Compound arrays for sample profiling

• US 9,709,558 B2
• Filed: 09/21/2012
• Issued: 07/18/2017
• Est. Priority Date: 06/19/2009
• Status: Active Grant

• Current Assignee: Arizona Board of Regents (University of Arizona)
• Original Assignee: Arizona Board of Regents (University of Arizona)
• Inventors: Johnston, Stephen Albert, Stafford, Phillip
• Primary Examiner(s): Andres, Janet L
• Assistant Examiner(s): Chestnut, Barry A
• Application Number:
  US13/624,386
• Publication Number:
  US 20130079242A1
• Time in Patent Office: 1,761 Days
• CPC Class Codes: C40B 40/10 Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: G01N 33/53 Immunoassay; Biospecific binding assay; Materials therefor
• CPC Class Codes: G01N 33/543 with an insoluble carrier for immobilising immunochemicals
• CPC Class Codes: G01N 33/54306 Solid-phase reaction mechanisms
• CPC Class Codes: G01N 33/6845 Methods of identifying protein-protein interactions in protein mixtures
• CPC Class Codes: G01N 33/6854 Immunoglobulins

Abstract

The invention provides arrays of compound for use in profiling samples. The arrays include compounds bind to components of the samples at relatively low affinities. The avidity of compounds binding to components of the samples can be increased by forming arrays such that multivalent components of the samples (e.g., antibodies or cells) can bind to more than one molecule of a compound at the same time. When a sample is applied to an array under such conditions, the compounds of the array bind to component(s) of the sample with significantly different avidities generating a profile characteristic of the sample.

Claims

1. A method of testing a vaccine, comprising

(a) contacting antibodies in a blood sample of a subject immunized with a vaccine against a pathogenic microorganism with an array of different peptides of between 10-30 amino acids in length immobilized on the surface of the array, wherein each different peptide has a unique amino acid sequence, each of the different peptides occupying a distinct feature of the array, wherein each distinct feature of the array comprises peptides of a same sequence, wherein at least 50 of the different peptides have dissociation constants of between 1 mM and 1 μ

M to at least one antibody in the subject'"'"'s sample, and wherein the array comprises at least 100,000 immobilized different peptides;

(b) detecting a pattern of antibody binding of the blood sample to the immobilized different peptides in the array, wherein the pattern comprises binding interactions with dissociation constants of between 1 mM and 1 μ

M; and

(c) comparing the binding interactions with dissociation constants of between 1 mM and 1 μ

M in the pattern of antibody binding of the blood sample of the subject to the pattern of antibody binding of one or more reference samples, wherein the reference samples are from subjects who have survived an infection with the pathogenic microorganism, wherein a plurality of peptides common to the pattern of antibody binding of the subject and pattern of antibody binding of the one or more reference samples indicates that the vaccine is effective against the pathogenic microorganism.

2. The method of claim 1, wherein the subject has been immunized with a vaccine before exposure to the pathogenic microorganism.

3. The method of claim 1, wherein the pathogenic microorganism is a virus.

5. The method of claim 1, wherein the peptides are 15 to 25 amino acids long.

6. The method of claim 1, wherein the peptides are 20 amino acids long.

7. The method of claim 1, wherein the peptides comprise the synthetic amino acids ornithine or norleucine.

8. The method of claim 1, wherein the peptides comprise naturally occurring amino acids.

9. The method of claim 1, wherein the peptides are spotted onto a surface of the array.

10. The method of claim 1, wherein the peptides are synthesized onto a surface of the array.

11. The method of claim 1, wherein the array contains from 100,000-1,000,000 peptides.

12. The method of claim 1, wherein the array contains from 500,000-2,000,000 peptides.

13. The method of claim 1, wherein peptides of a same sequence are spaced less than 6 nm apart.

14. The method of claim 1, wherein peptides of a same sequence-on the array have an average spacing of less than 4 nm apart.

15. The method of claim 1, wherein peptides of a same sequence have an average spacing of 2-4 nm.

16. The method of claim 1, wherein at least 1000 of the different peptides have dissociation constants of between 1 mM and 1 μ

M to at least one antibody in the sample.

17. The method of claim 1, wherein at least 1% of the different peptides have dissociation constants of between 1 mM and 1 μ

M to at least one antibody in the sample.

18. The method of claim 1, wherein the comparison is performed by a computer system that measures the euclidean distance between two vectors.

19. The method of claim 1, wherein at least 0.1% of the different peptides distinguish a protective antibody response from a non-protective antibody response.

20. The method of claim 19, wherein at least 1% of the different peptides distinguish a protective antibody response from a non-protective antibody response.

21. The method of claim 1, further comprising identifying the sequence of at least one different peptide having a dissociation constant of between 1 mM and 1 μ

M to at least one antibody in the sample.

22. The method of claim 1, wherein the amino-acid sequence of the peptides is random or semi-random.

23. The method of claim 1, wherein the comparison is performed by a computer system that provides a Spearman Correlation.

4. The method of 1, wherein the peptides are 12 to 35 amino acids long.