Peptides having tetrahedral mimicking groups as inhibitors of rhomboid proteases

Patent metadata

Field	Value
Publication number	US-2019144498-A1
Application number	US-201716307068-A
Country	US
Kind code	A1
Filing date	Jun 6, 2017
Priority date	Jun 6, 2016
Publication date	May 16, 2019
Grant date	—

Abstract

The present invention describes rhomboid protease inhibitors having high specificity and inhibition characteristics providing novel antibiotics, anti-malarial pharmaceutical agents, and provides a strategy for designing RiBns (rhomboid-inhibiting boronates) to target rhomboid selectively in unrelated organisms.

First claim

1 . A compound of formula I:
P−W   (I)
wherein P is a composition selected from the group comprising a peptide, a peptomimetic, or combination thereof comprising from 3 to 15 residues selected from natural amino acids, unnatural amino acids, or a combination thereof, attached to W, wherein W is a tetrahedral mimicking group comprising a chemical or biological structure that mimics a tetrahedral group in a substrate attached to a Rhomboid Protease.

2 . The compound of claim 1 wherein the peptide comprises from 4 to 10 amino acids.

3 . The compound of claim 1 wherein the peptide is selected from the group comprising Ac-VRMA (SEQ ID NO: 2), Ac-KRFRSMQYSA (SEQ ID NO: 3), Ac-KRFRSNQYSA (SEQ ID NO: 4), Ac-EAFSSMPYYA (SEQ ID NO: 5), or a combination thereof wherein Ac is an N-terminal acetyl moiety and W is attached to a C-terminal.

4 . A polypeptide having rhomboid protease inhibition activity comprising:
a) an amino acid sequence selected from the group comprising Ac-VRMA (SEQ ID NO: 2), Ac-KRFRSMQYSA (SEQ ID NO: 3), Ac-KRFRSNQYSA (SEQ ID NO: 4), Ac-EAFSSMPYYA (SEQ ID NO: 5), or a combination thereof attached to a tetrahedral mimicking group; b) peptomimetic of a) c) a functional fragment of a); d) a functional homolog of a) or b) or functional fragment thereof; and e) a fusion polypeptide comprising an amino acid sequence of any of a) to d).

5 . A method for inhibiting a rhomboid protease comprising the steps of providing a compound of claim 1 and applying it to a rhomboid protease.

6 . The method of claim 5 wherein the rhomboid protease is selected from the group consisting of a Entamoeba rhomboid protease, a Trichomonas rhomboid protease, a rhomboid protease, or a combination thereof.

7 . The method of claim 6 wherein the rhomboid protease is a Plasmodium rhomboid protease.

8 . The method of claim 7 wherein the rhomboid protease is PfROM4

9 . A method of inhibiting a rhomboid protease in a subject comprising administering to a subject comprising a rhomboid protease an effective amount of a composition, solvate, or stereoisomer of claim 1 ; and inhibiting the rhomboid protease.

10 . The method of claim 9 wherein the subject is a human and the rhomboid protease inhibited is a Plasmodium rhomboid protease.

11 . The method of claim 10 wherein the Plasmodium rhomboid protease is PfROM4.

12 . A method of using a compound of claim 1 to treat or prevent malaria in a subject comprising:
administering to a subject comprising malaria or exposed to malaria an effective amount of a composition, salt, solvate, or stereoisomer of claim 1 ; and
treating or preventing malaria in the subject.

13 . The method of claim 12 wherein the subject is a human and the treating or preventing malaria in the subject is determined when the activity of a Plasmodium rhomboid protease is inhibited in the subject when compared to a reference subject that has not been administered the composition.

14 . The method of claim 13 wherein the inhibition is in the range of 10 fold to 150 fold inhibition.

15 . The method of claim 13 wherein the inhibition is in the range of 50 fold to 110 fold inhibition.

16 . A method of directed substrate evolution providing the steps of:
providing a first rhomboid protease substrate; changing an amino acid of the first rhomboid protease substrate forming a mutated rhomboid protease substrate; evaluating the cleavage of the mutated rhomboid protease substrate; mapping a cleavage site of the mutated rhomboid protease substrate; forming a substrate mutant sequence having an enhanced cleavage in the range of 2 to 200-fold when compared to the cleavage of the rhomboid protease substrate and wherein the cleavage site is the same for the mutated rhomboid protease substrate and the first rhomboid protease substrate; and synthesizing a RiBn by attaching a tetrahedral mimicking group on the C-terminus of the substrate mutant sequence.

17 . The method of claim 16 , wherein the tetrahedral mimicking group is selected from group consisting of B (OH) 2 , trifluoromethylketone, or a combination thereof.

18 . The method of claim 1 wherein the tetrahedral mimicking group is selected from group consisting of B (OH) 2 , trifluoromethylketone, or a combination thereof.

19 . A method of using a compound of claim 1 to treat or prevent a parasite infection in a subject comprising
administering to a subject comprising a parasite or exposed to a parasite an effective amount of a composition, salt, solvate, or stereoisomer of claim 1 ; and
treating or preventing a parasite in the subject.

20 . The method of claim 19 wherein the parasite is antibiotic resistant.

21 . The method of claim 12 wherein the malaria is antibiotic resistant.

Assignees

• Univ Johns Hopkins

Inventors

• Urban Sinisa
• Gandhi Shiv
• Cho Sangwoo

Classifications

• Y02A50/30

  Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change · CPC title

• C07K2319/00

  Fusion polypeptide · CPC title

• C07K7/06

  having 5 to 11 amino acids · CPC title

• C07K5/101 Primary

  the side chain containing 2 to 4 carbon atoms, e.g. Val, Ile, Leu · CPC title

• C07K2319/50

  containing protease site · CPC title