# US 10,307,433 B2 · Composition and methods of use of small molecules as binding ligands for the modulation of proprotein convertase subtilisin/kexin type 9(PCSK9) protein activity

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- Number: US 10,307,433 B2
- Document ID: US10307433B2
- Status: Granted
- Kind: B2
- Application number: 15/989,360
- Filed: 2018-05-25
- Published: 2018-10-25
- Granted: 2019-06-04
- Earliest claimed: 2014-08-21
- Assignees: SRX Cardio, LLC
- Applicants: Srx Cardio, LLC
- Inventors: Thomas E. Barta; Jonathan W. Bourne; Kyle D. Monroe; Michael M. Muehlemann
- Web page: https://patentgrep.com/patent/US10307433B2

## CPC

- A61K 31/675: having nitrogen as a ring hetero atom, e.g. pyridoxal phosphate
- A61K 31/41: having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
- A61K 31/4245: Oxadiazoles
- A61K 31/454: containing a five-membered ring with nitrogen as a ring hetero atom, e.g. pimozide, domperidone
- A61K 31/683: Diesters of a phosphorus acid with two hydroxy compounds, e.g. phosphatidylinositols
- A61K 38/005: {Enzyme inhibitors (protease inhibitors A61K38/55)}
- A61K 38/05: Dipeptides
- A61K 45/06: Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
- A61P 3/00: Drugs for disorders of the metabolism (of the blood or the extracellular fluid A61P7/00)
- A61P 3/06: Antihyperlipidemics
- A61P 43/00: Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
- C07D 401/12: linked by a chain containing hetero atoms as chain links
- C07D 403/12: linked by a chain containing hetero atoms as chain links
- C07D 413/14: containing three or more hetero rings
- C07F 9/59: Hydrogenated pyridine rings
- C07F 9/6518: Five-membered rings
- C07F 9/65312: {having the two nitrogen atoms in positions 1 and 2}
- C07K 5/06078: {and aromatic or cycloaliphatic}
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- C07D: HETEROCYCLIC COMPOUNDS (macromolecular compounds C08)
- C07F: ACYCLIC, CARBOCYCLIC OR HETEROCYCLIC COMPOUNDS CONTAINING ELEMENTS OTHER THAN CARBON, HYDROGEN, HALOGEN, OXYGEN, NITROGEN, SULFUR, SELENIUM OR TELLURIUM (metal-containing porphyrins C07D487/22)
- 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

This invention is related to the field of PCSK9 biology and the composition and methods of use of small molecule ligands for modulation of PCSK9 biological activity. In particular, the invention provides compositions of small molecule compounds that modulate circulating levels of low density lipoproteins by altering the conformation of the protein PCSK9. Binding these small molecule ligands to PCSK9 alters the conformation of the protein, modifying the interaction between PCSK9 and an endogenous low density lipoprotein receptor, and can lead to reduced or increased levels of circulating LDL-cholesterol. High LDL cholesterol levels are associated with increased risk for heart disease. Low LDL-cholesterol levels may be problematic in other conditions, such as liver dysfunction; thus, there is also utility for small molecule ligands that can raise LDL levels.

## Claims

### Claim 1

A method, comprising:
a) providing;
i) a PCSK9 protein, wherein said protein comprises a binding site that induces allosteric modulation and a low density lipoprotein receptor binding site;
ii) a pharmaceutical formulation comprising a small molecule ligand capable of binding said binding site, wherein said small molecule ligand is an allosteric inhibitor ligand;
iii) a plurality of hepatocyte cells comprising a population of low density lipoprotein receptors; and
iv) low density lipoproteins;
b) binding said small molecule ligand to said binding site, wherein said small molecule ligand induces a conformational shift of said protein; and
c) modulating said population of said low density lipoprotein receptors by said conformational shift.

### Claim 2 (depends on 1)

The method of claim 1, wherein said pharmaceutical formulation further comprises a first pharmaceutical drug.

### Claim 3 (depends on 2)

The method of claim 2, wherein said first pharmaceutical drug comprises a cardiovascular drug.

### Claim 4 (depends on 3)

The method of claim 3, wherein said cardiovascular drug is selected from the group consisting of a statin and ezetimibe.

### Claim 5 (depends on 1)

The method of claim 1, wherein said small molecule ligand is an organic chemical compound less than 800 Da.

### Claim 6 (depends on 1)

The method of claim 1, wherein said PCSK9 protein allosteric inhibitor ligand increases the population of low density lipoprotein receptors measurable on the cell surface of said plurality of hepatocytes.

### Claim 7 (depends on 1)

The method of claim 1, wherein said PCSK9 protein allosteric inhibitor ligand decreases the affinity of the PCSK9 protein's low density lipoprotein receptor binding site for the low density lipoprotein receptor on said plurality of hepatocytes.

### Claim 8 (depends on 1)

The method of claim 1, wherein said allosteric inhibitor ligand increases the internalization of said low density lipoproteins by said hepatocytes.

### Claim 9

A method, comprising binding a small molecule compound to a PCSK9 protein allosteric modulation site, to increase the population of low density lipoprotein receptors measurable on the cell surface of a plurality of hepatocytes.

### Claim 10 (depends on 9)

The method of claim 9, wherein said small molecule compound increases the internalization of low density lipoproteins by said hepatocytes.

### Claim 11

A method of administering to a subject a small molecule compound, the method comprising binding said small molecule compound to a PCSK9 protein allosteric binding site, wherein said subject has at least one symptom of cardiovascular disease under conditions such that said at least one symptom of a cardiovascular disease is reduced.

### Claim 12 (depends on 11)

The method of claim 11, wherein said at least one symptom comprises elevated circulating low density lipoprotein.

### Claim 13 (depends on 11)

The method of claim 11, wherein said at least one symptom is reduced between 10%-85%.

### Claim 14 (depends on 11)

The method of claim 11, wherein said cardiovascular disease is selected from the group consisting of a coronary disease, hypertension, hypercholesterolemia and atherosclerosis.

### Claim 15 (depends on 11)

The method of claim 11, wherein said administering comprises an effective dose of said small molecule compound.

### Claim 16 (depends on 11)

The method of claim 11, wherein said small molecule compound is a pharmaceutical composition.

### Claim 17 (depends on 11)

The method of claim 11, wherein said small molecule compound is an organic chemical compound less than 800 Da.

### Claim 18 (depends on 11)

The method of claim 11, wherein said small molecule compound binds said PCSK9 protein with a binding affinity of less than 500 nM.

### Claim 19 (depends on 16)

The method of claim 16, wherein said pharmaceutical composition is further combined with a second pharmaceutical compound.

### Claim 20 (depends on 11)

The method of claim 11, wherein said small molecule compound is selected from the group consisting of SRX75, SRX76, SRX200, SRX201, SRX204, SRX205, SRX206, SRX207, SRX208, SRX209, SRX210, SRX211, SRX212, SRX213, SRX214, SRX215, SRX216, SRX217, SRX218, SRX219, SRX220, SRX221, SRX222, SRX223, SRX224, and SRX225.