WO2023041041A1 - D3-binding molecules and uses thereof - Google Patents

D3-binding molecules and uses thereof Download PDF

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WO2023041041A1
WO2023041041A1 PCT/CN2022/119334 CN2022119334W WO2023041041A1 WO 2023041041 A1 WO2023041041 A1 WO 2023041041A1 CN 2022119334 W CN2022119334 W CN 2022119334W WO 2023041041 A1 WO2023041041 A1 WO 2023041041A1
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seq
set forth
amino acid
antibody
binding molecule
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French (fr)
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Yunying CHEN
Yongqing Cheng
Xia Wang
Jijie Gu
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Wuxi Biologics Shanghai Co Ltd
Wuxi Biologics Ireland Ltd
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Wuxi Biologics Shanghai Co Ltd
Wuxi Biologics Ireland Ltd
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Priority to CN202280072803.0A priority Critical patent/CN118234510A/zh
Priority to EP22869407.1A priority patent/EP4401775A4/en
Priority to CA3231586A priority patent/CA3231586A1/en
Priority to KR1020247012198A priority patent/KR20240055852A/ko
Priority to PE2024000473A priority patent/PE20241133A1/es
Priority to US18/692,311 priority patent/US20240376194A1/en
Priority to IL311510A priority patent/IL311510A/en
Priority to JP2024516855A priority patent/JP2024535851A/ja
Priority to CR20240135A priority patent/CR20240135A/es
Priority to MX2024003331A priority patent/MX2024003331A/es
Priority to CN202411637479.XA priority patent/CN119462942A/zh
Priority to AU2022345323A priority patent/AU2022345323A1/en
Application filed by Wuxi Biologics Shanghai Co Ltd, Wuxi Biologics Ireland Ltd filed Critical Wuxi Biologics Shanghai Co Ltd
Publication of WO2023041041A1 publication Critical patent/WO2023041041A1/en
Priority to DO2024000052A priority patent/DOP2024000052A/es
Priority to CL2024000785A priority patent/CL2024000785A1/es
Priority to CONC2024/0003144A priority patent/CO2024003144A2/es
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Definitions

  • D3-binding molecules such as monoclonal antibodies, against D3 which can be used to treat D3-overexpressing tumor have been developed.
  • the CDR3 comprises an amino acid sequence as set forth in SEQ ID NO: 3, 6 or 9.
  • a D3-binding molecule as disclosed herein comprises a single variable domain as set forth in any one of SEQ ID NOs: 12-18 and 55, and IgG constant domains as set forth in SEQ ID NO: 19.
  • Figure 8 shows exemplary cross-family binding results of antibodies with human D1 and human D4, measured by ELISA.
  • a “functional Fc region” possesses an “effector function” of a native sequence Fc region.
  • effector functions include C1q binding; complement dependent cytotoxicity (CDC) ; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC) ; phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor; BCR) , etc.
  • CDC complement dependent cytotoxicity
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • phagocytosis e.g., B cell receptor; BCR
  • Such effector functions generally require the Fc region to be combined with a binding region or binding domain (e.g., an antibody variable region or domain, including a VHH domain) and can be assessed using various assays as disclosed.
  • humanized antibody is intended to refer to antibodies in which CDR sequences derived from the germline of another mammalian species, such as a mouse, llama or alpaca, have been grafted onto human framework sequences. Additional framework region modifications may be made within the human framework sequences.
  • epitope refers to a portion of an antigen that an immunoglobulin or antibody specifically binds to. “Epitope” is also known as “antigenic determinant” .
  • Epitope or antigenic determinant generally comprises chemically active surface groups of a molecule such as amino acids, carbohydrates or sugar side chains, and generally has a specific three-dimensional structure and a specific charge characteristic.
  • an epitope generally comprises at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 consecutive or non-consecutive amino acids in a unique steric conformation, which may be “linear” or “conformational” . See, for example, Epitope Mapping Protocols in Methods in Molecular Biology, Vol.
  • cancer refers to any tumor or any malignant cell growth or proliferation, primary or metastasis-mediated, including solid tumors and non-solid tumors such as leukemia.
  • multispecific (e.g., bispecific) antibody molecules can bind more than one (e.g., two or more) epitopes on the same target (e.g., antigen) .
  • one of the binding specificities is D3 and the other is for one or more of Cytotoxic T-lymphocyte antigen-4 (CTLA-4) , CD80, CD86, Programmed cell death 1 (PD-1) , Programmed cell death ligand 1 (PD-L1) , Programmed cell death ligand 2 (PD-L2) , Lymphocyte activation gene-3 (LAG-3; also known as CD223) , Galectin-3, B and T lymphocyte attenuator (BTLA) , T-cell membrane protein 3 (TIM3) , Galectin-9 (GAL9) , B7-H1, B7-H3, B7-H4, T-Cell immunoreceptor with Ig and ITIM domains (TIGIT/Vstm3/WUCAM/VSIG9) , V-domain
  • Anti-D3 antibodies comprising VHH CDRs
  • Variable regions and CDRs in an antibody sequence can be identified according to general rules that have been developed in the art (for example, the Kabat, AbM, Chothia, Contact, and IMGT numbering system) or by aligning the sequences against a database of known variable regions. Methods for identifying these regions are described in Kontermann and Dubel, eds., Antibody Engineering, Springer, New York, NY, 2001 and Dinarello et al., Current Protocols in Immunology, John Wiley and Sons Inc., Hoboken, NJ, 2000. Exemplary databases of antibody sequences are described in, and can be accessed through, the “Abysis” website at www. bioinf. org. uk/abs (maintained by A.C.
  • anti-D3 antibodies may contain conservative substitution or modification of amino acids in the variable regions and/or constant regions. It is understood in the art that certain conservative sequence modification can be made which do not remove antigen binding. See, e.g., Brummell et al. (1993) Biochem 32: 1180-8; de Wildt et al. (1997) Prot. Eng. 10: 835-41; Komissarov et al. (1997) J. Biol. Chem. 272: 26864-26870; Hall et al. (1992) J. Immunol. 149: 1605-12; Kelley and O’ Connell (1993) Biochem. 32: 6862-35; Adib-Conquy et al. (1998) Int. Immunol. 10: 341-6 and Beers et al. (2000) Clin. Can. Res. 6: 2835-43.
  • an anti-D3 antibody is a humanized antibody comprising a VHH and an Fc region of human IgG1.
  • the addition, deletion and/or substitution of at least one of the amino acids in the VHH region is not in any of the CDR sequences, but in the framework (FRW) sequences.
  • an antibody or antigen-binding portion thereof as described above may comprise one or more substitutions of the amino acids in the framework sequences, e.g. FRW1, FRW2, FRW3, and/or FRW4 of the VHH region.
  • an antibody or antigen-binding portion thereof comprises a VHH domain comprising an amino acid sequence as set forth in any one of SEQ ID NOs: 12-18 and 55, and a Fc region comprising an amino acid sequence as set forth in SEQ ID NO: 19.
  • the nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of:
  • excipients include, for example, water, alcohols, polyols, glycerol, vegetable oils, and the like.
  • suitable isotonic carriers for use in such formulations include Sodium Chloride Injection, Ringer's Solution, or Lactated Ringer's Injection.
  • the particular dosage regimen, including dose, timing and repetition, will depend on the particular individual and that individual's medical history, as well as empirical considerations such as pharmacokinetics (e.g., half-life, clearance rate, etc. ) .
  • anti-cancer agents that may be used in combination with D3-binding molecules (e.g., anti-D3 antibodies) of the present disclosure (either as a component of a site specific conjugate or in an unconjugated state) include, but are not limited to, alkylating agents, alkyl sulfonates, aziridines, ethylenimines and methylamelamines, acetogenins, a camptothecin, bryostatin, callystatin, CC-1065, cryptophycins, dolastatin, duocarmycin, eleutherobin, pancratistatin, a sarcodictyin, spongistatin, nitrogen mustards, antibiotics, enediyne antibiotics, dynemicin, bisphosphonates, esperamicin, chromoprotein enediyne antiobiotic chromophores, aclacinomysins, actinomycin, authramycin,
  • a composition may be provided as a lyophilized powder that may be reconstituted upon addition of an appropriate liquid, for example, sterile water or saline solution.
  • the composition comprises one or more substances that inhibit protein aggregation, including, but not limited to, sucrose and arginine. Any label on, or associated with, the container (s) indicates that the enclosed composition is used for treating the neoplastic disease condition of choice.
  • VHH humanization was done by “Best Fit” approach. Briefly, amino acid sequences of VHH framework regions were blasted against human germline V-gene database, and humanized VHH sequences were generated by replacing human CDR sequences in the top hit with VHH CDR sequences using Kabat CDR definition. Then key residues in framework which play an important role in antibody affinity or developability were back mutated to parental residues alone or in combination.
  • the variants were codon optimized for mammalian expression and then synthesized by GENEWIZ (SuZhou, China) .
  • the designed VHH variants and parental VHH proteins were cloned into human IgG1 expression vectors to generate human IgG1 constructs. Antibodies were produced in HEK293 cells and purified using Protein A chromatography. The variants with desired affinity were finally selected as the humanized leads.
  • na The EC50 value was not fitted.
  • the cells were washed with 1 ⁇ PBS/1%BSA and resuspended in 4%paraformaldehyde, and incubated with cells at 4 °C in dark for 0.5 hour. Then change the buffer with 1 ⁇ PBS/1%BSA and filter the cells. MFI of the cells was measured by a flow cytometer and analyzed by FlowJo.
  • Anti-human D3 antibodies WT115-BMK1-Biotin and WT115-BMK2-Biotin were used as positive controls.
  • WT114-BMK1-Biotin antibody was used as a negative control.
  • Binding of antibodies to the immobilized mouse D3 was detected by HRP-labeled secondary antibody (Invitrogen, SNN1004) , which was diluted in 1 ⁇ PBS/2%BSA at a concentration of 1: 30000. After incubation, the plates were washed using 1 ⁇ PBST for 6 times. The color was developed by dispensing 100 ⁇ L of TMB substrate, and then reaction was stopped by adding 100 ⁇ L of 2M HCl. Absorbance was read at 450nm and 540nm using a microplate spectrophotometer. All samples were tested in duplicate.
  • the binding epitopes of WT1156 antibodies were tested by ELISA with truncated D3 proteins, as described in 1.1 and Figure 7c.
  • the ELISA tests were performed by pre-coating plates with either antibodies or antigens. The results are shown in Figures 7a and 7b, respectively.
  • WT1156-P3R2-1C2-uIgG1 binds to WT115-hPro1. V1. ECD. MBP. AVI. His, WT115-hPro1. V2. ECD. MBP. AVI. His and partially to WT115-hPro1. V3. ECD. MBP. AVI. His, but not to the other isoforms, indicating its binding epitope is located in EGF1-2. WT1156-P3R2-1C9-uIgG1 and WT1156-P3R2-1H6-uIgG1 bind to WT115-hPro1. ECD.
  • Plates were pre-coated with 1 ⁇ g/mL, 100 ⁇ L per well of WT115-hPro1.
  • the antigen was diluted in coating buffer (0.02 M Na2CO3 and 0.18 M NaHCO3, pH9.2) from stock solution. Next day, the plates were washed using 1 ⁇ PBST (PBS containing 0.05%tween-20) for one time, and blocking was done by adding 200 ⁇ L of 1 ⁇ PBS/2%BSA per well.
  • the stability of the samples was tested by binding to human D3 using ELISA. Briefly, plates were pre-coated with 100 ⁇ L /well of 1 ⁇ g/mL WT115-hPro1. ECD. His at 4°C overnight. Next day, the plates were washed using 1 ⁇ PBST (PBS containing 0.05%tween-20) for one time, and blocking was done by adding 200 ⁇ L of 1 ⁇ PBS/2%BSA per well. During blocking, testing antibodies were added to the plates at various concentrations (4-fold serially diluted from 3 nM to 0.00018 nM) . The plates were incubated at ambient temperature for 1 hour.
  • PBST PBS containing 0.05%tween-20

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Priority Applications (16)

Application Number Priority Date Filing Date Title
EP22869407.1A EP4401775A4 (en) 2021-09-17 2022-09-16 D3-binding molecules and uses thereof
CA3231586A CA3231586A1 (en) 2021-09-17 2022-09-16 D3-binding molecules and uses thereof
KR1020247012198A KR20240055852A (ko) 2021-09-17 2022-09-16 D3-결합 분자 및 이의 용도
PE2024000473A PE20241133A1 (es) 2021-09-17 2022-09-16 Moleculas de union a d3 y usos de estas
US18/692,311 US20240376194A1 (en) 2021-09-17 2022-09-16 D3-binding molecules and uses thereof
IL311510A IL311510A (en) 2021-09-17 2022-09-16 D3 binding molecules and uses thereof
JP2024516855A JP2024535851A (ja) 2021-09-17 2022-09-16 D3結合分子及びその使用
MX2024003331A MX2024003331A (es) 2021-09-17 2022-09-16 Moleculas de union a d3 y usos de estas.
CR20240135A CR20240135A (es) 2021-09-17 2022-09-16 Moléculas de unión a d3 y usos de estas
CN202280072803.0A CN118234510A (zh) 2021-09-17 2022-09-16 D3结合分子及其用途
AU2022345323A AU2022345323A1 (en) 2021-09-17 2022-09-16 D3-binding molecules and uses thereof
CN202411637479.XA CN119462942A (zh) 2021-09-17 2022-09-16 D3结合分子及其用途
DO2024000052A DOP2024000052A (es) 2021-09-17 2024-03-15 Moléculas de unión a d3 y usos de estas
CL2024000785A CL2024000785A1 (es) 2021-09-17 2024-03-15 Moléculas de unión a d3 y usos de estas
CONC2024/0003144A CO2024003144A2 (es) 2021-09-17 2024-03-15 Moléculas de unión a d3 y usos de estas
ECSENADI202421498A ECSP24021498A (es) 2021-09-17 2024-03-18 Moléculas de unión a d3 y usos de estas

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EP3328889B1 (en) * 2015-07-31 2021-06-23 Amgen Research (Munich) GmbH Bispecific antibody constructs binding dll3 and cd3
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