# US 2014/0154180 A1 · Pharmacophores for Amyloid Fibers Involved in Alzheimer's Disease

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- Number: US 2014/0154180 A1
- Document ID: US20140154180A1
- Status: Published application
- Kind: A1
- Application number: 14/232,866
- Filed: 2012-07-16
- Published: 2014-06-05
- Earliest claimed: 2011-07-14
- Assignees: The Regents of the University of California
- Inventors: David S. Eisenberg; Lin Jiang; Meytal Landau; Cong Liu
- Web page: https://patentgrep.com/patent/US20140154180A1

## CPC

- G16B 15/30: Drug targeting using structural data; Docking or binding prediction
- A61K 31/12: Ketones
- A61K 31/121: acyclic
- A61K 31/122: having the oxygen directly attached to a ring, e.g. quinones, vitamin K1, anthralin
- A61K 31/15: Oximes (>C=N—O—); Hydrazines (>N—N<); Hydrazones (>N—N=) {; Imines (C—N=C)}
- A61K 31/185: Acids; Anhydrides, halides or salts thereof, e.g. sulfur acids, imidic, hydrazonic or hydroximic acids (hydroxamic acids A61K31/16; peroxy acids A61K31/327)
- A61K 31/473: ortho- or peri-condensed with carbocyclic ring systems, e.g. acridines, phenanthridines
- A61K 31/536: ortho- or peri-condensed with carbocyclic ring systems
- A61K 31/538: ortho- or peri-condensed with carbocyclic ring systems
- A61K 31/655: Azo (—N=N—), diazo (=N2), azoxy (>N—O—N< or N(=O)—N<), azido (—N3) or diazoamino (—N=N—N<) compounds
- A61K 31/704: attached to a condensed carbocyclic ring system, e.g. sennosides, thiocolchicosides, escin, daunorubicin {(digitoxin A61K31/7048)}
- A61K 51/08: Peptides, e.g. proteins {, carriers being peptides, polyamino acids, proteins}
- A61P 25/28: for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
- G01N 33/6896: {Neurological disorders, e.g. Alzheimer's disease}
- G16B 15/00: ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
- G01N 2333/4709: Amyloid plaque core protein
- G01N 2500/20: cell-free systems
- G01N 2800/2821: Alzheimer
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- 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
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)

## Abstract

This invention relates, e.g., to a method for designing or selecting on a computer a candidate small molecule amyloid binder or inhibitor, comprising: a) docking test compounds to the binding site or binding surface determined from the three-dimensional structure of a co-crystal of a protofilament of an amyloid protein bound to a small molecule which is known to bind to the amyloid protein, and (b) selecting test compounds which exhibit an energy below that of the small molecule used to form the co-crystal made in a), as candidate amyloid binders.

## Claims

### Claim 1

A method for determining on a computer the relevant criteria for designing or selecting on a computer a small molecule amyloid binder or inhibitor, comprising
a) co-crystallizing a protofilament of an amyloid protein with a small molecule that is known to bind to the amyloid protein; and
b) determining on a computer the three-dimensional structure of the co-crystal, thereby determining the atomic coordinates of the binding surface or binding pocket

### Claim 2 (depends on 1)

The method of claim 1, further comprising designing or selecting on a computer a small molecule amyloid binder or inhibitor, comprising
a) docking test compounds to the crystal structure determined in b) on a computer, and
b) selecting test compounds which exhibit a calculated binding energy below that of the small molecule used to form the co-crystal made in a), as candidate amyloid binders.

### Claim 3 (depends on 1)

The method of claim 1, wherein the amyloid protein is Aβ, and the small molecule is a charged or polar molecule comprising one or more flat aromatic rings.

### Claim 4 (depends on 3)

The method of claim 3, wherein the charged or polar molecule is Orange-G.

### Claim 5 (depends on 2)

The method of claim 2, wherein the atomic coordinates of the three-dimensional structure are shown in Table 3, and the amino acid residues of the amyloid molecule which contact the amyloid binder are selected from one or more of Lys16, Leu17, Val18, Phe19, or Phe20, or combinations thereof.

### Claim 6 (depends on 1)

The method of claim 1, wherein the amyloid protein is tau, and the small molecule is a charged or polar molecule comprising one or more flat aromatic rings.

### Claim 7 (depends on 6)

The method of claim 6, wherein the charged or polar molecule is Orange-G.

### Claim 8 (depends on 7)

The method of claim 7, wherein the atomic coordinates of the three-dimensional structure are shown in Table 4, and the amino acid residues of the amyloid molecule which contact the amyloid binder are selected from one or more of Gln2, Val4, or Lys6, or combinations thereof.

### Claim 9 (depends on 1)

The method of claim 1, wherein the amyloid protein is tau, and the small molecule is an elongated apolar molecule.

### Claim 10 (depends on 9)

The method of claim 9, wherein the elongated apolar molecule is curcumin or DDNP.

### Claim 11 (depends on 10)

The method of claim 10, wherein the atomic coordinates of the three-dimensional structure are shown in Table 5 or 6, and the amino acid residues of the amyloid molecule which contact the amyloid binder are selected from one or more of Val1, Gln2, Ile3, Val4, Tyr5 or Lys6, or combinations thereof.

### Claim 12

A method for designing or selecting on a computer a candidate small molecule amyloid binder or inhibitor, comprising
a) docking test compounds to the binding site or binding surface determined from the three-dimensional structure of a co-crystal of a protofilament of an amyloid protein bound to a small molecule which is known to bind to the amyloid protein, wherein the atomic coordinates of the binding site or binding surface are as set forth in the following Tables 3-6, and amino acid residues of the amyloid molecule which contacts the amyloid binder are as indicated:
(i) Table 3 (based on an Orange-G/Aβ co-crystal), wherein the amino acid residues of the amyloid molecule are selected from one or more of Lys16, Leu17, Val18, Phe19, or Phe20, or combinations thereof; or
(ii) Table 4, (based on an Orange-G/tau co-crystal), wherein the amino acid residues of the amyloid molecule are selected from one or more of Gln2, Val4, or Lys6, or combinations thereof; or
(iii) Table 5 (based on a co-crystal of tau with curcumin), wherein the amino acid residues of the amyloid molecule are selected from one or more of Val1, Gln2, Ile3, Val4, Tyr5 or Lys6, or combinations thereof;
(iv) Table 6 (based on a co-crystal of tau with DDNP), wherein the amino acid residues of the amyloid molecule are selected from one or more of Val1, Gln2, Ile3, Val4, Tyr5 or Lys6, or combinations thereof;
(b) selecting test compounds which exhibit an energy below that of the small molecule used to form the co-crystal made in a), as candidate amyloid binders.

### Claim 13 (depends on 2)

The method of claim 2, wherein the docking is accomplished by a docking program in which the test molecule and protein side chain torsion angles and small molecule rotamers are sampled in a near native perturbation fashion.

### Claim 14 (depends on 2)

The method of claim 2, further comprising testing the candidate amyloid binders for their ability to inhibit amyloid-mediated cell toxicity, and identifying and selecting candidate amyloid inhibitors which inhibit amyloid-mediated cell toxicity to a greater degree than the small molecule which was co-crystallized with the amyloid.

### Claim 15 (depends on 2)

The method of claim 2, further comprising characterizing and validating the candidate binders by X-ray crystallography, NMR spectroscopy (titration), ITC (isothermal titration calorimetry), thermal denaturation, mass spectrography, or SPR (surface plasmon resonance), to measure the binding affinity to amyloid fibers or oligomers, and/or an activity assay.

### Claim 16 (depends on 2)

The method of claim 2, further comprising deriving on a computer a refined pharmacophore based on the identified candidate amyloid inhibitors.

### Claim 17 (depends on 16)

Starting with the refined pharmacophore derived in claim 16, testing a new set of candidate amyloid binders by repeating the docking and selecting steps, and testing the candidate amyloid binders for their ability to inhibit amyloid-mediated cell toxicity, in order to identify a further refined pharmacophore.

### Claim 18 (depends on 17)

Starting with the further refined pharmacophore derived in claim 17, repeating the docking and screening steps, and testing the candidate amyloid binders for their ability to inhibit amyloid-mediated cell toxicity in order to identify a yet further refined pharmacophore; and repeat.

### Claim 19

A pharmaceutical composition comprising one or more of the compounds BAF4, BAF8, BAF11, BAF12, BAF14, BAF30 or BAF31, as shown in FIG. 18, or the derivatives of BAF11—the isomer, σR1, σR3 or ΔOHσR—as shown in FIG. 19, or the derivative of BAF30-αR1—as shown in FIG. 20, or a pharmaceutically acceptable salt, hydrate, solvate or metal chelate thereof, and a pharmaceutically acceptable carrier.

### Claim 20 (depends on 19)

The pharmaceutical composition of claim 19, wherein the compound is detectably labeled.

### Claim 21 (depends on 20)

The pharmaceutical composition of claim 20, wherein the label is a radioactive or fluorescent label.

### Claim 22 (depends on 5)

The pharmaceutical composition of claim 5, wherein the label is suitable for detection by PET.

### Claim 23

A method for determining the presence of Aβ or tau oligomers or fibers in a sample, comprising contacting a sample suspected of comprising such fibers with an effective amount of one or more of BAF4, BAF8, BAF11, BAF12, BAF14, BAF30 or BAF31, as shown in FIG. 18, or the derivatives of BAF11—the isomer, σR1, σR3 or ΔOHσR—as shown in FIG. 19, or the derivative of BAF30σR1—as shown in FIG. 20, or a pharmaceutically acceptable salt, hydrate, solvate or metal chelate thereof, wherein the compound is detectably labeled; and
measuring the amount of bound label in the sample,
wherein a statistically significantly higher amount of label than that in a control sample lacking the fibers indicates the presence of the fibers in the sample.

### Claim 24 (depends on 23)

The method of claim 23, which is carried out in vitro or in vivo.

### Claim 25 (depends on 23)

The method of claim 23, which is a method for diagnosing the presence of an amyloid disease.

### Claim 26 (depends on 23)

The method of claim 23, which is a method for diagnosing Alzheimer's disease.

### Claim 27

A method for detecting the presence of Aβ or tau fibers in a subject, comprising introducing into the subject a compound with an effective amount of one or more of the compounds BAF4, BAF8, BAF11, BAF12, BAF14, BAF30 or BAF31, as shown in FIG. 18, or the derivatives of BAF11—the isomer, σR1, σR3 or ΔOHσR—as shown in FIG. 19, or the derivative of BAF30-αR1— as shown in FIG. 20, or a pharmaceutically acceptable salt, hydrate, solvate or metal chelate thereof, wherein the compound is labeled with a nuclide that can be detected by PET; and
measuring the amount of bound label in the brain by PET,
wherein a statistically significantly higher signal than that in a control sample lacking the fibers indicates the presence of the fibrils in the brain of the subject.

### Claim 28

A method for reducing or inhibiting amyloid-based cellular toxicity, comprising contacting amyloid protofilaments with an effective amount of BAF4, BAF8, BAF11, BAF12, BAF14, BAF30 or BAF31, as shown in FIG. 18, or the derivatives of BAF11—the isomer, σR1, σR3 or ΔOHσR—as shown in FIG. 19, or the derivative of BAF30-σR1— as shown in FIG. 20, or a pharmaceutically acceptable salt, hydrate, solvate or metal chelate thereof.

### Claim 29 (depends on 28)

The method of claim 28, which is carried out in vitro.

### Claim 30 (depends on 28)

The method of claim 28, which is carried out in vivo.

### Claim 31

A method for treating an amyloid-mediated disease or condition, comprising administering to a subject having or likely to have the disease or condition an effective amount of BAF4, BAF8, BAF11, BAF12, BAF14, BAF30 or BAF31, as shown in FIG. 18, or the derivatives of BAF11—the isomer, σR1, σR3 or ΔOHσR—as shown in FIG. 19, or the derivative of BAF30-αR1— as shown in FIG. 20, or a pharmaceutically acceptable salt, hydrate, solvate or metal chelate thereof.

### Claim 32

A computer readable medium providing the structural representation of a co-crystal of a protofilament of an amyloid protein with a small molecule that is known to bind to the amyloid protein.

### Claim 33

A kit for detecting the presence of Abeta or tau in a sample, comprising a compound of the invention in a container.