# US 2013/0158232 A1 · Method for selecting a candidate drug compound

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- Number: US 2013/0158232 A1
- Document ID: US20130158232A1
- Status: Published application
- Kind: A1
- Application number: 13/443,706
- Filed: 2012-04-10
- Published: 2013-06-20
- Earliest claimed: 2003-02-27
- Assignees: Pepscan Systems B.V.
- Inventors: Peter TIMMERMAN; Joris Beld; Robbert Hans Meloen; Wouter Cornelis Puijk
- Web page: https://patentgrep.com/patent/US20130158232A1

## CPC

- G01N 33/54306: {Solid-phase reaction mechanisms}
- C07K 17/02: Peptides being immobilised on, or in, an organic carrier
- C40B 30/04: by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
- G01N 33/54353: {with ligand attached to the carrier via a chemical coupling agent (coatings G01N33/54393)}
- 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)
- 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)
- C40B: COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES (in silico combinatorial libraries of nucleic acids, proteins or peptides G16B35/00; in silico combinatorial chemistry G16C20/60)

## Abstract

The disclosure relates to the field of candidate drug testing and drug development. Described are methods for providing a compound composed of at least one molecule attached via at least two linkages to a molecular scaffold, the method comprising providing a scaffold comprising at least a first and a second reactive group; providing at least one molecule able to react with the at least first and second reactive group; and contacting the scaffold with at least one molecule to form at least two linkages between the scaffold and the molecule in a coupling reaction, wherein the formation of a linkage accelerates the formation of a consecutive linkage. The coupling reaction may be performed in solution, such as an aqueous solution. Furthermore, described is a method for selecting a candidate drug compound comprising providing a library of the compounds and determining the binding of a target molecule to the compounds.

## Claims

### Claim at position 1

1-20. (canceled)

### Claim 21

A compound comprising at least two looped peptide structures attached via at least three thioether linkages to an aromatic or heteroaromatic molecule, wherein each of the at least three thioether linkages comprises a sulfur at a benzylic position on said aromatic or heteroaromatic molecule.

### Claim 22 (depends on 21)

The compound of claim 21, wherein the aromatic or heteroaromatic molecule comprises a 5- or 6-membered aromatic or heteroaromatic ring.

### Claim 23 (depends on 21)

The compound of claim 21, wherein each of the at least three thioether linkages is formed by reacting
a halomethyl group on an aromatic or heteroaromatic ring with
an SH functionality comprised within the peptide structure,
thereby forming at least three thioether linkages, each comprising a sulfur at a benzylic position on said aromatic or heteroaromatic molecule.

### Claim 24 (depends on 23)

The compound of claim 23, wherein the aromatic molecule is an arene.

### Claim 25 (depends on 21)

The compound of claim 21, wherein each of the at least three thioether linkages is formed by reacting
one of the halomethyl groups on a tris-, or tetrakis(halomethyl)-substituted aromatic or heteroaromatic ring with
an SH functionality comprised within the peptide structure,
thereby forming at least three thioether linkages, each comprising a sulfur at a benzylic position on said aromatic or heteroaromatic molecule.

### Claim 26 (depends on 25)

The compound of claim 25, wherein the aromatic molecule is an arene.

### Claim 27 (depends on 21)

The compound of claim 21, wherein the compound functions as a peptidomimetic of a biologically active protein.

### Claim 28 (depends on 21)

The compound of claim 21, wherein the looped peptide structure is constrained in the compound, so as to allow the presentation of the looped peptide structure as a stable binding domain.

### Claim 29 (depends on 21)

The compound of claim 21, wherein the looped peptide structure is between three and twenty-seven amino acid residues in length.

### Claim 30

A compound comprising at least one looped peptide structure attached via at least two thioether linkages to an aromatic or heteroaromatic molecule,
wherein the peptide comprises a cysteine knot structural motif, and
wherein each of the at least two thioether linkages comprises a sulfur at a benzylic position on said aromatic or heteroaromatic molecule.

### Claim 31 (depends on 30)

The compound of claim 30, wherein the aromatic or heteroaromatic molecule comprises a 5- or 6-membered aromatic or heteroaromatic ring.

### Claim 32 (depends on 30)

The compound of claim 30, wherein each of the at least two thioether linkages is formed by reacting
a halomethyl group on an aromatic or heteroaromatic ring with
an SH functionality comprised within the peptide structure,
thereby forming at least two thioether linkages, each comprising a sulfur at a benzylic position on said aromatic or heteroaromatic molecule.

### Claim 33 (depends on 32)

The compound of claim 32, wherein the aromatic molecule is an arene.

### Claim 34 (depends on 30)

The compound of claim 30, wherein each of the at least two thioether linkages is formed by reacting
one of the halomethyl groups on a bis-, tris- or tetrakis(halomethyl)-substituted aromatic or heteroaromatic ring with
an SH functionality comprised within the peptide structure,
thereby forming at least two thioether linkages, each comprising a sulfur at a benzylic position on said aromatic or heteroaromatic molecule.

### Claim 35 (depends on 34)

The compound of claim 34, wherein the aromatic molecule is an arene.

### Claim 36 (depends on 30)

The compound of claim 30, wherein the compound functions as a peptidomimetic of a biologically active protein.

### Claim 37 (depends on 30)

The compound of claim 30, wherein the looped peptide structure is constrained in the compound, so as to allow the presentation of the looped peptide structure as a stable binding domain.

### Claim 38 (depends on 30)

The compound of claim 30, wherein the looped peptide structure is between three and twenty-seven amino acid residues in length.