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CN-116583298-B - PD-1 targeted IL-15/IL-15RαFC fusion proteins with improved properties

CN116583298BCN 116583298 BCN116583298 BCN 116583298BCN-116583298-B

Abstract

The present invention relates to fusion proteins comprising a variant IL-15 protein, fusion proteins comprising a variant anti-PD-1 antigen-binding domain, and fusion proteins comprising a variant IL-15 protein and a variant anti-PD-1 antigen-binding domain. The invention also relates to nucleic acid molecules, expression vectors, host cells and methods for preparing such fusion proteins and the use of such fusion proteins in cancer treatment.

Inventors

  • J. Desijialaisi
  • C.HUANG
  • M. Burnett
  • M. Hedwatt
  • R. Valma
  • SCHUBERT STEPHAN
  • C. Bunsen
  • R. Rachid
  • DIAZ JORGE
  • P. Holder

Assignees

  • 基因泰克公司
  • XENCOR股份有限公司

Dates

Publication Date
20260512
Application Date
20201009
Priority Date
20191011

Claims (20)

  1. 1. A composition comprising a variant IL-15 protein, wherein in the variant IL-15 protein, N at position 71 is substituted with Q, N at position 79 is substituted with Q, and S at position 114 is substituted with a, as compared to SEQ ID No. 2.
  2. 2. A composition comprising a variant IL-15 protein, wherein in the variant IL-15 protein, N at position 71 is substituted with Q, N at position 79 is substituted with Q, and S at position 114 is deleted compared to SEQ ID No. 2.
  3. 3. A composition comprising a variant IL-15 protein, wherein in the variant IL-15 protein, N at position 71 is substituted with Q, N at position 79 is substituted with Q, and N at position 112 is substituted with Q, as compared to SEQ ID No. 2.
  4. 4. A composition comprising a variant IL-15 protein, wherein in the variant IL-15 protein, N at position 71 is substituted with Q, N at position 79 is substituted with Q, S at position 114 is substituted with a, D at position 30 is substituted with N, and N at position 65 is substituted with D, as compared to SEQ ID No. 2.
  5. 5. A composition comprising a variant IL-15 protein, wherein in the variant IL-15 protein, N at position 71 is substituted with Q, N at position 79 is substituted with Q, S at position 114 is deleted, D at position 30 is substituted with N, and N at position 65 is substituted with D, as compared to SEQ ID No. 2.
  6. 6. A composition comprising a variant IL-15 protein, wherein in the variant IL-15 protein, N at position 71 is substituted with Q, N at position 79 is substituted with Q, N at position 112 is substituted with Q, D at position 30 is substituted with N, and N at position 65 is substituted with D, as compared to SEQ ID No. 2.
  7. 7. A composition comprising a variant IL-15 protein, wherein in the variant IL-15 protein, N at position 71 is substituted with Q, N at position 79 is substituted with Q, S at position 114 is substituted with a, D at position 30 is substituted with N, E at position 64 is substituted with Q, and N at position 65 is substituted with D, as compared to SEQ ID No. 2.
  8. 8. A composition comprising a variant IL-15 protein, wherein in the variant IL-15 protein, N at position 71 is substituted with Q, N at position 79 is substituted with Q, S at position 114 is deleted, D at position 30 is substituted with N, E at position 64 is substituted with Q, and N at position 65 is substituted with D, as compared to SEQ ID No. 2.
  9. 9. A composition comprising a variant IL-15 protein, wherein in the variant IL-15 protein, N at position 71 is substituted with Q, N at position 79 is substituted with Q, N at position 112 is substituted with Q, D at position 30 is substituted with N, E at position 64 is substituted with Q, and N at position 65 is substituted with D, as compared to SEQ ID No. 2.
  10. 10. The composition of claim 9, wherein the amino acid sequence of the variant IL-15 protein consists of SEQ ID NO: 319.
  11. 11. A nucleic acid composition comprising a nucleic acid molecule encoding the variant IL-15 protein of any one of claims 1 to 10.
  12. 12. An expression vector comprising the nucleic acid molecule of claim 11.
  13. 13. A host cell comprising the nucleic acid molecule of claim 11 or the expression vector of claim 12.
  14. 14. A method of making a composition comprising a variant IL-15 protein, the method comprising culturing the host cell of claim 13 under conditions wherein the variant IL-15 protein is produced and recovering the variant IL-15 protein.
  15. 15. A pharmaceutical composition comprising a variant IL-15 protein according to any one of claims 1 to 10 and a pharmaceutically acceptable carrier.
  16. 16. Use of the variant IL-15 protein of any one of claims 1 to 10 for the manufacture of a medicament for treating cancer in a subject in need thereof, wherein the cancer is breast cancer or colon cancer.
  17. 17. The use of claim 16, wherein the composition comprising the variant IL-15 protein is formulated for administration in combination with a therapeutically effective amount of a checkpoint blocking antibody, wherein the checkpoint blocking antibody is an anti-PD-1 antibody or an anti-PD-L1 antibody.
  18. 18. Use of the pharmaceutical composition according to claim 15 for the manufacture of a medicament for treating cancer in a subject in need thereof, wherein the cancer is breast cancer or colon cancer.
  19. 19. The use of claim 18, wherein the pharmaceutical composition is formulated for administration in combination with a therapeutically effective amount of a checkpoint blocking antibody, wherein the checkpoint blocking antibody is an anti-PD-1 antibody or an anti-PD-L1 antibody.
  20. 20. The use of claim 17 or 19, wherein the checkpoint blocking antibody is nal Wu Liyou mab or pamt Li Zhushan antibody.

Description

PD-1 targeted IL-15/IL-15RαFC fusion proteins with improved properties Cross Reference to Related Applications The present application claims priority from U.S. provisional application No. 62/914,265, U.S. provisional application No. 62/914,317, and U.S. provisional application No. 63/011,208, 16, 10, 2020, 10, 11, 2019, each of which is incorporated herein by reference in its entirety. Sequence listing The present application comprises a sequence listing that has been electronically submitted in ASCII format and is incorporated by reference herein in its entirety. The ASCII copy was created on 10/9 of 2020 and named 000218-0005-WO 1-sequence_LISTING.TXT, size 764,863 bytes. Background In cancer immunotherapy, two very promising approaches include cytokine-based therapies and blockade of immune checkpoint proteins such as PD-1. Cytokines such as IL-2 and IL-15 contribute to proliferation and differentiation of B cells, T cells and NK cells. Both cytokines exert their cell signaling functions by binding to a trimeric complex composed of two co-receptors, the common gamma chain (yc; CD 132) and the IL-2 receptor beta chain (IL-2rβ; CD 122), and the alpha chain receptor (IL-2 receptor alpha (IL-2rα; CD 25) or IL-15 receptor alpha (IL-15 rα; CD 215) that is unique to each cytokine. Both cytokines are considered potential valuable therapeutic agents in oncology, and IL-2 has been approved for the treatment of metastatic renal cell carcinoma and malignant melanoma patients. At present, although several clinical trials are underway, the use of recombinant IL-15 has not been approved. But as a potential drug, both cytokines have very rapid clearance with half-lives in minutes. Systemic toxicity can be caused when large doses of IL-2 immunotherapy are used to overcome the rapid clearance problem. In recent clinical trials, this systemic toxicity has also been described in relation to IL-15 immunotherapy (Guo et al, J Immunol,2015,195 (5): 2353-64). Upon T cell activation, immune checkpoint proteins such as PD-1 are upregulated, depleting activated T cells by binding to immune checkpoint ligands such as PD-L1, thereby preventing autoimmunity. However, immune checkpoint proteins are also up-regulated in Tumor Infiltrating Lymphocytes (TILs) and immune checkpoint ligands are over-expressed on tumor cells, thereby promoting immune escape from tumor cells. Research proves that by medicine(Na Wu Liyou mab) and(Palbociclizumab) blocks immune checkpoint interactions to eliminate inhibition of TIL, and can effectively treat cancer. Although checkpoint blocking therapies such as nal Wu Liyou mab and palbociclib have good prospects, many patients still fail to achieve adequate response to checkpoint blockade alone. Thus, there remains a need for therapeutic strategies comprising cytokines in tumor therapy that do not require high dose administration and have anti-tumor effects that avoid systemic toxicity. In addition, there is a need to identify other treatments that combine with checkpoint blockade to increase patient remission rates. This may be particularly complex as other treatments should not compete with checkpoint blockers. The present invention addresses these needs and warnings by providing PD-1 targeted IL-15 fusion proteins that have an extended half-life and target TIL with higher selectivity to improve safety features, and that do not compete with checkpoint blocker antibodies that may bind together. Disclosure of Invention The first aspect of the invention provides a targeted IL-15/Rα heterodimeric Fc fusion protein comprising a) a first monomer comprising from N-terminus to C-terminus i) an IL-15/Rα sushi domain, ii) a first domain linker, iii) an IL-15 domain, and iv) a first variant Fc domain, b) a second monomer comprising a heavy chain comprising a VH-CH 1-hinge-CH 2-CH3, wherein the CH2-CH3 is a second variant Fc domain, C) a third monomer comprising a light chain comprising a VL-CL, wherein the VH and VL domains form an Antigen Binding Domain (ABD) that binds to human PD-1, wherein the VH is a variant variable heavy domain comprising an F32L/W100F amino acid substitution according to SEQ ID NO:5, and wherein the VH is a variant variable domain comprising an N27dH/K30Y/S93 according to SEQ ID NO: 168. In some embodiments, the VH comprises the amino acid sequence of SEQ ID NO. 318 and the VL comprises the amino acid sequence of SEQ ID NO. 176. In some embodiments, the IL-15 domain is a variant IL-15 domain comprising an amino acid substitution ：D30N/E64Q/N65D、N1D/N4D/D8N、N1D/N4D/N65D、N1D/D30N、N1D/D61N、N1D/D61N/E64Q/Q108E、N1D/E64Q、N1D/N65D、N1D/Q108E、N4D/D30N、N4D/D61N、N4D/D61N/N65D、N4D/D61N/E64Q/Q108E、N4D/E64Q、N4D/N65D、D8N/D61N、D8N/E64Q、D30N/E64Q、D30N/N65D、D30N/Q180E、D61N/E64Q/N65D、E64Q/N65D、E64Q/Q108E selected from the group consisting of N65D/Q108E. In some embodiments, the IL-15 domain is a variant IL-15 domain comprising an amino acid substitution selected from the group consisting of N71Q, N79Q, N112Q,