Methods and systems for predicting misfolded protein epitopes

Patent metadata

Field	Value
Publication number	US-10475525-B2
Application number	US-201614997951-A
Country	US
Kind code	B2
Filing date	Jan 18, 2016
Priority date	Oct 6, 2008
Publication date	Nov 12, 2019
Grant date	Nov 12, 2019

Abstract

A method and system to identify an epitope unique to a misfolded form of a protein is provided. Sets of one or more amino acid residues are selected from a model representing the structure of the protein; the free energy of unfolding of each set is determined; and the epitope is identified from the sets having a total probability of unfolding above a minimum probability or a free energy of unfolding below a minimum energy. In other aspects, the invention provides for the use of epitopes identified by the epitope prediction methods, and related antibodies, to diagnose and treat disease and to screen samples for the presence of such epitopes.

First claim

We claim:

1. A method for obtaining an immunogen useful to produce an antibody that binds selectively to a misfolded form of a protein relative to the natively folded form of that protein, the method comprising:
applying a method of operating a system to identify an epitope unique to a misfolded form of a protein of interest, the system comprising a processor and one or more memories coupled to the processor, the one or more memories containing instructions recorded thereon that, when executed by the processor, cause the processor to:
(a) receive a model representing at least a portion of the structure of the protein of interest;
(b) select one or more sets from the model, each set comprising one or more amino acid residues;
(c) determine the free energy of unfolding of each set; and
(d) identify the epitope by:
(i) determining the total probability of unfolding of each set based on the free energy of unfolding of one or more of the sets in isolation, and identifying the epitope from the sets having a total probability of unfolding above a minimum probability; or
(ii) identifying the epitope from the sets having a free energy of unfolding below a minimum energy;
wherein the identifying comprises storing data describing the epitope in the one or more memories of the system, or presenting graphical or numerical depiction of the epitope on a display or printed medium;

preparing a peptide comprising the epitope identified in step (d) by solid or solution phase synthesis; and
isolating the peptide and producing the immunogen comprising the peptide that comprises the epitope unique to the misfolded form of the protein of interest.

2. The method of claim 1 , wherein:
(a) the method further comprises receiving by the processor a selection of a region in the model; and
(b) each of the one or more sets selected by the processor comprise at least one residue in the region.

3. The method of claim 1 , wherein selecting by the processor one or more sets from the model comprises selecting all sets comprising a sequence of one or more contiguous amino acid residues in the model.

4. The method of claim 1 , wherein selecting by the processor one or more sets from the model comprises selecting all sets comprising two or more non-contiguous sequences of one or more contiguous amino acid residues in the model.

5. The method of claim 3 , wherein each sequence comprises a length between a minimum length and a maximum length.

6. The method of claim 1 , wherein determining by the processor the free energy of unfolding of each set comprises determining the enthalpy of unfolding of the set by:
(a) determining the total number of pairs of polar atoms in the model that (i) are comprised of at least one polar atom in the set, (ii) are more than one amino acid residue apart in the amino acid sequence of the model, and (iii) are within a cutoff distance from one another; and
(b) determining the enthalpy of unfolding of the set as the product of the total number of pairs determined in (a) by a fixed interaction energy.

7. The method of claim 1 , wherein determining by the processor the free energy of unfolding of each set comprises determining the enthalpy of unfolding of the set by summing the results of solving the following equation for each pair of polar atoms in the model that are comprised of at least one atom in the set:
wherein:

Δ
⁢

⁢
H

=

∈
′

⁢

cos
4

⁡

(
θ
)

⁢

(

(

1
r

)

10

-

β
⁡

(

1
r

)

12

)

ΔH is enthalpy of unfolding of the pair of polar atoms;
{acute over (ε)} is a fitting parameter;
θ is an angle between covalent bonds to carbon involving the polar atoms;
r is distance between the pair of polar atoms; and
β is a fitting parameter.

8. The method of claim 1 , wherein determining by the processor the free energy of unfolding of each set comprises determining the enthalpy of unfolding of the set by:
(a) determining the solvent accessible surface area of the polar, nonpolar and hydroxyl functional groups that comprise the amino acid residues in the model;
(b) determining the solvent accessible surface area of the polar, nonpolar and hydroxyl functional groups that comprise the amino acid residues in the model with the set removed;
(c) determining the solvent accessible surface area of the polar, nonpolar and hydroxyl functional groups that comprise the amino acid residues of the set in isolation;
(d) determining the sum of the solvent accessible surface area of the polar functional groups determined in (b) and (c) minus the solvent accessible surface area of the polar functional groups determined in (a);
(e) determining the sum of the solvent accessible surface area of the nonpolar functional groups determined in (b) and (c) minus the solvent accessible surface area of the nonpolar functional groups determined in (a);
(f) determining the sum of the solvent accessible surface area of the hydroxyl functional groups determined in (b) and (c) minus the solvent accessible surface area of the hydroxyl functional groups determined in (a);
(g) determining the enthalpy of unfolding of the set by solving the following equation:

Δ
⁢

⁢

H
⁡

(
T
)

=

(

-
8.44

⁢
Δ
⁢

⁢

ASA
nonpolar

+

31.4
⁢

Assignees

• Univ British Columbia

Inventors

• Cashman Neil R
• Plotkin Steven S
• Guest William C

Classifications

• A61P43/00

  Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00 · CPC title

• A61P37/04

  Immunostimulants · CPC title

• A61P35/04

  specific for metastasis · CPC title

• A61P35/02

  specific for leukemia · CPC title

• A61P35/00

  Antineoplastic agents · CPC title