CD20-binding proteins comprising Shiga toxin A subunit effector regions for inducing cellular internalization and methods using same

Patent metadata

Field	Value
Publication number	US-11142584-B2
Application number	US-201514643619-A
Country	US
Kind code	B2
Filing date	Mar 10, 2015
Priority date	Mar 11, 2014
Publication date	Oct 12, 2021
Grant date	Oct 12, 2021

Abstract

The present invention provides CD20-binding proteins that bind to and rapidly internalize in a CD20-mediated fashion from a cell surface location to the interior of the cell. CD20-binding proteins of the invention comprise a CD20 binding region and a Shiga toxin effector region. Certain of the disclosed CD20-binding proteins kill cells that express CD20 on their surface. Further, the presently disclosed CD20-binding proteins can comprise additional exogenous materials, such as, e.g., antigens, and are capable of targeted delivery of these additional exogenous materials into the interior of CD20 expressing cells. These CD20-binding proteins have uses in methods such as, e.g., methods involving the efficient cellular internalization of CD20, targeted killing of CD20 expressing cells, delivering exogenous materials inside CD20 expressing cells, detecting CD20 expressing cells, and treating a variety of conditions involving CD20 expressing cells including cancers, tumors, growth abnormalities, and immune disorders.

First claim

The invention is claimed as follows:

1. A CD20-binding protein comprising:
a) a CD20 binding region capable of specifically binding an extracellular part of CD20, wherein the CD20 binding region comprises the polypeptide represented by amino acids 2 to 245 of any one of SEQ ID NOs: 46-63, 90-98, 103-105, 108-110, and 112, and
b) a Shiga toxin A Subunit effector region polypeptide comprising an amino acid sequence that is at least 95% identical to an amino acid sequence selected from:
i) amino acids 75 to 251 of SEQ ID NO: 1 or SEQ ID NO: 2;
ii) amino acids 1 to 251 of SEQ ID NO: 1 or SEQ ID NO: 2; and
iii) amino acids 1 to 261 of SEQ ID NO: 1 or SEQ ID NO: 2;
wherein the CD20 binding region is linked via one or more peptide linker(s) to the Shiga toxin A Subunit effector region polypeptide;

wherein, when the CD20-binding protein is administered to CD20 positive cells at a concentration equivalent to 50% cell-surface CD20 occupancy, the CD20-binding protein internalizes into one or more of the CD20 positive cells within five hours at 37 degrees Celsius.

2. The CD20-binding protein of claim 1 , wherein, when the CD20-binding protein is administered to CD20 positive cells at a concentration equivalent to 50% cell-surface CD20 occupancy, the CD20-binding protein internalizes into one or more of the CD20 positive cells within one hour at 37 degrees Celsius.

3. The CD20-binding protein of claim 1 , wherein the CD20 positive cell is a descendant or member of a B-cell lineage.

4. The CD20-binding protein of claim 1 , wherein the CD20 positive cell is a:
malignant B-cell, B-cell leukemia cell, B-cell lymphoma cell, B-cell myeloma cell, acute myeloid leukemia cell, acute non-lymphocytic leukemia cell, B-cell chronic lymphocytic leukemia cell, B-cell lymphoma cell, B-cell non-Hodgkin's lymphoma cell, B-cell precursor acute lymphoblastic leukemia cell, B-cell prolymphocytic leukemia cell, Burkitt's lymphoma cell, chronic lymphocytic leukemia cell, chronic myeloid leukemia cell, diffuse large B-cell lymphoma cell, follicular lymphoma cell, hairy cell leukemia cell, Hodgkin's lymphoma cell, immunoblastic large cell lymphoma cell, mantle cell lymphoma cell, melanoma cell, multiple myeloma cell, neoplastic plasma cell, nodular lymphocyte predominant Hodgkin's lymphoma cell, non-Hodgkin's lymphoma cell, plasmablastic lymphoma cell, plasma cell myeloma cell, precursor B-lymphoblastic lymphoma cell, small lymphocytic lymphoma cell, malignant T-cell, T-cell leukemia cell, T-cell lymphoma cell, T-cell large granular lymphocyte leukemia cell, T-cell prolymphocytic leukemia cell, healthy B-cell lineage cell, or healthy T-cell.

5. The CD20-binding protein of claim 1 , wherein, when the CD20-binding protein is administered to one or more CD20 positive cells at a physiological temperature, the CD20-binding protein is capable of one or more of the following behaviors in said one or more CD20 positive cells:
(i) internalizing inside said one or more CD20 positive cells within one hour,
(ii) subcellular routing at least one Shiga toxin A Subunit effector region polypeptide to the cytosol of said one or more CD20 positive cells,
(iii) disrupting the ribosome function of said one or more CD20 positive cells, and
(iv) killing of said one or more CD20 positive cells.

6. The CD20-binding protein of claim 5 , wherein the CD20-binding protein exhibits a cytotoxic effect that is at least 3-fold greater to a first population cells whose members are CD20 positive relative to a second population of cells whose members do not express CD20 at a cellular surface.

7. The CD20-binding protein of claim 1 , wherein the Shiga toxin A Subunit effector region polypeptide comprises a polypeptide comprising the amino acid sequence selected from:
a) amino acids 75 to 251 of SEQ ID NO: 1 or SEQ ID NO: 2;
b) amino acids 1 to 251 of SEQ ID NO: 1 or SEQ ID NO: 2; and
c) amino acids 1 to 261 of SEQ ID NO: 1 or SEQ ID NO: 2.

8. A CD20-binding protein comprising:
a) a CD20 binding region capable of specifically binding an extracellular part of CD20,
and comprising the polypeptide represented by amino acids 2 to 245 of any one of SEQ ID NOs: 46-112, and

b) a Shiga toxin A Subunit effector region polypeptide, wherein the polypeptide is represented by amino acids 75 to 251 of SEQ ID NO:1
wherein the CD20 binding region is linked via one or more peptide linker(s) to the Shiga toxin A Subunit effector region polypeptide; and
wherein, when the CD20-binding protein is administered to CD20 positive cells at a concentration equivalent to 50% cell-surface CD20 occupancy, the CD20-binding protein internalizes into one or more of the CD20 positive cells within five hours at 37 degrees Celsius.

9. The CD20-binding protein of claim 8 , which comprises the polypeptide shown in any one of SEQ ID NOs: 47-51 and 53-63.

10. The CD20-binding protein of claim 1 , further comprising an additional exogenous peptide.

11. A pharmaceutical composition comprising
the CD20-binding protein of claim 1 ; and
at least one pharmaceutically acceptable excipient or carrier.

12. A diagnostic composition comprising
the CD20-binding protein of claim 1 ; and
a detection promoting agent.

13. A kit comprising:
(i) the CD20-binding protein of claim 1 ;
(ii) the pharmaceutical composition according to claim 11 ; or
(iii) the diagnostic composition according to claim 12 ; and
an additional reagent and/or pharmaceutical delivery device.

14. The CD20-binding protein of claim 1 or 8 , wherein the amino acid residue corresponding to position 75 of SEQ ID NO: 1 or 2 is asparagine, the amino acid residue corresponding to position 77 of SEQ ID NO: 1 or 2 is tyrosine, the amino acid residue corresponding to position 167 of SEQ ID NO: 1 or 2 is glutamate, the amino acid residue corresponding to position 170 of SEQ ID NO: 1 or 2 is arginine, and the amino acid residue corresponding to position 176 of SEQ ID NO: 1 or 2 is arginine.

15. The CD20-binding protein of claim 1 or 8 , wherein at least one of the one or more peptide linker(s) comprises an IgG3 linker.

16. The pharmaceutical composition of claim 11 , wherein the amino acid residue corresponding to position 75 of SEQ ID NO: 1 or 2 is asparagine, the amino acid residue corresponding to position 77 of SEQ ID NO: 1 or 2 is tyrosine, the amino acid residue corresponding to position 167 of SEQ ID NO: 1 or 2 is glutamate, the amino acid residue corresponding to position 170 of SEQ ID NO: 1 or 2 is arginine, and the amino acid residue corresponding to position 176 of SEQ ID NO: 1 or 2 is arginine.

17. The diagnostic composition of claim 12 , wherein the amino acid residue corresponding to position 75 of SEQ ID NO: 1 or 2 is asparagine, the amino acid residue corresponding to position 77 of SEQ ID NO: 1 or 2 is tyrosine, the amino acid residue corresponding to position 167 of SEQ ID NO: 1 or 2 is glutamate, the amino acid residue corresponding to position 170 of SEQ ID NO: 1 or 2 is arginine, and the amino acid residue corresponding to position 176 of SEQ ID NO: 1 or 2 is arginine.

18. A method of delivering an exogenous peptide to a cell, the method comprising administering the exogenous peptide of claim 10 to a CD20-expressing cell, wherein the CD20-binding protein delivers the additional exogenous material into the interior of the cell within five hours at 37 degrees Celsius.

Assignees

• Molecular Templates Inc

Inventors

• Poma Eric
• Kim Jason
• Higgins Jack
• Willert Erin
• Rajagopalan Sangeetha

Classifications

• G01N33/57505

  of the blood, e.g. leukaemia · CPC title

• A61K2039/6056

  Antibodies · CPC title

• A61K47/6829

  Bacterial toxins, e.g. diphteria toxins or Pseudomonas exotoxin A · CPC title

• C12N2760/16134

  Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein · CPC title

• A61K39/12

  Viral antigens · CPC title