Techniques for predicting, detecting and reducing aspecific protein interference in assays involving immunoglobulin single variable domains

Patent metadata

Field	Value
Publication number	US-10858418-B2
Application number	US-202016822186-A
Country	US
Kind code	B2
Filing date	Mar 18, 2020
Priority date	Jun 23, 2011
Publication date	Dec 8, 2020
Grant date	Dec 8, 2020

Abstract

This invention provides, and in certain specific but non-limiting aspects relates to: assays that can be used to predict whether a given ISV will be subject to protein interference as described herein and/or give rise to an (aspecific) signal in such an assay (such as for example in an ADA immunoassay). Such predictive assays could for example be used to test whether a given ISV could have a tendency to give rise to such protein interference and/or such a signal; to select ISV's that are not or less prone to such protein interference or to giving such a signal; as an assay or test that can be used to test whether certain modification(s) to an ISV will (fully or partially) reduce its tendency to give rise to such interference or such a signal; and/or as an assay or test that can be used to guide modification or improvement of an ISV so as to reduce its tendency to give rise to such protein interference or signal; —methods for modifying and/or improving ISV's to as to remove or reduce their tendency to give rise to such protein interference or such a signal; —modifications that can be introduced into an ISV that remove or reduce its tendency to give rise to such protein interference or such a signal; ISV's that have been specifically selected (for example, using the assay(s) described herein) to have no or low(er)/reduced tendency to give rise to such protein interference or such a signal; modified and/or improved ISV's that have no or a low(er)/reduced tendency to give rise to such protein interference or such a signal.

First claim

The invention claimed is:

1. A method of modifying a protein comprising an amino acid sequence of an immunoglobulin single variable domain (VH or VHH) and ending with the sequence VTVSS (SEQ ID NO: 33) to have reduced aspecific protein binding to the C-terminal end of said protein, the method comprising extending the C-terminal end of said protein by 1 to 5 amino acid residues to generate an extended protein ending with the sequence VTVSS(X) n (SEQ ID NO: 34), in which n is 1 to 5, with each X being independently chosen from any amino acid.

2. The method of claim 1 , wherein the extended protein has reduced aspecific protein binding to its C-terminal end in a biological fluid of a human subject.

3. The method of claim 1 , wherein the biological fluid is a whole blood sample, a serum sample, a plasma sample, an ocular fluid sample, a bronchoalveolar fluid sample, or a cerebrospinal fluid sample.

4. The method of claim 1 , wherein n is 1 to 5 , with each X being independently chosen from any naturally occurring amino acid.

5. The method of claim 1 , wherein n is 1 to 5 , with each X being independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) and isoleucine (I).

6. The method of claim 5 , wherein the amino acid sequence of the immunoglobulin single variable domain has valine at position 11 according to Kabat numbering.

7. The method of claim 1 , wherein n is 1 or 2.

8. The method of claim 1 , in which:
(a) n=1, 2 or 3 in which each X=Ala or Gly; or
(b) n=1, 2 or 3 in which each X=Ala; or
(c) n=1, 2 or 3 in which each X=Gly; or
(d) n=2 or 3 in which at least one X=Ala or Gly, with any remaining amino acid residue X being independently chosen from any naturally occurring amino acid; or
(e) n =2 or 3 in which all but one X=Ala or Gly, with any remaining amino acid residue X being independently chosen from any naturally occurring amino acid.

9. The method of claim 8 , in which in (d) or (e) the remaining amino acid residue X is independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) and isoleucine (I).

10. The method of claim 8 , wherein n=1 or n=2.

11. The method of claim 1 , wherein the immunoglobulin single variable domain is a VHH or humanized VHH.

12. The method of claim 1 , wherein the immunoglobulin single variable domain is a VH or a camelized VH.

13. A method of modifying a protein comprising an amino acid sequence of an immunoglobulin single variable domain (VH or VHH) and ending with the sequence VTVSS (SEQ ID NO: 33) to have reduced aspecific protein binding to the C-terminal end of said protein, the method comprising extending the C-terminal end of said protein by 1 to 5 amino acid residues to generate an extended protein ending with the sequence VTVSS(X) n (SEQ ID NO: 34), in which n is 1 to 5, with each X being independently chosen from any amino acid; wherein the protein comprises an amino acid sequence of two or more immunoglobulin single variable domains (VH or VHH), wherein at least one of the immunoglobulin single variable domains binds a therapeutic target.

14. The method of claim 13 , wherein the protein further comprises an amino acid sequence of one or more linkers separating the amino acid sequences of two or more immunoglobulin single variable domains of the protein.

15. The method of claim 13 , in which:
(a) n=1, 2 or 3 in which each X=Ala or Gly; or
(b) n=1, 2 or 3 in which each X=Ala; or
(c) n=1, 2 or 3 in which each X=Gly; or
(d) n=2 or 3 in which at least one X=Ala or Gly, with any remaining amino acid residue X being independently chosen from any naturally occurring amino acid; or
(e) n=2 or 3 in which all but one X=Ala or Gly, with any remaining amino acid residue X being independently chosen from any naturally occurring amino acid.

16. A method of modifying a protein comprising an amino acid sequence of an immunoglobulin single variable domain (VH or VHH) and ending with the sequence VTVSS (SEQ ID NO: 33) to have reduced aspecific protein binding to the C-terminal end of said protein, the method comprising extending the C-terminal end of said protein by 1 to 5 amino acid residues to generate an extended protein ending with the sequence VTVSS(X) n (SEQ ID NO: 34), in which n is 1 to 5, with each X being independently chosen from any amino acid; wherein the protein comprises an amino acid sequence of two or more immunoglobulin single variable domains (VH or VHH), wherein one of the immunoglobulin single variable domains binds serum albumin.

17. The method of claim 16 , wherein the immunoglobulin single variable domain that binds serum albumin is at the C-terminal end of the protein.

18. The method of claim 16 , wherein the immunoglobulin single variable domain that binds serum albumin is not at the C-terminal end of the protein.

19. The method of claim 16 , wherein, the protein further comprises an amino acid sequence of one or more linkers separating the amino acid sequences of two or more immunoglobulin single variable domains of the protein.

20. The method of claim 16 , in which:
(a) n=1, 2 or 3 in which each X=Ala or Gly; or
(b) n=1, 2 or 3 in which each X=Ala; or
(c) n=1, 2 or 3 in which each X=Gly; or
(d) n=2 or 3 in which at least one X=Ala or Gly, with any remaining amino acid residue X being independently chosen from any naturally occurring amino acid; or
(e) n=2 or 3 in which all but one X=Ala or Gly, with any remaining amino acid residue X being independently chosen from any naturally occurring amino acid.

Assignees

• Ablynx Nv

Inventors

• Baumeister Judith
• Bouche Marie-Paule Lucienne Armanda
• Boutton Carlo
• Buyse Marie-Ange
• Snoeck Veerle
• Staelens Stephanie
• Dombrecht Bruno
• Schotte Peter
• Ververken Cedric Jozef Neotere
• Beste Gerald
• Hermans Guy
• Steffensen Soren
• Szyroki Alexander
• Denayer Tinneke

Classifications

• C07K2317/76

  Antagonist effect on antigen, e.g. neutralization or inhibition of binding · CPC title

• C07K16/00 Primary

  Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies · CPC title

• C07K2317/92

  Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value · CPC title

• C07K2317/569

  Single domain, e.g. dAb, sdAb, VHH, VNAR or nanobody® · CPC title

• C07K2317/567

  Framework region [FR] · CPC title