1
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Guo X, Song J, Liu M, Ou X, Guo Y. The interplay between the tumor microenvironment and tumor-derived small extracellular vesicles in cancer development and therapeutic response. Cancer Biol Ther 2024; 25:2356831. [PMID: 38767879 PMCID: PMC11110713 DOI: 10.1080/15384047.2024.2356831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
The tumor microenvironment (TME) plays an essential role in tumor cell survival by profoundly influencing their proliferation, metastasis, immune evasion, and resistance to treatment. Extracellular vesicles (EVs) are small particles released by all cell types and often reflect the state of their parental cells and modulate other cells' functions through the various cargo they transport. Tumor-derived small EVs (TDSEVs) can transport specific proteins, nucleic acids and lipids tailored to propagate tumor signals and establish a favorable TME. Thus, the TME's biological characteristics can affect TDSEV heterogeneity, and this interplay can amplify tumor growth, dissemination, and resistance to therapy. This review discusses the interplay between TME and TDSEVs based on their biological characteristics and summarizes strategies for targeting cancer cells. Additionally, it reviews the current issues and challenges in this field to offer fresh insights into comprehending tumor development mechanisms and exploring innovative clinical applications.
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Affiliation(s)
- Xuanyu Guo
- The Affiliated Hospital, Southwest Medical University, Luzhou, PR China
| | - Jiajun Song
- Department of Clinical Laboratory Medicine, the Affiliated Hospital, Southwest Medical University, Luzhou, PR China
| | - Miao Liu
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, PR China
| | - Xinyi Ou
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, PR China
| | - Yongcan Guo
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, PR China
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2
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Paul S, Konig MF, Pardoll DM, Bettegowda C, Papadopoulos N, Wright KM, Gabelli SB, Ho M, van Elsas A, Zhou S. Cancer therapy with antibodies. Nat Rev Cancer 2024; 24:399-426. [PMID: 38740967 DOI: 10.1038/s41568-024-00690-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/29/2024] [Indexed: 05/16/2024]
Abstract
The greatest challenge in cancer therapy is to eradicate cancer cells with minimal damage to normal cells. Targeted therapy has been developed to meet that challenge, showing a substantially increased therapeutic index compared with conventional cancer therapies. Antibodies are important members of the family of targeted therapeutic agents because of their extraordinarily high specificity to the target antigens. Therapeutic antibodies use a range of mechanisms that directly or indirectly kill the cancer cells. Early antibodies were developed to directly antagonize targets on cancer cells. This was followed by advancements in linker technologies that allowed the production of antibody-drug conjugates (ADCs) that guide cytotoxic payloads to the cancer cells. Improvement in our understanding of the biology of T cells led to the production of immune checkpoint-inhibiting antibodies that indirectly kill the cancer cells through activation of the T cells. Even more recently, bispecific antibodies were synthetically designed to redirect the T cells of a patient to kill the cancer cells. In this Review, we summarize the different approaches used by therapeutic antibodies to target cancer cells. We discuss their mechanisms of action, the structural basis for target specificity, clinical applications and the ongoing research to improve efficacy and reduce toxicity.
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Affiliation(s)
- Suman Paul
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Maximilian F Konig
- Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chetan Bettegowda
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Katharine M Wright
- Discovery Chemistry, Merck Research Laboratory, Merck and Co, West Point, PA, USA
| | - Sandra B Gabelli
- Discovery Chemistry, Merck Research Laboratory, Merck and Co, West Point, PA, USA.
| | - Mitchell Ho
- Antibody Engineering Program, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | | | - Shibin Zhou
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
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3
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Qin X, Ning W, Liu H, Liu X, Luo W, Xia N. Stepping forward: T-cell redirecting bispecific antibodies in cancer therapy. Acta Pharm Sin B 2024; 14:2361-2377. [PMID: 38828136 PMCID: PMC11143529 DOI: 10.1016/j.apsb.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/26/2023] [Accepted: 02/28/2024] [Indexed: 06/05/2024] Open
Abstract
T cell-redirecting bispecific antibodies are specifically designed to bind to tumor-associated antigens, thereby engaging with CD3 on the T cell receptor. This linkage between tumor cells and T cells actively triggers T cell activation and initiates targeted killing of the identified tumor cells. These antibodies have emerged as one of the most promising avenues within tumor immunotherapy. However, despite success in treating hematological malignancies, significant advancements in solid tumors have yet to be explored. In this review, we aim to address the critical challenges associated with T cell-redirecting bispecific antibodies and explore novel strategies to overcome these obstacles, with the ultimate goal of expanding the application of this therapy to include solid tumors.
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Affiliation(s)
- Xiaojing Qin
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry–Education Integration in Vaccine Research, the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen University, Xiamen 361102, China
| | - Wenjing Ning
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry–Education Integration in Vaccine Research, the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen University, Xiamen 361102, China
| | - Han Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry–Education Integration in Vaccine Research, the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen University, Xiamen 361102, China
| | - Xue Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry–Education Integration in Vaccine Research, the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen University, Xiamen 361102, China
| | - Wenxin Luo
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry–Education Integration in Vaccine Research, the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry–Education Integration in Vaccine Research, the Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen University, Xiamen 361102, China
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4
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Gavade A, Nagraj AK, Patel R, Pais R, Dhanure P, Scheele J, Seiz W, Patil J. Understanding the Specific Implications of Amino Acids in the Antibody Development. Protein J 2024; 43:405-424. [PMID: 38724751 DOI: 10.1007/s10930-024-10201-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 06/01/2024]
Abstract
As the demand for immunotherapy to treat and manage cancers, infectious diseases and other disorders grows, a comprehensive understanding of amino acids and their intricate role in antibody engineering has become a prime requirement. Naturally produced antibodies may not have the most suitable amino acids at the complementarity determining regions (CDR) and framework regions, for therapeutic purposes. Therefore, to enhance the binding affinity and therapeutic properties of an antibody, the specific impact of certain amino acids on the antibody's architecture must be thoroughly studied. In antibody engineering, it is crucial to identify the key amino acid residues that significantly contribute to improving antibody properties. Therapeutic antibodies with higher binding affinity and improved functionality can be achieved through modifications or substitutions with highly suitable amino acid residues. Here, we have indicated the frequency of amino acids and their association with the binding free energy in CDRs. The review also analyzes the experimental outcome of two studies that reveal the frequency of amino acids in CDRs and provides their significant correlation between the outcomes. Additionally, it discusses the various bond interactions within the antibody structure and antigen binding. A detailed understanding of these amino acid properties should assist in the analysis of antibody sequences and structures needed for designing and enhancing the overall performance of therapeutic antibodies.
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Affiliation(s)
- Akshata Gavade
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Anil Kumar Nagraj
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Riya Patel
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Roylan Pais
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Pratiksha Dhanure
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | | | | | - Jaspal Patil
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India.
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5
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Sun J, Zhang X, Xue L, Cheng L, Zhang J, Chen X, Shen Z, Li K, Wang L, Huang C, Song J. Structural insights into the unique pH-responsive characteristics of the anti-TIGIT therapeutic antibody Ociperlimab. Structure 2024; 32:550-561.e5. [PMID: 38460520 DOI: 10.1016/j.str.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/28/2023] [Accepted: 02/13/2024] [Indexed: 03/11/2024]
Abstract
TIGIT is mainly expressed on T cells and is an inhibitory checkpoint receptor that binds to its ligand PVR in the tumor microenvironment. Anti-TIGIT monoclonal antibodies (mAbs) such as Ociperlimab and Tiragolumab block the TIGIT-PVR interaction and are in clinical development. However, the molecular blockade mechanism of these mAbs remains elusive. Here, we report the crystal structures of TIGIT in complex with Ociperlimab_Fab and Tiragolumab_Fab revealing that both mAbs bind TIGIT with a large steric clash with PVR. Furthermore, several critical epitopic residues are identified. Interestingly, the binding affinity of Ociperlimab toward TIGIT increases approximately 17-fold when lowering the pH from 7.4 to 6.0. Our structure shows a strong electrostatic interaction between ASP103HCDR3 and HIS76TIGIT explaining the pH-responsive mechanism of Ociperlimab. In contrast, Tiragolumab does not show an acidic pH-dependent binding enhancement. Our results provide valuable information that could help to improve the efficacy of therapeutic antibodies for cancer treatment.
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MESH Headings
- Hydrogen-Ion Concentration
- Humans
- Models, Molecular
- Receptors, Immunologic/metabolism
- Receptors, Immunologic/chemistry
- Crystallography, X-Ray
- Protein Binding
- Antibodies, Monoclonal/chemistry
- Binding Sites
- Antibodies, Monoclonal, Humanized/chemistry
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/immunology
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Affiliation(s)
- Jian Sun
- Department of Biologics, BeiGene (Beijing) Co., Ltd, Beijing, China
| | - Xiangxiang Zhang
- Department of Biologics, BeiGene (Beijing) Co., Ltd, Beijing, China
| | - Liu Xue
- Department of Biologics, BeiGene (Beijing) Co., Ltd, Beijing, China
| | - Liang Cheng
- Department of Biologics, BeiGene (Beijing) Co., Ltd, Beijing, China
| | - Jing Zhang
- Department of Biologics, BeiGene (Beijing) Co., Ltd, Beijing, China
| | - Xin Chen
- Department of Translational Science, BeiGene (Beijing) Co., Ltd, Beijing, China
| | - Zhirong Shen
- Department of Translational Science, BeiGene (Beijing) Co., Ltd, Beijing, China
| | - Kang Li
- Department of Biologics, BeiGene (Beijing) Co., Ltd, Beijing, China
| | - Lai Wang
- Department of Biology, BeiGene (Beijing) Co., Ltd, Beijing, China
| | - Chichi Huang
- Department of Biologics, BeiGene (Beijing) Co., Ltd, Beijing, China
| | - Jing Song
- Department of Biologics, BeiGene (Beijing) Co., Ltd, Beijing, China.
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6
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Dombrowsky CS, Happel D, Habermann J, Hofmann S, Otmi S, Cohen B, Kolmar H. A Conditionally Activated Cytosol-Penetrating Antibody for TME-Dependent Intracellular Cargo Delivery. Antibodies (Basel) 2024; 13:37. [PMID: 38804305 PMCID: PMC11130931 DOI: 10.3390/antib13020037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/29/2024] Open
Abstract
Currently, therapeutic and diagnostic applications of antibodies are primarily limited to cell surface-exposed and extracellular proteins. However, research has been conducted on cell-penetrating peptides (CPP), as well as cytosol-penetrating antibodies, to overcome these limitations. In this context, a heparin sulfate proteoglycan (HSPG)-binding antibody was serendipitously discovered, which eventually localizes to the cytosol of target cells. Functional characterization revealed that the tested antibody has beneficial cytosol-penetrating capabilities and can deliver cargo proteins (up to 70 kDa) to the cytosol. To achieve tumor-specific cell targeting and cargo delivery through conditional activation of the cell-penetrating antibody in the tumor microenvironment, a single-chain Fc fragment (scFv) and a VL domain were isolated as masking units. Several in vitro assays demonstrated that fusing the masking protein with a cleavable linker to the cell penetration antibody results in the inactivation of antibody cell binding and internalization. Removal of the mask via MMP-9 protease cleavage, a protease that is frequently overexpressed in the tumor microenvironment (TME), led to complete regeneration of binding and cytosol-penetrating capabilities. Masked and conditionally activated cytosol-penetrating antibodies have the potential to serve as a modular platform for delivering protein cargoes addressing intracellular targets in tumor cells.
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Affiliation(s)
- Carolin Sophie Dombrowsky
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Dominic Happel
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Jan Habermann
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Sarah Hofmann
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Sasi Otmi
- Inter-Lab, a Subsidiary of Merck KGaA, South Industrial Area, Yavne 8122004, Israel
| | - Benny Cohen
- Inter-Lab, a Subsidiary of Merck KGaA, South Industrial Area, Yavne 8122004, Israel
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
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7
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Li Y, Cai Z, Gu J, Chen J, Zhang Y. Naphthalimide-based Functional Glycopolymeric Nanoparticles as Fluorescent Probes for Selective Imaging of Tumor Cells. Chemistry 2024; 30:e202304165. [PMID: 38246871 DOI: 10.1002/chem.202304165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/23/2024]
Abstract
A series of functional glycopolymer nanoparticles with 1,8-naphthalimide motif was designed, synthesized and applied for tumor cell imaging. With the pH-sensitive and aggregation-induced emission (AIE) effect of the 1,8-naphthalimide fluorescent probe, the presence of glucose-based glycopolymers enhanced its water-solubility and biocompatibility. Owing to the dual tumor-targeting effects of the dense glucose part and the boronic ester modification, the obtained glycopolymers showed high affinity to tumor cells, with a much faster staining rate than normal cells, indicating a great potential for diagnosis and treatments of cancers.
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Affiliation(s)
- Yi Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, P.R. China
| | - Zhi Cai
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, P.R. China
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, P.R. China
| | - Jieyu Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, P.R. China
| | - Jinghua Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, P.R. China
| | - Yan Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, P.R. China
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8
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Tsuchikama K, Anami Y, Ha SYY, Yamazaki CM. Exploring the next generation of antibody-drug conjugates. Nat Rev Clin Oncol 2024; 21:203-223. [PMID: 38191923 DOI: 10.1038/s41571-023-00850-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/10/2024]
Abstract
Antibody-drug conjugates (ADCs) are a promising cancer treatment modality that enables the selective delivery of highly cytotoxic payloads to tumours. However, realizing the full potential of this platform necessitates innovative molecular designs to tackle several clinical challenges such as drug resistance, tumour heterogeneity and treatment-related adverse effects. Several emerging ADC formats exist, including bispecific ADCs, conditionally active ADCs (also known as probody-drug conjugates), immune-stimulating ADCs, protein-degrader ADCs and dual-drug ADCs, and each offers unique capabilities for tackling these various challenges. For example, probody-drug conjugates can enhance tumour specificity, whereas bispecific ADCs and dual-drug ADCs can address resistance and heterogeneity with enhanced activity. The incorporation of immune-stimulating and protein-degrader ADCs, which have distinct mechanisms of action, into existing treatment strategies could enable multimodal cancer treatment. Despite the promising outlook, the importance of patient stratification and biomarker identification cannot be overstated for these emerging ADCs, as these factors are crucial to identify patients who are most likely to derive benefit. As we continue to deepen our understanding of tumour biology and refine ADC design, we will edge closer to developing truly effective and safe ADCs for patients with treatment-refractory cancers. In this Review, we highlight advances in each ADC component (the monoclonal antibody, payload, linker and conjugation chemistry) and provide more-detailed discussions on selected examples of emerging novel ADCs of each format, enabled by engineering of one or more of these components.
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Affiliation(s)
- Kyoji Tsuchikama
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Yasuaki Anami
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Summer Y Y Ha
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Chisato M Yamazaki
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
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9
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Biewenga L, Vermathen R, Rosier BJ, Merkx M. A Generic Antibody-Blocking Protein That Enables pH-Switchable Activation of Antibody Activity. ACS Chem Biol 2024; 19:48-57. [PMID: 38110237 PMCID: PMC10804362 DOI: 10.1021/acschembio.3c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023]
Abstract
Molecular strategies that allow for reversible control of antibody activity have drawn considerable interest for both therapeutic and diagnostic applications. Protein M is a generic antibody-binding protein that binds to the Fv domain of IgGs and, in doing so, blocks antigen binding. However, the dissociation of protein M is essentially irreversible, which has precluded its use as an antibody affinity reagent and molecular mask to control antibody activity. Here, we show that introduction of 8 histidine residues on the Fv binding interface of protein M results in a variant that shows pH-switchable IgG binding. This protein M-8his variant provides an attractive and universal affinity resin for the purification of IgGs, antibody fragments (Fab and single-chain variable fragments (scFv)), and antibody conjugates. Moreover, protein M-8his enables the pH-dependent blocking of therapeutic antibodies, allowing the selective targeting of cells at pH 6.0.
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Affiliation(s)
- Lieuwe Biewenga
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Robin Vermathen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Bas J.H.M. Rosier
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
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10
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Xu F, Yu F. Sensing and regulation of plant extracellular pH. TRENDS IN PLANT SCIENCE 2023; 28:1422-1437. [PMID: 37596188 DOI: 10.1016/j.tplants.2023.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/03/2023] [Accepted: 06/19/2023] [Indexed: 08/20/2023]
Abstract
In plants, pH determines nutrient acquisition and sensing, and triggers responses to osmotic stress, whereas pH homeostasis protects the cellular machinery. Extracellular pH (pHe) controls the chemistry and rheology of the cell wall to adjust its elasticity and regulate cell expansion in space and time. Plasma membrane (PM)-localized proton pumps, cell-wall components, and cell wall-remodeling enzymes jointly maintain pHe homeostasis. To adapt to their environment and modulate growth and development, plant cells must sense subtle changes in pHe caused by the environment or neighboring cells. Accumulating evidence indicates that PM-localized cell-surface peptide-receptor pairs sense pHe. We highlight recent advances in understanding how plants perceive and maintain pHe, and discuss future perspectives.
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Affiliation(s)
- Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, PR China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, PR China.
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11
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Hajjar S, Zhou X. pH sensing at the intersection of tissue homeostasis and inflammation. Trends Immunol 2023; 44:807-825. [PMID: 37714775 PMCID: PMC10543622 DOI: 10.1016/j.it.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/13/2023] [Accepted: 08/13/2023] [Indexed: 09/17/2023]
Abstract
pH is tightly maintained at cellular, tissue, and systemic levels, and altered pH - particularly in the acidic range - is associated with infection, injury, solid tumors, and physiological and pathological inflammation. However, how pH is sensed and regulated and how it influences immune responses remain poorly understood at the tissue level. Applying conceptual frameworks of homeostatic and inflammatory circuitries, we categorize cellular and tissue components engaged in pH regulation, drawing parallels from established cases in physiology. By expressing various intracellular (pHi) and extracellular pH (pHe)-sensing receptors, the immune system may integrate information on tissue and cellular states into the regulation of homeostatic and inflammatory programs. We introduce the novel concept of resistance and adaptation responses to rationalize pH-dependent immunomodulation intertwined with homeostatic equilibrium and inflammatory control. We discuss emerging challenges and opportunities in understanding the immunological roles of pH sensing, which might reveal new strategies to combat inflammation and restore tissue homeostasis.
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Affiliation(s)
- Stephanie Hajjar
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, 300 Longwood Ave, Boston, MA 02115, USA
| | - Xu Zhou
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, 300 Longwood Ave, Boston, MA 02115, USA.
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12
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Smith FD, Pierce RH, Thisted T, van der Horst EH. Conditionally Active, pH-Sensitive Immunoregulatory Antibodies Targeting VISTA and CTLA-4 Lead an Emerging Class of Cancer Therapeutics. Antibodies (Basel) 2023; 12:55. [PMID: 37753969 PMCID: PMC10525963 DOI: 10.3390/antib12030055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/28/2023] Open
Abstract
Immune checkpoints and other immunoregulatory targets can be difficult to precisely target due to expression on non-tumor immune cells critical to maintaining immune homeostasis in healthy tissues. On-target/off-tumor binding of therapeutics results in significant pharmacokinetic and pharmacodynamic problems. Target-mediated drug disposition (TMDD) significantly limits effective intratumoral drug levels and adversely affects anti-tumor efficacy. Target engagement outside the tumor environment may lead to severe immune-related adverse events (irAEs), resulting in a narrowing of the therapeutic window, sub-optimal dosing, or cessation of drug development altogether. Overcoming these challenges has become tractable through recent advances in antibody engineering and screening approaches. Here, we review the discovery and development of conditionally active antibodies with minimal binding to target at physiologic pH but high-affinity target binding at the low pH of the tumor microenvironment by focusing on the discovery and improved properties of pH-dependent mAbs targeting two T cell checkpoints, VISTA and CTLA-4.
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Affiliation(s)
- F. Donelson Smith
- Sensei Biotherapeutics, Inc., 1405 Research Blvd., Suite 125, Rockville, MD 20850, USA;
| | | | - Thomas Thisted
- Sensei Biotherapeutics, Inc., 1405 Research Blvd., Suite 125, Rockville, MD 20850, USA;
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13
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Wei W, Hogues H, Sulea T. Comparative Performance of High-Throughput Methods for Protein p Ka Predictions. J Chem Inf Model 2023; 63:5169-5181. [PMID: 37549424 PMCID: PMC10466379 DOI: 10.1021/acs.jcim.3c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Indexed: 08/09/2023]
Abstract
The medically relevant field of protein-based therapeutics has triggered a demand for protein engineering in different pH environments of biological relevance. In silico engineering workflows typically employ high-throughput screening campaigns that require evaluating large sets of protein residues and point mutations by fast yet accurate computational algorithms. While several high-throughput pKa prediction methods exist, their accuracies are unclear due to the lack of a current comprehensive benchmarking. Here, seven fast, efficient, and accessible approaches including PROPKA3, DeepKa, PKAI, PKAI+, DelPhiPKa, MCCE2, and H++ were systematically tested on a nonredundant subset of 408 measured protein residue pKa shifts from the pKa database (PKAD). While no method outperformed the null hypotheses with confidence, as illustrated by statistical bootstrapping, DeepKa, PKAI+, PROPKA3, and H++ had utility. More specifically, DeepKa consistently performed well in tests across multiple and individual amino acid residue types, as reflected by lower errors, higher correlations, and improved classifications. Arithmetic averaging of the best empirical predictors into simple consensuses improved overall transferability and accuracy up to a root-mean-square error of 0.76 pKa units and a correlation coefficient (R2) of 0.45 to experimental pKa shifts. This analysis should provide a basis for further methodological developments and guide future applications, which require embedding of computationally inexpensive pKa prediction methods, such as the optimization of antibodies for pH-dependent antigen binding.
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Affiliation(s)
- Wanlei Wei
- Human Health Therapeutics
Research Centre, National Research Council
Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
| | - Hervé Hogues
- Human Health Therapeutics
Research Centre, National Research Council
Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
| | - Traian Sulea
- Human Health Therapeutics
Research Centre, National Research Council
Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
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14
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Liu X, Tan Q, Wen J, Wang X, Yang G, Li Y, Lu M, Ye W, Si A, Ma S, Ding T, Sun L, Liu F, Zhang M, Jiang T, Gao W. Improving the cytotoxicity of immunotoxins by reducing the affinity of the antibody in acidic pH. J Transl Med 2023; 21:572. [PMID: 37626430 PMCID: PMC10463491 DOI: 10.1186/s12967-023-04210-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 05/19/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Immunotoxins are antibody-toxin conjugates that bind to surface antigens and exert effective cytotoxic activity after internalization into tumor cells. Immunotoxins exhibit effective cytotoxicity and have been approved by the FDA to treat multiple hematological malignancies, such as hairy cell leukemia and cutaneous T-cell lymphoma. However, most of the internalized immunotoxin is degraded in lysosomes, and only approximately 5% of free toxin escapes into the cytosol to exert cytotoxicity. Many studies have improved immunotoxins by engineering the toxin fragment to reduce immunogenicity or increase stability, but how the antibody fragment contributes to the activity of immunotoxins has not been well demonstrated. METHODS In the current study, we used 32A9 and 42A1, two anti-GPC3 antibodies with similar antigen-binding capabilities and internalization rates, to construct scFv-mPE24 immunotoxins and evaluated their in vitro and in vivo antitumor activities. Next, the antigen-binding capacity, trafficking, intracellular protein stability and release of free toxin of 32A9 scFv-mPE24 and 42A1 scFv-mPE24 were compared to elucidate their different antitumor activities. Furthermore, we used a lysosome inhibitor to evaluate the degradation behavior of 32A9 scFv-mPE24 and 42A1 scFv-mPE24. Finally, the antigen-binding patterns of 32A9 and 42A1 were compared under neutral and acidic pH conditions. RESULTS Although 32A9 and 42A1 had similar antigen binding capacities and internalization rates, 32A9 scFv-mPE24 had superior antitumor activity compared to 42A1 scFv-mPE24. We found that 32A9 scFv-mPE24 exhibited faster degradation and drove efficient free toxin release compared to 42A1 scFv-mPE24. These phenomena were determined by the different degradation behaviors of 32A9 scFv-mPE24 and 42A1 scFv-mPE24 in lysosomes. Moreover, 32A9 was sensitive to the low-pH environment, which made the 32A9 conjugate easily lose antigen binding and undergo degradation in lysosomes, and the free toxin was then efficiently produced to exert cytotoxicity, whereas 42A1 was resistant to the acidic environment, which kept the 42A1 conjugate relatively stable in lysosomes and delayed the release of free toxin. CONCLUSIONS These results showed that a low pH-sensitive antibody-based immunotoxin degraded faster in lysosomes, caused effective free toxin release, and led to improved cytotoxicity compared to an immunotoxin based on a normal antibody. Our findings suggested that a low pH-sensitive antibody might have an advantage in the design of immunotoxins and other lysosomal degradation-dependent antibody conjugate drugs.
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Affiliation(s)
- Xiaoyu Liu
- School of Basic Medical Sciences and Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, 101 Longmian Road, Xuehai Building, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Qingqing Tan
- Department of Gynecology Oncology, Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, China
| | - Jiaqi Wen
- School of Basic Medical Sciences and Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, 101 Longmian Road, Xuehai Building, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Xufei Wang
- School of Basic Medical Sciences and Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, 101 Longmian Road, Xuehai Building, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Gang Yang
- School of Basic Medical Sciences and Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, 101 Longmian Road, Xuehai Building, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Yuxiao Li
- Department of Endocrinology, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Ming Lu
- School of Basic Medical Sciences and Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, 101 Longmian Road, Xuehai Building, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Wei Ye
- School of Basic Medical Sciences and Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, 101 Longmian Road, Xuehai Building, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Anfeng Si
- Department of Surgical Oncology, Jinling Hospital, Medical School of Nanjing University, 34 Yanggongjing Road, Nanjing, 210000, Jiangsu, People's Republic of China
| | - Sujuan Ma
- School of Basic Medical Sciences and Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, 101 Longmian Road, Xuehai Building, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Tong Ding
- School of Basic Medical Sciences and Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, 101 Longmian Road, Xuehai Building, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Luan Sun
- School of Basic Medical Sciences and Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, 101 Longmian Road, Xuehai Building, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Fang Liu
- School of Basic Medical Sciences and Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, 101 Longmian Road, Xuehai Building, Nanjing, 211166, Jiangsu, People's Republic of China
| | - Mei Zhang
- Department of Endocrinology, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Tao Jiang
- Department of Surgical Oncology, Jinling Hospital, Medical School of Nanjing University, 34 Yanggongjing Road, Nanjing, 210000, Jiangsu, People's Republic of China.
| | - Wei Gao
- School of Basic Medical Sciences and Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, 101 Longmian Road, Xuehai Building, Nanjing, 211166, Jiangsu, People's Republic of China.
- The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou Second People's Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, China.
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15
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Purisima EO, Corbeil CR, Gaudreault F, Wei W, Deprez C, Sulea T. Solvated interaction energy: from small-molecule to antibody drug design. Front Mol Biosci 2023; 10:1210576. [PMID: 37351549 PMCID: PMC10282643 DOI: 10.3389/fmolb.2023.1210576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023] Open
Abstract
Scoring functions are ubiquitous in structure-based drug design as an aid to predicting binding modes and estimating binding affinities. Ideally, a scoring function should be broadly applicable, obviating the need to recalibrate and refit its parameters for every new target and class of ligands. Traditionally, drugs have been small molecules, but in recent years biologics, particularly antibodies, have become an increasingly important if not dominant class of therapeutics. This makes the goal of having a transferable scoring function, i.e., one that spans the range of small-molecule to protein ligands, even more challenging. One such broadly applicable scoring function is the Solvated Interaction Energy (SIE), which has been developed and applied in our lab for the last 15 years, leading to several important applications. This physics-based method arose from efforts to understand the physics governing binding events, with particular care given to the role played by solvation. SIE has been used by us and many independent labs worldwide for virtual screening and discovery of novel small-molecule binders or optimization of known drugs. Moreover, without any retraining, it is found to be transferrable to predictions of antibody-antigen relative binding affinities and as accurate as functions trained on protein-protein binding affinities. SIE has been incorporated in conjunction with other scoring functions into ADAPT (Assisted Design of Antibody and Protein Therapeutics), our platform for affinity modulation of antibodies. Application of ADAPT resulted in the optimization of several antibodies with 10-to-100-fold improvements in binding affinity. Further applications included broadening the specificity of a single-domain antibody to be cross-reactive with virus variants of both SARS-CoV-1 and SARS-CoV-2, and the design of safer antibodies by engineering of a pH switch to make them more selective towards acidic tumors while sparing normal tissues at physiological pH.
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16
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Qian L, Lin X, Gao X, Khan RU, Liao JY, Du S, Ge J, Zeng S, Yao SQ. The Dawn of a New Era: Targeting the "Undruggables" with Antibody-Based Therapeutics. Chem Rev 2023. [PMID: 37186942 DOI: 10.1021/acs.chemrev.2c00915] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The high selectivity and affinity of antibodies toward their antigens have made them a highly valuable tool in disease therapy, diagnosis, and basic research. A plethora of chemical and genetic approaches have been devised to make antibodies accessible to more "undruggable" targets and equipped with new functions of illustrating or regulating biological processes more precisely. In this Review, in addition to introducing how naked antibodies and various antibody conjugates (such as antibody-drug conjugates, antibody-oligonucleotide conjugates, antibody-enzyme conjugates, etc.) work in therapeutic applications, special attention has been paid to how chemistry tools have helped to optimize the therapeutic outcome (i.e., with enhanced efficacy and reduced side effects) or facilitate the multifunctionalization of antibodies, with a focus on emerging fields such as targeted protein degradation, real-time live-cell imaging, catalytic labeling or decaging with spatiotemporal control as well as the engagement of antibodies inside cells. With advances in modern chemistry and biotechnology, well-designed antibodies and their derivatives via size miniaturization or multifunctionalization together with efficient delivery systems have emerged, which have gradually improved our understanding of important biological processes and paved the way to pursue novel targets for potential treatments of various diseases.
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Affiliation(s)
- Linghui Qian
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xuefen Lin
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xue Gao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rizwan Ullah Khan
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jia-Yu Liao
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shubo Du
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Cancer Center, & Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544
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17
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Li Y, Liu J, Chen W, Wang W, Yang F, Liu X, Sheng Y, Du K, He M, Lyu X, Li H, Zhao L, Wei Z, Wang F, Zheng S, Sui J. A pH-dependent anti-CD47 antibody that selectively targets solid tumors and improves therapeutic efficacy and safety. J Hematol Oncol 2023; 16:2. [PMID: 36650558 PMCID: PMC9844003 DOI: 10.1186/s13045-023-01399-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The antiphagocytic molecule CD47 is overexpressed in a wide variety of cancer cells, and antibodies targeting CD47 for cancer therapies are currently under intensive investigation. However, owing to the ubiquitous expression of CD47 on healthy cells, anti-CD47 therapies often achieve only weak therapeutic benefits and can induce severe side effects. Here, we report the generation of a pH-dependent anti-CD47 antibody (BC31M4) which selectively binds to tumors under the acidic solid tumor microenvironment. METHODS BC31M4 was generated using antibody phage display and a pH-dependent selection strategy. The pH-dependent binding and blocking activities of BC31M4 were verified using in vitro assays, and the structural basis of the pH-dependent binding property was characterized. BC31M4's antitumor effect was confirmed by both phagocytosis assays and studies in xenograft models. The tumor selectivity, mechanism of action, PK properties, side effects, and therapeutic efficacy were further evaluated in humanized (hCD47 and its receptor hSIRPα) immunocompetent syngeneic mouse models. RESULTS The crystal structure reveals that two histidines locate within the CDRs of the light chain directly contribute to the pH-dependent binding of BC31M4. BC31M4 promotes macrophage phagocytosis of tumor cells more potently at acidic-pH than at physiological-pH. Our hCD47/hSIRPα humanized syngeneic mouse model results demonstrated that BC31M4 selectively accumulates in tumors but not in normal tissues. BC31M4 causes minimal side effects and exhibits superior PK properties as compared to the other examined anti-CD47 antibodies. When combined with adoptive T cell transfer, BC31M4 efficiently promotes adaptive immune responses against tumors and also induces immune memory. Moreover, we show that BC31M4's antitumor effects rely on an Fc that mediates strong effector functions. CONCLUSIONS Our study illustrates that the development of a tumor-selective, pH-dependent anti-CD47 antibody safely confers strong therapeutic effects against solid tumors, thus providing a promising therapeutic strategy to overcome the challenges of anti-CD47 therapy.
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Affiliation(s)
- Yulu Li
- Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint Graduate Program, School of Life Sciences, Peking University, Beijing, China.,National Institute of Biological Sciences (NIBS), Beijing, China
| | - Juan Liu
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Wei Chen
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Wei Wang
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Fang Yang
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Ximing Liu
- Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint Graduate Program, School of Life Sciences, Peking University, Beijing, China.,National Institute of Biological Sciences (NIBS), Beijing, China
| | - Yao Sheng
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Kaixin Du
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Miaomiao He
- National Institute of Biological Sciences (NIBS), Beijing, China.,Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xueyuan Lyu
- National Institute of Biological Sciences (NIBS), Beijing, China.,PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huiyu Li
- National Institute of Biological Sciences (NIBS), Beijing, China.,PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Linlin Zhao
- National Institute of Biological Sciences (NIBS), Beijing, China.,PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhizhong Wei
- National Institute of Biological Sciences (NIBS), Beijing, China.,PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fengchao Wang
- National Institute of Biological Sciences (NIBS), Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Sanduo Zheng
- National Institute of Biological Sciences (NIBS), Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Jianhua Sui
- National Institute of Biological Sciences (NIBS), Beijing, China. .,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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18
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An anti-CD98 antibody displaying pH-dependent Fc-mediated tumour-specific activity against multiple cancers in CD98-humanized mice. Nat Biomed Eng 2023; 7:8-23. [PMID: 36424464 DOI: 10.1038/s41551-022-00956-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 09/27/2022] [Indexed: 11/27/2022]
Abstract
The cell-surface glycoprotein CD98-a subunit of the LAT1/CD98 amino acid transporter-is an attractive target for cancer immunotherapies, but its widespread expression has hampered the development of CD98-targeting antibody therapeutics. Here we report that an anti-CD98 antibody, identified via the screening of phage-display libraries of CD98 single-chain variable fragments with mutated complementarity-determining regions, preserves the physiological function of CD98 and elicits broad-spectrum crystallizable-fragment (Fc)-mediated anti-tumour activity (requiring Fcγ receptors for immunoglobulins, macrophages, dendritic cells and CD8+ T cells, as well as other components of the innate and adaptive immune systems) in multiple xenograft and syngeneic tumour models established in CD98-humanized mice. We also show that a variant of the anti-CD98 antibody with pH-dependent binding, generated by solving the structure of the antibody-CD98 complex, displayed enhanced tumour-specific activity and pharmacokinetics. pH-dependent antibody variants targeting widely expressed antigens may lead to superior therapeutic outcomes.
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19
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Kakuzaki T, Koga H, Takizawa S, Metsugi S, Shiraiwa H, Sampei Z, Yoshida K, Tsunoda H, Teramoto R. Monte Carlo Thompson sampling-guided design for antibody engineering. MAbs 2023; 15:2244214. [PMID: 37605371 PMCID: PMC10446805 DOI: 10.1080/19420862.2023.2244214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 07/27/2023] [Accepted: 07/29/2023] [Indexed: 08/23/2023] Open
Abstract
Antibodies are one of the predominant treatment modalities for various diseases. To improve the characteristics of a lead antibody, such as antigen-binding affinity and stability, we conducted comprehensive substitutions and exhaustively explored their sequence space. However, it is practically unfeasible to evaluate all possible combinations of mutations owing to combinatorial explosion when multiple amino acid residues are incorporated. It was recently reported that a machine-learning guided protein engineering approach such as Thompson sampling (TS) has been used to efficiently explore sequence space in the framework of Bayesian optimization. For TS, over-exploration occurs when the initial data are biasedly distributed in the vicinity of the lead antibody. We handle a large-scale virtual library that includes numerous mutations. When the number of experiments is limited, this over-exploration causes a serious issue. Thus, we conducted Monte Carlo Thompson sampling (MTS) to balance the exploration-exploitation trade-off by defining the posterior distribution via the Monte Carlo method and compared its performance with TS in antibody engineering. Our results demonstrated that MTS largely outperforms TS in discovering desirable candidates at an earlier round when over-exploration occurs on TS. Thus, the MTS method is a powerful technique for efficiently discovering antibodies with desired characteristics when the number of rounds is limited.
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Affiliation(s)
- Taro Kakuzaki
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Hikaru Koga
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Shuuki Takizawa
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Shoichi Metsugi
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | | | - Zenjiro Sampei
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Kenji Yoshida
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Hiroyuki Tsunoda
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
| | - Reiji Teramoto
- Research Division, Chugai Pharmaceutical Co., Ltd., Yokohama, Japan
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20
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Sulea T, Deprez C, Corbeil CR, Purisima EO. Optimizing Antibody-Antigen Binding Affinities with the ADAPT Platform. Methods Mol Biol 2023; 2552:361-374. [PMID: 36346603 DOI: 10.1007/978-1-0716-2609-2_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The ADAPT (Assisted Design of Antibody and Protein Therapeutics) platform guides the selection of mutants that improve/modulate the affinity of antibodies and other biologics. Predicted affinities are based on a consensus z-score from three scoring functions. Computational predictions are interleaved with experimental validation, significantly enhancing the robustness of the design and selection of mutants. A key step is an initial exhaustive virtual single-mutant scan that identifies hot spots and the mutations predicted to improve affinity. A small number of proposed single mutants are then produced and assayed. Only the validated single mutants (i.e., having improved affinity) are used to design double and higher-order mutants in subsequent rounds of design, avoiding the combinatorial explosion that arises from random mutagenesis. Typically, with a total of about 30-50 designed single, double, and triple mutants, affinity improvements of 10- to 100-fold are obtained.
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Affiliation(s)
- Traian Sulea
- National Research Council Canada, Human Health Therapeutics Research Centre, Montreal, QC, Canada
| | - Christophe Deprez
- National Research Council Canada, Human Health Therapeutics Research Centre, Montreal, QC, Canada
| | - Christopher R Corbeil
- National Research Council Canada, Human Health Therapeutics Research Centre, Montreal, QC, Canada
| | - Enrico O Purisima
- National Research Council Canada, Human Health Therapeutics Research Centre, Montreal, QC, Canada.
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21
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Karaçam S, Tunçer S. Exploiting the Acidic Extracellular pH: Evaluation of Streptococcus salivarius M18 Postbiotics to Target Cancer Cells. Probiotics Antimicrob Proteins 2022; 14:995-1011. [PMID: 34080175 DOI: 10.1007/s12602-021-09806-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 12/24/2022]
Abstract
Previously, we showed that the growth, antibiotic resistance, and biofilm formation properties of the pathogens Pseudomonas aeruginosa and Klebsiella pneumonia were tremendously inhibited by the cell-free supernatant of the oral probiotic Streptococcus salivarius M18. These anti-pathogenic activities of the supernatant were more efficient under acidic conditions. The present approach takes advantage of the acidic nature of the tumor microenvironment to evaluate the effect of the S. salivarius M18 postbiotics on colon cancer cells. In both two-dimensional (2D) and three-dimensional (3D) cell culture models, S. salivarius M18 cell-free supernatant showed anti-cancer actions in the pH conditions mimicking the acidity of the tumor. The inhibitory effect was more prominent when the colon cancer cells have been treated with the cell-free supernatant obtained from the inulin incubated S. salivarius M18. The results of this study point out the potential of the S. salivarius M18 functional probiotic products to be used for targeting low pH environments including the unique acidic microenvironment of tumors.
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Affiliation(s)
- Sevinç Karaçam
- Department of Biotechnology, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey
| | - Sinem Tunçer
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey.
- Department of Medical Services and Techniques, Vocational School of Health Services, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey.
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22
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Liu Y, Nguyen AW, Maynard JA. Engineering antibodies for conditional activity in the solid tumor microenvironment. Curr Opin Biotechnol 2022; 78:102809. [PMID: 36182870 DOI: 10.1016/j.copbio.2022.102809] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022]
Abstract
Antibody-based therapeutics enjoy considerable clinical and commercial successes as cancer treatments. However, they can also cause serious toxicities due to recognition of tumor-associated antigens in noncancerous tissues, which can prevent antibody use in certain patient populations and therapeutic modalities. Here, we discuss recent efforts to develop advanced antibody therapeutics with activities restricted to the solid tumor microenvironment. With the intent of decreasing toxicities and expanding therapeutic windows, protein engineering strategies can render ligand binding sensitive to multiple tumor-specific characteristics. These triggers can be intrinsic to solid tumor microenvironments, such as low pH, high extracellular ATP, and the presence of specific proteases. Emerging strategies rely instead on exogenous triggers such as light and ultrasound to provide spatial and temporal control over antibody activation. These multilayered approaches to targeting diseased tissues are expected to usher in a new generation of precision therapeutics.
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Affiliation(s)
- Yutong Liu
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
| | - Annalee W Nguyen
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA.
| | - Jennifer A Maynard
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA.
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23
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Furuya G, Katoh H, Atsumi S, Hashimoto I, Komura D, Hatanaka R, Senga S, Hayashi S, Akita S, Matsumura H, Miura A, Mita H, Nakakido M, Nagatoishi S, Sugiyama A, Suzuki R, Konishi H, Yamamoto A, Abe H, Hiraoka N, Aoki K, Kato Y, Seto Y, Yoshimura C, Miyadera K, Tsumoto K, Ushiku T, Ishikawa S. Nucleic acid-triggered tumoral immunity propagates pH-selective therapeutic antibodies through tumor-driven epitope spreading. Cancer Sci 2022; 114:321-338. [PMID: 36136061 PMCID: PMC9807517 DOI: 10.1111/cas.15596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 01/07/2023] Open
Abstract
Important roles of humoral tumor immunity are often pointed out; however, precise profiles of dominant antigens and developmental mechanisms remain elusive. We systematically investigated the humoral antigens of dominant intratumor immunoglobulin clones found in human cancers. We found that approximately half of the corresponding antigens were restricted to strongly and densely negatively charged polymers, resulting in simultaneous reactivities of the antibodies to both densely sulfated glycosaminoglycans (dsGAGs) and nucleic acids (NAs). These anti-dsGAG/NA antibodies matured and expanded via intratumoral immunological driving force of innate immunity via NAs. These human cancer-derived antibodies exhibited acidic pH-selective affinity across both antigens and showed specific reactivity to diverse spectrums of human tumor cells. The antibody-drug conjugate exerted therapeutic effects against multiple cancers in vivo by targeting cell surface dsGAG antigens. This study reveals that intratumoral immunological reactions propagate tumor-oriented immunoglobulin clones and demonstrates a new therapeutic modality for the universal treatment of human malignancies.
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Affiliation(s)
- Genta Furuya
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroto Katoh
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shinichiro Atsumi
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Itaru Hashimoto
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Daisuke Komura
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Ryo Hatanaka
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Shogo Senga
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Shuto Hayashi
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shoji Akita
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Hirofumi Matsumura
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Akihiro Miura
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Hideaki Mita
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Makoto Nakakido
- Laboratory of Medical Proteomics, Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Satoru Nagatoishi
- Laboratory of Medical Proteomics, Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Akira Sugiyama
- Laboratory of Systems Biology and MedicineResearch Center for Advanced Science and Technology, The University of TokyoTokyoJapan
| | - Ryohei Suzuki
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroki Konishi
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Asami Yamamoto
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Nobuyoshi Hiraoka
- Department of Analytical PathologyNational Cancer Center Research InstituteTokyoJapan
| | - Kazunori Aoki
- Division of Molecular and Cellular MedicineNational Cancer Center Research InstituteTokyoJapan
| | - Yasumasa Kato
- Department of Oral Function and Molecular BiologyOhu University School of DentistryFukushimaJapan
| | - Yasuyuki Seto
- Department of Gastrointestinal SurgeryGraduate School of Medicine, The University of TokyoTokyoJapan
| | - Chihoko Yoshimura
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Kazutaka Miyadera
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Kouhei Tsumoto
- Laboratory of Medical Proteomics, Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shumpei Ishikawa
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
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24
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Wei W, Corbeil CR, Gaudreault F, Deprez C, Purisima EO, Sulea T. Antibody mutations favoring
pH
‐dependent binding in solid tumor microenvironments: Insights from large‐scale structure‐based calculations. Proteins 2022; 90:1538-1546. [DOI: 10.1002/prot.26340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/26/2022] [Accepted: 03/23/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Wanlei Wei
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
| | - Christopher R. Corbeil
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
| | - Francis Gaudreault
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
| | - Christophe Deprez
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
| | - Enrico O. Purisima
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
| | - Traian Sulea
- Human Health Therapeutics Research Center National Research Council Canada Montreal Quebec Canada
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25
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Chen TT. Conditionally active T cell engagers for the treatment of solid tumors: rationale and clinical development. Expert Opin Biol Ther 2022; 22:955-963. [PMID: 35857922 DOI: 10.1080/14712598.2022.2098674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION T cell engagers are a class of bispecific molecules that induce highly potent T cell-dependent cytotoxicity by bringing T cell activating receptors into proximity with cancer-associated cell surface antigens. However, because of their high potency, there is a greater risk of on-target/off-tumor toxicity owing to normal tissues having tumor antigen expression even at low levels. To reduce these adverse events, the dysregulated activity of proteases within the tumor microenvironment has recently been explored to create inert prodrugs that become conditionally active engagers after their cleavage by these enzymes. AREAS COVERED T-cell engagers that have been introduced for clinical use, and their respective successes and failures are reviewed. The unique challenges of these bispecific molecules for treating solid tumors and prior technologies used to exploit the proteolytic tumor microenvironment to create better-tolerated prodrugs and how that experience has led to the current series of conditionally active T-cell engagers, are discussed. EXPERT OPINION Methods for modulating the serum half-life of both inert and activated T cell engagers could have important ramifications in how they infiltrate tumors and prevent toxicity. Alternative features of the tumor microenvironment can also be leveraged in the development of conditional T cell engagers.
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Affiliation(s)
- T Timothy Chen
- Maverick Therapeutics, Inc., a wholly owned subsidiary of Takeda Development Center Americas, Inc
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26
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Sulea T, Baardsnes J, Stuible M, Rohani N, Tran A, Parat M, Cepero Donates Y, Duchesne M, Plante P, Kour G, Durocher Y. Structure-based dual affinity optimization of a SARS-CoV-1/2 cross-reactive single-domain antibody. PLoS One 2022; 17:e0266250. [PMID: 35353868 PMCID: PMC8967028 DOI: 10.1371/journal.pone.0266250] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/17/2022] [Indexed: 11/23/2022] Open
Abstract
The SARS coronavirus 2 (SARS-CoV-2) spike (S) protein binding to the human ACE2 receptor is the molecular event that initiates viral entry into host cells and leads to infection and virus replication. There is a need for agents blocking viral entry into host cells that are cross-reactive with emerging virus variants. VHH-72 is an anti-SARS-CoV-1 single-domain antibody that also exhibits cross-specificity with SARS-CoV-2 but with decreased binding affinity. Here we applied a structure-based approach to affinity-mature VHH-72 for the SARS-CoV-2 spike protein while retaining the original affinity for SARS-CoV-1. This was achieved by employing the computational platform ADAPT in a constrained dual-affinity optimization mode as a means of broadening specificity. Select mutants designed by ADAPT were formatted as fusions with a human IgG1-Fc fragment. These mutants demonstrated improved binding to the SARS-CoV-2 spike protein due to decreased dissociation rates. Functional testing for virus neutralization revealed improvements relative to the parental VHH72-Fc up to 10-fold using a SARS-CoV-2 pseudotyped lentivirus and 20-fold against the SARS-CoV-2 authentic live virus (Wuhan variant). Binding and neutralization improvements were maintained for some other SARS-CoV-2 variants currently in circulation. These improved VHH-72 mutants are predicted to establish novel interactions with the S antigen. They will be useful, alone or as fusions with other functional modules, in the global quest for treatments of COVID-19 infections.
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Affiliation(s)
- Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
- * E-mail:
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Matthew Stuible
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Nazanin Rohani
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Anh Tran
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Marie Parat
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yuneivy Cepero Donates
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mélanie Duchesne
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Pierre Plante
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Guneet Kour
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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27
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An antibody Fc engineered for conditional antibody-dependent cellular cytotoxicity at the low tumor microenvironment pH. J Biol Chem 2022; 298:101798. [PMID: 35248534 PMCID: PMC9006656 DOI: 10.1016/j.jbc.2022.101798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
Despite the exquisite specificity and high affinity of antibody-based cancer therapies, treatment side effects can occur since the tumor-associated antigens targeted are also present on healthy cells. However, the low pH of the tumor microenvironment provides an opportunity to develop conditionally active antibodies with enhanced tumor specificity. Here, we engineered the human IgG1 Fc domain to enhance pH-selective binding to the receptor FcγRIIIa and subsequent antibody-dependent cellular cytotoxicity (ADCC). We displayed the Fc domain on the surface of mammalian cells and generated a site-directed library by altering Fc residues at the Fc-FcγRIIIa interface to support interactions with positively charged histidine residues. We then used a competitive staining and flow cytometric selection strategy to isolate Fc variants exhibiting reduced FcγRIIIa affinities at neutral pH, but physiological affinities at the tumor-typical pH 6.5. We demonstrate that antibodies composed of Fab arms binding the breast cell epithelial marker Her2 and the lead Fc variant, termed acid-Fc, exhibited an ∼2-fold pH-selectivity for FcγRIIIa binding based on the ratio of equilibrium dissociation constants Kd,7.4/Kd,6.5, due to a faster dissociation rate at pH 7.4. Finally, in vitro ADCC assays with human FcγRIIIa-positive natural killer and Her2-positive target cells demonstrated similar activities for anti-Her2 antibodies bearing the wild-type or acid-Fc at pH 6.5, but nearly 20-fold reduced ADCC for acid-Fc at pH 7.4, based on EC50 ratios. This work shows the promise of mammalian cell display for Fc engineering and the feasibility of pH-selective Fc activation to provide a second dimension of selective tumor cell targeting.
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28
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Lee PS, MacDonald KG, Massi E, Chew PV, Bee C, Perkins P, Chau B, Thudium K, Lohre J, Nandi P, Deyanova EG, Barman I, Gudmundsson O, Dollinger G, Sproul T, Engelhardt JJ, Strop P, Rajpal A. Improved therapeutic index of an acidic pH-selective antibody. MAbs 2022; 14:2024642. [PMID: 35192429 PMCID: PMC8865267 DOI: 10.1080/19420862.2021.2024642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Although therapeutically efficacious, ipilimumab can exhibit dose-limiting toxicity that prevents maximal efficacious clinical outcomes and can lead to discontinuation of treatment. We hypothesized that an acidic pH-selective ipilimumab (pH Ipi), which preferentially and reversibly targets the acidic tumor microenvironment over the neutral periphery, may have a more favorable therapeutic index. While ipilimumab has pH-independent CTLA-4 affinity, pH Ipi variants have been engineered to have up to 50-fold enhanced affinity to CTLA-4 at pH 6.0 compared to pH 7.4. In hCTLA-4 knock-in mice, these variants have maintained anti-tumor activity and reduced peripheral activation, a surrogate marker for toxicity. pH-sensitive therapeutic antibodies may be a differentiating paradigm and a novel modality for enhanced tumor targeting and improved safety profiles.
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Affiliation(s)
- Peter S Lee
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, CA, USA
| | | | - Evan Massi
- Immuno-Oncology Research, Bristol Myers Squibb, Redwood City, CA, USA
| | - Pamela V Chew
- Oncology Biology, Gilead Sciences, Foster City, CA, USA
| | - Christine Bee
- Discovery Biology, Frontier Medicines, South San Francisco, CA, USA
| | - Padma Perkins
- Immuno-Oncology Research, Bristol Myers Squibb, Redwood City, CA, USA
| | - Bryant Chau
- Kyverna, Synthetic Biology, Emeryville, CA, USA
| | - Kent Thudium
- Immuno-Oncology Research, Bristol Myers Squibb, Redwood City, CA, USA
| | - Jack Lohre
- In Vivo Pharmacology, Bristol Myers Squibb, Redwood City, CA, USA
| | - Pradyot Nandi
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - Ekaterina G Deyanova
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - Ishita Barman
- Therapeutic Discovery, 3T Biosciences, South San Francisco, CA, USA
| | - Olafur Gudmundsson
- Pharmaceutical Candidate Optimization, Bristol Myers Squibb, Lawrenceville, NJ, USA
| | - Gavin Dollinger
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, CA, USA
| | - Tim Sproul
- In Vivo Pharmacology, UNITY Biotechnology, South San Francisco, CA, USA
| | | | - Pavel Strop
- Biologics Discovery, Tallac Therapeutics, Burlingame, CA, USA
| | - Arvind Rajpal
- Large Molecule Drug Discovery, Genentech Research and Early Development, South San Francisco, CA, USA
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29
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Warwicker J. The Physical Basis for pH Sensitivity in Biomolecular Structure and Function, With Application to the Spike Protein of SARS-CoV-2. Front Mol Biosci 2022; 9:834011. [PMID: 35252354 PMCID: PMC8894873 DOI: 10.3389/fmolb.2022.834011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/19/2022] [Indexed: 11/24/2022] Open
Abstract
Since pH sensitivity has a fundamental role in biology, much effort has been committed to establishing physical models to rationalize and predict pH dependence from molecular structures. Two of the key challenges are to accurately calculate ionizable group solvation and hydration and then to apply this modeling to all conformations relevant to the process in question. Explicit solvent methods coupled to molecular dynamics simulation are increasingly complementing lower resolution implicit solvent techniques, but equally, the scale of biological data acquisition leaves a role for high-throughput modeling. Additionally, determination of ranges of structures for a system allows sampling of key stages in solvation. In a review of the area, it is emphasized that pH sensors in biology beyond the most obvious candidate (histidine side chain, with an unshifted pK a near neutral pH) should be considered; that modeling can benefit from other concepts in bioinformatics, in particular modulation of interactions and function in families of homologs; and that it can also be beneficial to incorporate as many experimental structures as possible, to mitigate against small variations in conformation and to analyze larger, functional, conformational changes. These aspects are then demonstrated with new work on the spike protein of SARS-CoV-2, looking at the pH dependence of variants, including prediction of a change in the balance of locked, closed, and open forms at neutral pH for the Omicron variant spike protein.
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Affiliation(s)
- Jim Warwicker
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
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30
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Chen Q, Che C, Liu J, Gong Z, Si M, Yang S, Yang G. Construction of an exosome-functionalized graphene oxide based composite bionic smart drug delivery system and its anticancer activity. NANOTECHNOLOGY 2022; 33:175101. [PMID: 35008083 DOI: 10.1088/1361-6528/ac49bf] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Graphene oxide has covalently modified by chito oligosaccharides andγ-polyglutamic acid to form GO-CO-γ-PGA, which exhibits excellent performance as a drug delivery carrier, but this carrier did not have the ability to actively target. In this study, the targeting property of breast cancer tumor cell exosomes was exploited to give GO-CO-γ-PGA the ability to target breast tumor cells (MDA-MB-231), and the drug mitoxantrone (MIT) was loaded to finally form EXO-GO-CO-γ-PGA-MIT with an encapsulation efficiency of 73.02%. The pH response of EXO-GO-CO-γ-PGA showed a maximum cumulative release rate of 56.59% (pH 5.0, 120 h) and 6.73% (pH 7.4, 120 h) for MIT at different pH conditions.In vitrocellular assays showed that EXO-GO-CO-γ-PGA-MIT was more potent in killing MDA-MB-231 cells due to its targeting ability and had a significantly higher pro-apoptotic capacity compared to GO-CO-γ-PGA-MIT. The results showed that this bionic nano-intelligent drug delivery system has good drug slow release function and it can increase the local drug concentration of tumor and enhance the pro-apoptotic ability of MIT, so this newly synthesized bionic drug delivery carriers (EXO-GO-CO-γ-PGA-MIT) has potential application in breast cancer treatment.
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Affiliation(s)
- Qi Chen
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, People's Republic of China
| | - Chengchuan Che
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, People's Republic of China
| | - Jinfeng Liu
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, People's Republic of China
| | - Zhijin Gong
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, People's Republic of China
| | - Meiru Si
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, People's Republic of China
| | - Shanshan Yang
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, People's Republic of China
| | - Ge Yang
- College of Life Sciences, Qufu Normal University, Qufu 273165, Shandong, People's Republic of China
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31
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Zou W, Huang C, Sun Q, Zhao K, Gao H, Su R, Li Y. A stepwise mutagenesis approach using histidine and acidic amino acid to engineer highly pH-dependent protein switches. 3 Biotech 2022; 12:21. [PMID: 34956814 PMCID: PMC8686790 DOI: 10.1007/s13205-021-03079-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/26/2021] [Indexed: 10/26/2022] Open
Abstract
Antibody-based drugs can be highly toxic, because they target normal tissue as well as tumor tissue. The pH value of the extracellular microenvironments around tumor tissues is lower than that of normal tissues. Therefore, antibodies that engage in pH-dependent binding at slightly acidic pH are crucial for improving the safety of antibody-based drugs. Thus, we implemented a stepwise mutagenesis approach to engineering pH-dependent antibodies capable of selective binding in the acidic microenvironment in this study. The first step involved single-residue histidine scanning mutagenesis of the antibody's complementarity-determining regions to prescreen for pH-dependent mutants and identify ionizable sensitive hot-spot residues that could be substituted by acidic amino acids to obtain pH-dependent antibodies. The second step involved single-acidic amino acid residue substitutions of the identified residues and the assessment of pH-dependent binding. We identified six ionizable sensitive hot-spot residues using single-histidine scanning mutagenesis. Nine pH-dependent antibodies were isolated using single-acidic amino acid residue mutagenesis at the six hot-spot residue positions. Relative to wild-type anti-CEA chimera antibody, the binding selectivity of the best performing mutant was improved by approximately 32-fold according to ELISA and by tenfold according to FACS assay. The mutant had a high affinity in the pH range of 5.5-6.0. This study supports the development of pH-dependent protein switches and increases our understanding of the role of ionizable residues in protein interfaces. The stepwise mutagenesis approach is rapid, general, and robust and is expected to produce pH-sensitive protein affinity reagents for various applications.
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Affiliation(s)
- Wenjun Zou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Chuncui Huang
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qing Sun
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Keli Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Huanyu Gao
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Rong Su
- Department of Clinical Laboratory, Foshan Hospital of Traditional Chinese Medicine, Foshan, 528000 Guangdong China
| | - Yan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
- Key Laboratory of Interdisciplinary Research, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
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32
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Kuchroo JR, Hafler DA, Sharpe AH, Lucca LE. The double-edged sword: Harnessing PD-1 blockade in tumor and autoimmunity. Sci Immunol 2021; 6:eabf4034. [PMID: 34739340 DOI: 10.1126/sciimmunol.abf4034] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Juhi R Kuchroo
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Liliana E Lucca
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
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33
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Redesigning an antibody H3 loop by virtual screening of a small library of human germline-derived sequences. Sci Rep 2021; 11:21362. [PMID: 34725391 PMCID: PMC8560851 DOI: 10.1038/s41598-021-00669-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/05/2021] [Indexed: 01/01/2023] Open
Abstract
The design of superior biologic therapeutics, including antibodies and engineered proteins, involves optimizing their specific ability to bind to disease-related molecular targets. Previously, we developed and applied the Assisted Design of Antibody and Protein Therapeutics (ADAPT) platform for virtual affinity maturation of antibodies (Vivcharuk et al. in PLoS One 12(7):e0181490, 10.1371/journal.pone.0181490, 2017). However, ADAPT is limited to point mutations of hot-spot residues in existing CDR loops. In this study, we explore the possibility of wholesale replacement of the entire H3 loop with no restriction to maintain the parental loop length. This complements other currently published studies that sample replacements for the CDR loops L1, L2, L3, H1 and H2. Given the immense sequence space theoretically available to H3, we focused on the virtual grafting of over 5000 human germline-derived H3 sequences from the IGMT/LIGM database increasing the diversity of the sequence space when compared to using crystalized H3 loop sequences. H3 loop conformations are generated and scored to identify optimized H3 sequences. Experimental testing of high-ranking H3 sequences grafted into the framework of the bH1 antibody against human VEGF-A led to the discovery of multiple hits, some of which had similar or better affinities relative to the parental antibody. In over 75% of the tested designs, the re-designed H3 loop contributed favorably to overall binding affinity. The hits also demonstrated good developability attributes such as high thermal stability and no aggregation. Crystal structures of select re-designed H3 variants were solved and indicated that although some deviations from predicted structures were seen in the more solvent accessible regions of the H3 loop, they did not significantly affect predicted affinity scores.
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34
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Changing Cross-Reactivity for Different Immunoassays Using the Same Antibodies: Theoretical Description and Experimental Confirmation. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11146581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Many applications of immunoassays involve the possible presence of structurally similar compounds that bind with antibodies, but with different affinities. In this regard, an important characteristic of an immunoassay is its cross-reactivity: the possibility of detecting various compounds in comparison with a certain standard. Based on cross-reactivity, analytical systems are assessed as either high-selective (responding strictly to a specific compound) or low-selective (responding to a number of similar compounds). The present study demonstrates that cross-reactivity is not an intrinsic characteristic of antibodies but can vary for different formats of competitive immunoassays using the same antibodies. Assays with sensitive detection of markers and, accordingly, implementation at low concentrations of antibodies and modified (competing) antigens are characterized by lower cross-reactivities and are, thus, more specific than assays requiring high concentrations of markers and interacting reagents. This effect was confirmed by both mathematical modeling and experimental comparison of an enzyme immunoassay and a fluorescence polarization immunoassay of sulfonamides and fluoroquinolones. Thus, shifting to lower concentrations of reagents decreases cross-reactivities by up to five-fold. Moreover, the cross-reactivities are changed even in the same assay format by varying the ratio of immunoreactants’ concentrations and shifting from the kinetic or equilibrium mode of the antigen-antibody reaction. The described patterns demonstrate the possibility of modulating immunodetection selectivity without searching for new binding reactants.
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35
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Song L, Cohen D, Ouyang Z, Cao Y, Hu X, Liu XS. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nat Methods 2021; 18:627-630. [PMID: 33986545 PMCID: PMC9328942 DOI: 10.1038/s41592-021-01142-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/02/2021] [Indexed: 02/02/2023]
Abstract
We introduce the TRUST4 open-source algorithm for reconstruction of immune receptor repertoires in αβ/γδ T cells and B cells from RNA-sequencing (RNA-seq) data. Compared with competing methods, TRUST4 supports both FASTQ and BAM format and is faster and more sensitive in assembling longer-even full-length-receptor repertoires. TRUST4 can also call repertoire sequences from single-cell RNA-seq (scRNA-seq) data without V(D)J enrichment, and is compatible with both SMART-seq and 5' 10x Genomics platforms.
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Affiliation(s)
- Li Song
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - David Cohen
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zhangyi Ouyang
- Department of Biotechnology, Beijing Institue of Radiation Medicine, Beijing, China
| | - Yang Cao
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xihao Hu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - X. Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard T.H. Chan School of Public Health, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA,: Corresponding author.
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Lucchi R, Bentanachs J, Oller-Salvia B. The Masking Game: Design of Activatable Antibodies and Mimetics for Selective Therapeutics and Cell Control. ACS CENTRAL SCIENCE 2021; 7:724-738. [PMID: 34079893 PMCID: PMC8161478 DOI: 10.1021/acscentsci.0c01448] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Indexed: 05/04/2023]
Abstract
The high selectivity and affinity of antibody binding have made antibodies all-pervasive tools in therapy, diagnosis, and basic science. A plethora of chemogenetic approaches has been devised to make antibodies responsive to stimuli ranging from light to enzymatic activity, temperature, pH, ions, and effector molecules. Within a single decade, the field of activatable antibodies has yielded marketed therapeutics capable of engaging antigens that could not be targeted with traditional antibodies, as well as new tools to control intracellular protein location and investigate biological processes. Many opportunities remain untapped, waiting for more efficient and generally applicable masking strategies to be developed at the interface between chemistry and biotechnology.
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Affiliation(s)
- Roberta Lucchi
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Jordi Bentanachs
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Benjamí Oller-Salvia
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
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Hong ST, Su YC, Wang YJ, Cheng TL, Wang YT. Anti-TNF Alpha Antibody Humira with pH-dependent Binding Characteristics: A constant-pH Molecular Dynamics, Gaussian Accelerated Molecular Dynamics, and In Vitro Study. Biomolecules 2021; 11:334. [PMID: 33672169 PMCID: PMC7926962 DOI: 10.3390/biom11020334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 12/17/2022] Open
Abstract
Humira is a monoclonal antibody that binds to TNF alpha, inactivates TNF alpha receptors, and inhibits inflammation. Neonatal Fc receptors can mediate the transcytosis of Humira-TNF alpha complex structures and process them toward degradation pathways, which reduces the therapeutic effect of Humira. Allowing the Humira-TNF alpha complex structures to dissociate to Humira and soluble TNF alpha in the early endosome to enable Humira recycling is crucial. We used the cytoplasmic pH (7.4), the early endosomal pH (6.0), and pKa of histidine side chains (6.0-6.4) to mutate the residues of complementarity-determining regions with histidine. Our engineered Humira (W1-Humira) can bind to TNF alpha in plasma at neutral pH and dissociate from the TNF alpha in the endosome at acidic pH. We used the constant-pH molecular dynamics, Gaussian accelerated molecular dynamics, two-dimensional potential mean force profiles, and in vitro methods to investigate the characteristics of W1-Humira. Our results revealed that the proposed Humira can bind TNF alpha with pH-dependent affinity in vitro. The W1-Humira was weaker than wild-type Humira at neutral pH in vitro, and our prediction results were close to the in vitro results. Furthermore, our approach displayed a high accuracy in antibody pH-dependent binding characteristics prediction, which may facilitate antibody drug design. Advancements in computational methods and computing power may further aid in addressing the challenges in antibody drug design.
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Affiliation(s)
- Shih-Ting Hong
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Yu-Cheng Su
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsin-Chu 300, Taiwan;
| | - Yu-Jen Wang
- Department of Mechanical and Electromechanical Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
| | - Tian-Lu Cheng
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yeng-Tseng Wang
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
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Klaus T, Deshmukh S. pH-responsive antibodies for therapeutic applications. J Biomed Sci 2021; 28:11. [PMID: 33482842 PMCID: PMC7821552 DOI: 10.1186/s12929-021-00709-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/15/2021] [Indexed: 11/29/2022] Open
Abstract
Therapeutic antibodies are instrumental in improving the treatment outcome for certain disease conditions. However, to enhance their efficacy and specificity, many efforts are continuously made. One of the approaches that are increasingly explored in this field are pH-responsive antibodies capable of binding target antigens in a pH-dependent manner. We reviewed suitability and examples of these antibodies that are functionally modulated by the tumor microenvironment. Provided in this review is an update about antigens targeted by pH-responsive, sweeping, and recycling antibodies. Applicability of the pH-responsive antibodies in the engineering of chimeric antigen receptor T-cells (CAR-T) and in improving drug delivery to the brain by the enhanced crossing of the blood-brain barrier is also discussed. The pH-responsive antibodies possess strong treatment potential. They emerge as next-generation programmable engineered biologic drugs that are active only within the targeted biological space. Thus, they are valuable in targeting acidified tumor microenvironment because of improved spatial persistence and reduced on-target off-tumor toxicities. We predict that the programmable pH-dependent antibodies become powerful tools in therapies of cancer.
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Affiliation(s)
- Tomasz Klaus
- Research and Development Department, Pure Biologics, Inc., Dunska 11, 54427, Wrocław, Poland
| | - Sameer Deshmukh
- Research and Development Department, Pure Biologics, Inc., Dunska 11, 54427, Wrocław, Poland.
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Wang Y, Zhu M, Guo F, Song Y, Fan X, Qin G. Identification of Tumor Microenvironment-Related Prognostic Biomarkers in Luminal Breast Cancer. Front Genet 2020; 11:555865. [PMID: 33329695 PMCID: PMC7735391 DOI: 10.3389/fgene.2020.555865] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/23/2020] [Indexed: 12/24/2022] Open
Abstract
Background: The tumor microenvironment (TME) has been reported to have significant value in the diagnosis and prognosis of cancers. This study aimed to identify key biomarkers in the TME of luminal breast cancer (BC). Methods: We obtained immune scores (ISs) and stromal scores (SSs) for The Cancer Genome Atlas (TCGA) luminal BC cohort from the online ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data) portal. The relationships between ISs and SSs and the overall survival of luminal BC patients were assessed by the Kaplan-Meier method. The differentially expressed messenger RNAs (DEmRNAs) related to the ISs and SSs were subjected to functional enrichment analysis. Additionally, a competing endogenous RNA (ceRNA) network was constructed with differentially expressed microRNAs (DEmiRNAs) and long noncoding RNAs (DElncRNAs). Furthermore, a protein–protein interaction (PPI) network was established to analyze the DEmRNAs in the ceRNA network. Then, survival analysis of biomarkers involved in the ceRNA network was carried out to explore their prognostic value. Finally, these biomarkers were validated using the luminal BC dataset from the Gene Expression Omnibus (GEO) database. Results: The results showed that ISs were significantly associated with longer survival times of luminal BC patients. Functional enrichment analysis showed that the DEmRNAs were mainly associated with immune response, antigen binding, and the extracellular region. In the PPI network, the top 10 DEmRNAs were identified as hub genes that affected the TME of luminal BC. Finally, two DEmiRNAs, two DElncRNAs, and 17 DEmRNAs of the ceRNA network associated with the TME were shown to have prognostic value. Subsequently, the expression of 15 prognostic biomarkers was validated in one additional dataset (GSE81002). In particular, one lncRNA (GVINP1) and five mRNAs (CCDC69, DOCK2, IKZF1, JCHAIN, and NCKAP1L) were novel biomarkers. Conclusions: Our studies demonstrated that ISs were associated with the survival of luminal BC patients, and a set of novel biomarkers that might play a prognostic role in the TME of luminal BC was identified.
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Affiliation(s)
- Yanyan Wang
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mingzhi Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng Guo
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi Song
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xunjie Fan
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guijun Qin
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Song X, Qi W, Guo J, Sun L, Ding A, Zhao G, Li H, Qiu W, Lv J. Immune checkpoint inhibitor combination therapy for gastric cancer: Research progress. Oncol Lett 2020; 20:46. [PMID: 32802168 PMCID: PMC7412728 DOI: 10.3892/ol.2020.11905] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/25/2020] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer is one of the most common types of cancer; notably, gastric cancer is one of the top five malignancies with regards to incidence and mortality rates. The symptoms of early gastric cancer are not typical, exhibiting only slight upper abdominal discomfort. When the symptoms become more obvious, the lesion has usually progressed to an advanced stage. Notably, >90% of inpatients already have locally advanced or metastatic gastric cancer at the time of initial diagnosis, with limited treatment options for advanced gastric cancer. These options include chemotherapy, targeted therapy and immune checkpoint inhibitors (ICIs). With regards to ICIs, the clinical benefit of monotherapy for advanced gastric cancer is limited; however, combinations of ICIs and other therapies may have clinical benefit. Relevant clinical studies have demonstrated that combinations of ICIs with chemotherapy, anti-vascular targeted therapy or other molecular targeted therapies, and the use of two ICIs, improve outcomes for patients with advanced gastric cancer. This article is a review of progress in the use of ICIs in combination with other therapies for the treatment of gastric cancer. The purpose of this article was to advance gastric cancer immunotherapy and to improve the overall therapeutic benefit for patients with advanced gastric cancer.
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Affiliation(s)
- Xiaoxu Song
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Weiwei Qi
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Jing Guo
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Libin Sun
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Aiping Ding
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Guanghui Zhao
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Hui Li
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Wensheng Qiu
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Jing Lv
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
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Mangeat T, Gracia M, Martineau P, Robert B. Stratégies de ciblage spécifique de la tumeur fondées sur les caractéristiques des antigènes tumoraux et du microenvironnement tumoral. Med Sci (Paris) 2020; 36 Hors série n° 1:56-60. [DOI: 10.1051/medsci/2020194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
L’immunothérapie à base d’anticorps monoclonaux (AcM) connaît un plein essor en cancérologie. En 2020, plus de 40% des anticorps approuvés par la FDA (Food and Drug Administration) (34 sur 84 anticorps, selon The Antibody Society) ont une indication pour les thérapies anti-cancéreuses. Contrairement à la chimiothérapie standard, ils démontrent un bien meilleur profil de tolérance pour les patients. Malgré cela, des effets indésirables néfastes peuvent survenir en raison du ciblage de l’antigène qui est également exprimé au niveau des tissus sains. C’est pourquoi des stratégies émergentes visent à optimiser le format des anticorps et à tenir compte des particularités du microenvironnement tumoral pour conférer une action encore plus spécifique de l’anticorps au niveau tumoral.
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van Faassen H, Ryan S, Henry KA, Raphael S, Yang Q, Rossotti MA, Brunette E, Jiang S, Haqqani AS, Sulea T, MacKenzie CR, Tanha J, Hussack G. Serum albumin‐binding V
H
Hs with variable pH sensitivities enable tailored half‐life extension of biologics. FASEB J 2020; 34:8155-8171. [DOI: 10.1096/fj.201903231r] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/14/2020] [Accepted: 04/02/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Henk van Faassen
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Shannon Ryan
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Kevin A. Henry
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
- Department of Biochemistry, Microbiology & Immunology University of Ottawa Ottawa ON Canada
| | - Shalini Raphael
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Qingling Yang
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Martin A. Rossotti
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Eric Brunette
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Susan Jiang
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Arsalan S. Haqqani
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre National Research Council Canada Montréal QC Canada
| | - C. Roger MacKenzie
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
- Department of Biochemistry, Microbiology & Immunology University of Ottawa Ottawa ON Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre National Research Council Canada Ottawa ON Canada
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