aryl, a heteroaryl, a heterocyclyl, an arylalkyl, a peptide, a targeting moiety, or a tag;
and wherein:
the first coil comprises fourteen contiguous residues which correlate to positions f 0 -e 2 of Formula I, wherein said fourteen contiguous residues of the first coil have the amino acid sequence of SEQ ID NO: 4; and the second coil comprises fourteen contiguous residues which correlate to positions g′ 0 -f′ 2 of Formula II, wherein said fourteen contiguous residues of the second coil have the amino acid sequence of SEQ ID NO: 6.

2. The macrostructure of claim 1 , wherein:
the length of any linker between residue pairs g 0 -e′ 1 , g 1 -e′ 2 , g 2 -e′ 3 , e 1 -g′ 0 , e 2 -g′ 1 , and e 3 -g′ 2 is such that the spatial distance between the Ca positions of each residue in the pair is 10-25 Å; and
the length of any linker between residue pairs d 1 -d′ 1 , d 2 -d′ 2 , d 3 -d′ 3 , a 1 -a′ 1 , a 2 -a′ 2 , and a 3 -a′ 3 is such that the spatial distance between the Cα positions of each residue in the pair is 5-15 Å.

3. The macrostructure of claim 1 , wherein:
(1) at least f 0 , g 0 , a 1 , b 1 , c 1 , d 1 , e 1 , f 1 , g 1 , a 2 , b 2 , c 2 , d 2 , and e 2 are present in the first coil and at least g′ 0 , a′ 1 , b′ 1 , c′ 1 , d′ 1 , e′ 1 , f′ 1 , g′ 1 , a′ 2 , b′ 2 , c′ 2 , d′ 2 , e′ 2 , and f′ 2 are present in the second coil; or
(2) at least f 1 , g 1 , a 2 , b 2 , c 2 , d 2 , e 2 , f 2 , g 2 , a 3 , b 3 , c 3 , d 3 , and e 3 are present in the first coil and at least g′ 1 , a′ 2 , b′ 2 , c′ 2 , d′ 2 , e′ 2 , f′ 2 , g′ 2 , a′ 3 , b′ 3 , c′ 3 , d′ 3 , e′ 3 , and f′ 3 are present in the second coil.

4. The macrostructure of claim 1 , wherein a linker between at least one of residue pairs g 0 -e′ 1 , g 1 -e′ 2 , g 2 -e′ 3 , e 1 -g′ 0 , e 2 -g′ 1 , and e 3 -g′ 2 is present.

5. The macrostructure of claim 1 , wherein a linker between at least one of residue pairs g 0 -e′ 1 , g 1 -e′ 2 , g 2 -e′ 3 , e 1 -g′ 0 , e 2 -g′ 1 , and e 3 -g′ 2 has the formula —Z n —, wherein n is a number from 1 to 25 and each Z is independently selected at each occurrence thereof from the group consisting of alkylene, alkenylene, arylene, heteroarylene, triazole-diyl, thiazole-diyl, oxazole-diyl, ethers, amides, esters, maleimides, thioethers, O, S, and Se.

6. The macrostructure of claim 1 , wherein a linker between at least one of residue pairs g 0 -e′ 1 , g 1 -e′ 2 , g 2 -e′ 3 , e 1 -g′ 0 , e 2 -g′ 1 , and e 3 -g′ 2 has a formula selected from:
(a) the group consisting of:

wherein:
X is O, S, CR 2 , NR, or P;
each X 1 is independently O, S, NH, or NR;
each R is independently H, alkyl, or aryl; and
each Y is S;

(b) the group consisting of:

wherein:
X is O, S, CR 2 , NR, or P;
each X 1 is independently O, S, C, CR, N, NH, or NR;
each R is independently H, alkyl, or aryl; and
each Y is S; and

(c) the group consisting of:

7. The macrostructure of claim 1 , wherein the parallel coiled-coil has the formula set forth in FIG. 16.

8. The macrostructure of claim 1 , wherein, first coil comprises the amino acid sequence of SEQ ID NO: 13 and the second coil comprises the amino acid sequence of SEQ ID NO: 14.

9. A pharmaceutical composition comprising a macrostructure according to claim 1 and a pharmaceutically acceptable vehicle.

Assignees

• Univ New York

Inventors

• Arora Paramjit S
• Wuo Michael G

Classifications

• C07K14/4702 Primary

  Regulators; Modulating activity · CPC title

• A61K47/65

  Peptidic linkers, binders or spacers, e.g. peptidic enzyme-labile linkers · CPC title

• A61P35/00 Primary

  Antineoplastic agents · CPC title

• C07C49/04

  Saturated compounds containing keto groups bound to acyclic carbon atoms · CPC title

• C07D227/02

  with only hydrogen or carbon atoms directly attached to the ring nitrogen atom · CPC title