1
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Johann F, Wöll S, Gieseler H. "Negative" Impact: The Role of Payload Charge in the Physicochemical Stability of Auristatin Antibody-Drug Conjugates. J Pharm Sci 2024:S0022-3549(24)00150-3. [PMID: 38679233 DOI: 10.1016/j.xphs.2024.04.023] [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: 12/24/2023] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
Antibody-drug conjugates (ADCs) tend to be less stable than their parent antibodies, which is often attributed to the hydrophobic nature of their drug payloads. This study investigated how the payload charge affects ADC stability by comparing two interchain cysteine ADCs that had matched drug-to-antibody ratios and identical linkers but differently charged auristatin payloads, vcMMAE (neutral) and vcMMAF (negative). Both ADCs exhibited higher aggregation than their parent antibody under shaking stress and thermal stress conditions. However, conjugation with vcMMAF increased the aggregation rates to a greater extent than conjugation with uncharged but more hydrophobic vcMMAE. Consistent with the payload logD values, ADC-vcMMAE showed the greatest increase in hydrophobicity but minor changes in charge compared with the parent antibody, as indicated by hydrophobic interaction chromatography and capillary electrophoresis data. In contrast, ADC-vcMMAF showed a decrease in net charge and isoelectric point along with an increase in charge heterogeneity. This charge alteration likely contributed to a reduced electrostatic repulsion and increased surface activity in ADC-vcMMAF, thus affecting its aggregation propensity. These findings suggest that not only the hydrophobicity of the payload, but also its charge should be considered as a critical factor affecting the stability of ADCs.
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Affiliation(s)
- Florian Johann
- Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Department of Pharmaceutical Technology and Biopharmacy, Freeze Drying Focus Group (FDFG), Cauerstraße 4, 91058 Erlangen, Germany; Merck KGaA, Global CMC Development, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Steffen Wöll
- Merck KGaA, Global CMC Development, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Henning Gieseler
- Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Department of Pharmaceutical Technology and Biopharmacy, Freeze Drying Focus Group (FDFG), Cauerstraße 4, 91058 Erlangen, Germany; GILYOS GmbH, Friedrich-Bergius-Ring 15, 97076 Würzburg, Germany.
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2
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Prašnikar M, Proj M, Bjelošević Žiberna M, Lebar B, Knez B, Kržišnik N, Roškar R, Gobec S, Grabnar I, Žula A, Ahlin Grabnar P. The search for novel proline analogs for viscosity reduction and stabilization of highly concentrated monoclonal antibody solutions. Int J Pharm 2024; 655:124055. [PMID: 38554741 DOI: 10.1016/j.ijpharm.2024.124055] [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: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
Administration of monoclonal antibodies (mAbs) is currently focused on subcutaneous injection associated with increased patient adherence and reduced treatment cost, leading to sustainable healthcare. The main bottleneck is low volume that can be injected, requiring highly concentrated mAb solutions. The latter results in increased solution viscosity with pronounced mAb aggregation propensity because of intensive protein-protein interactions. Small molecule excipients have been proposed to restrict the protein-protein interactions, contributing to reduced viscosity. The aim of the study was to discover novel compounds that reduce the viscosity of highly concentrated mAb solution. First, the chemical space of proline analogs was explored and 35 compounds were determined. Viscosity measurements revealed that 18 proline analogs reduced the mAb solution viscosity similar to or more than proline. The compounds forming both electrostatic and hydrophobic interactions with mAb reduced the viscosity of the formulation more efficiently without detrimentally effecting mAb physical stability. A correlation between the level of interaction and viscosity-reducing effect was confirmed with molecular dynamic simulations. Structure rigidity of the compounds and aromaticity contributed to their viscosity-reducing effect, dependent on molecule size. The study results highlight the novel proline analogs as an effective approach in viscosity reduction in development of biopharmaceuticals for subcutaneous administration.
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Affiliation(s)
- Monika Prašnikar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Matic Proj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | | | - Blaž Lebar
- Biologics Drug Product, Technical Research and Development, Global Drug Development, Novartis, Slovenia
| | - Benjamin Knez
- Biologics Drug Product, Technical Research and Development, Global Drug Development, Novartis, Slovenia
| | - Nika Kržišnik
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Robert Roškar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Iztok Grabnar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Aleš Žula
- Biologics Drug Product, Technical Research and Development, Global Drug Development, Novartis, Slovenia
| | - Pegi Ahlin Grabnar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.
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3
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Rubio-Pérez L, Frago S, Compte M, Navarro R, Harwood SL, Lázaro-Gorines R, Gómez-Rosel M, Hangiu O, Silva-Pilipich N, Vanrell L, Smerdou C, Álvarez-Vallina L. Characterization of a Trispecific PD-L1 Blocking Antibody That Exhibits EGFR-Conditional 4-1BB Agonist Activity. Antibodies (Basel) 2024; 13:34. [PMID: 38804302 PMCID: PMC11130918 DOI: 10.3390/antib13020034] [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: 01/12/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024] Open
Abstract
Immune checkpoint blockade has changed the treatment paradigm for advanced solid tumors, but the overall response rates are still limited. The combination of checkpoint blockade with anti-4-1BB antibodies to stimulate tumor-infiltrating T cells has shown anti-tumor activity in human trials. However, the further clinical development of these antibodies has been hampered by significant off-tumor toxicities. Here, we generated an anti-4-1BB/EGFR/PD-L1 trispecific antibody consisting of a triple-targeting tandem trimerbody (TT) fused to an engineered silent Fc region. This antibody (IgTT-4E1-S) was designed to combine the blockade of the PD-L1/PD-1 axis with conditional 4-1BB costimulation specifically confined to the tumor microenvironment (TME). The antibody demonstrated simultaneous binding to purified EGFR, PD-L1, and 4-1BB in solution, effective blockade of the PD-L1/PD1 interaction, and potent 4-1BB-mediated costimulation, but only in the presence of EGFR-expressing cells. These results demonstrate the feasibility of IgTT-4E1-S specifically blocking the PD-L1/PD-1 axis and inducing EGFR-conditional 4-1BB agonist activity.
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Affiliation(s)
- Laura Rubio-Pérez
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario12 de Octubre (H12O), 28041 Madrid, Spain; (L.R.-P.); (R.L.-G.); (M.G.-R.); (O.H.)
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), 28041 Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
- Chair for Immunology UFV/Merck, Universidad Francisco de Vitoria (UFV), Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Susana Frago
- Department of Antibody Engineering, Leadartis SL, QUBE Technology Park, Tres Cantos, 28760 Madrid, Spain; (S.F.); (M.C.); (R.N.)
| | - Marta Compte
- Department of Antibody Engineering, Leadartis SL, QUBE Technology Park, Tres Cantos, 28760 Madrid, Spain; (S.F.); (M.C.); (R.N.)
| | - Rocío Navarro
- Department of Antibody Engineering, Leadartis SL, QUBE Technology Park, Tres Cantos, 28760 Madrid, Spain; (S.F.); (M.C.); (R.N.)
| | - Seandean L. Harwood
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark;
| | - Rodrigo Lázaro-Gorines
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario12 de Octubre (H12O), 28041 Madrid, Spain; (L.R.-P.); (R.L.-G.); (M.G.-R.); (O.H.)
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), 28041 Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Marina Gómez-Rosel
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario12 de Octubre (H12O), 28041 Madrid, Spain; (L.R.-P.); (R.L.-G.); (M.G.-R.); (O.H.)
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), 28041 Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Oana Hangiu
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario12 de Octubre (H12O), 28041 Madrid, Spain; (L.R.-P.); (R.L.-G.); (M.G.-R.); (O.H.)
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), 28041 Madrid, Spain
- Department of Antibody Engineering, Leadartis SL, QUBE Technology Park, Tres Cantos, 28760 Madrid, Spain; (S.F.); (M.C.); (R.N.)
| | - Noelia Silva-Pilipich
- Division of DNA and RNA Medicine, Cima Universidad de Navarra, 31008 Pamplona, Spain; (N.S.-P.); (C.S.)
- Instituto de Investigación Sanitaria de Navarra (IdISNA) and CCUN, 31008 Pamplona, Spain
| | - Lucía Vanrell
- Facultad de Ingeniería, Universidad ORT Uruguay, 11100 Montevideo, Uruguay;
- Nanogrow Biotech, Montevideo 11500, Uruguay
| | - Cristian Smerdou
- Division of DNA and RNA Medicine, Cima Universidad de Navarra, 31008 Pamplona, Spain; (N.S.-P.); (C.S.)
- Instituto de Investigación Sanitaria de Navarra (IdISNA) and CCUN, 31008 Pamplona, Spain
| | - Luis Álvarez-Vallina
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario12 de Octubre (H12O), 28041 Madrid, Spain; (L.R.-P.); (R.L.-G.); (M.G.-R.); (O.H.)
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), 28041 Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
- Chair for Immunology UFV/Merck, Universidad Francisco de Vitoria (UFV), Pozuelo de Alarcón, 28223 Madrid, Spain
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4
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Sadiki A, Liu S, Vaidya SR, Kercher EM, Lang RT, McIsaac J, Spring BQ, Auclair JR, Zhou ZS. Site-Specific Conjugation of Native Antibody: Transglutaminase-Mediated Modification of a Conserved Glutamine While Maintaining the Primary Sequence and Core Fc Glycan via Trimming with an Endoglycosidase. Bioconjug Chem 2024; 35:465-471. [PMID: 38499390 PMCID: PMC11036358 DOI: 10.1021/acs.bioconjchem.4c00013] [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: 01/15/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/20/2024]
Abstract
A versatile chemo-enzymatic tool to site-specifically modify native (nonengineered) antibodies is using transglutaminase (TGase, E.C. 2.3.2.13). With various amines as cosubstrates, this enzyme converts the unsubstituted side chain amide of glutamine (Gln or Q) in peptides and proteins into substituted amides (i.e., conjugates). A pleasant surprise is that only a single conserved glutamine (Gln295) in the Fc region of IgG is modified by microbial TGase (mTGase, EC 2.3.2.13), thereby providing a highly specific and generally applicable conjugation method. However, prior to the transamidation (access to the glutamine residue by mTGase), the steric hindrance from the nearby conserved N-glycan (Asn297 in IgG1) must be reduced. In previous approaches, amidase (PNGase F, EC 3.5.1.52) was used to completely remove the N-glycan. However, PNGase F also converts a net neutral asparagine (Asn297) to a negatively charged aspartic acid (Asp297). This charge alteration may markedly change the structure, function, and immunogenicity of an IgG antibody. In contrast, in our new method presented herein, the N-glycan is trimmed by an endoglycosidase (EndoS2, EC 3.2.1.96), hence retaining both the core N-acetylglucosamine (GlcNAc) moiety and the neutral asparaginyl amide. The trimmed glycan also reduces or abolishes Fc receptor-mediated functions, which results in better imaging agents by decreasing nonspecific binding to other cells (e.g., immune cells). Moreover, the remaining core glycan allows further derivatization such as glycan remodeling and dual conjugation. Practical and robust, our method generates conjugates in near quantitative yields, and both enzymes are commercially available.
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Affiliation(s)
- Amissi Sadiki
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
| | - Shanshan Liu
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
| | - Shefali R. Vaidya
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
| | - Eric M. Kercher
- Translational
Biophotonics Cluster, Department of Physics, Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ryan T. Lang
- Translational
Biophotonics Cluster, Department of Physics, Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - James McIsaac
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
| | - Bryan Q. Spring
- Translational
Biophotonics Cluster, Department of Physics, Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Jared R. Auclair
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
| | - Zhaohui Sunny Zhou
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
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5
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Hess R, Faessler J, Yun D, Mama A, Saleh D, Grosch JH, Wang G, Schwab T, Hubbuch J. Predicting multimodal chromatography of therapeutic antibodies using multiscale modeling. J Chromatogr A 2024; 1718:464706. [PMID: 38335881 DOI: 10.1016/j.chroma.2024.464706] [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: 11/04/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
Multimodal chromatography has emerged as a powerful method for the purification of therapeutic antibodies. However, process development of this separation technique remains challenging because of an intricate and molecule-specific interaction towards multimodal ligands, leading to time-consuming and costly experimental optimization. This study presents a multiscale modeling approach to predict the multimodal chromatographic behavior of therapeutic antibodies based on their sequence information. Linear gradient elution (LGE) experiments were performed on an anionic multimodal resin for 59 full-length antibodies, including five different antibody formats at pH 5.0, 6.0, and 7.0 that were used for parameter determination of a linear adsorption model at low loading density conditions. Quantitative structure-property relationship (QSPR) modeling was utilized to correlate the adsorption parameters with up to 1374 global and local physicochemical descriptors calculated from antibody homology models. The final QSPR models employed less than eight descriptors per model and demonstrated high training accuracy (R² > 0.93) and reasonable test set prediction accuracy (Q² > 0.83) for the adsorption parameters. Model evaluation revealed the significance of electrostatic interaction and hydrophobicity in determining the chromatographic behavior of antibodies, as well as the importance of the HFR3 region in antibody binding to the multimodal resin. Chromatographic simulations using the predicted adsorption parameters showed good agreement with the experimental data for the vast majority of antibodies not employed during the model training. The results of this study demonstrate the potential of sequence-based prediction for determining chromatographic behavior in therapeutic antibody purification. This approach leads to more efficient and cost-effective process development, providing a valuable tool for the biopharmaceutical industry.
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Affiliation(s)
- Rudger Hess
- Karlsruhe Institute of Technology (KIT), Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe, Germany; DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jan Faessler
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Doil Yun
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Ahmed Mama
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - David Saleh
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jan-Hendrik Grosch
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Gang Wang
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Thomas Schwab
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jürgen Hubbuch
- Karlsruhe Institute of Technology (KIT), Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe, Germany.
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6
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Foss S, Sakya SA, Aguinagalde L, Lustig M, Shaughnessy J, Cruz AR, Scheepmaker L, Mathiesen L, Ruso-Julve F, Anthi AK, Gjølberg TT, Mester S, Bern M, Evers M, Bratlie DB, Michaelsen TE, Schlothauer T, Sok D, Bhattacharya J, Leusen J, Valerius T, Ram S, Rooijakkers SHM, Sandlie I, Andersen JT. Human IgG Fc-engineering for enhanced plasma half-life, mucosal distribution and killing of cancer cells and bacteria. Nat Commun 2024; 15:2007. [PMID: 38453922 PMCID: PMC10920689 DOI: 10.1038/s41467-024-46321-9] [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: 04/07/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Monoclonal IgG antibodies constitute the fastest growing class of therapeutics. Thus, there is an intense interest to design more potent antibody formats, where long plasma half-life is a commercially competitive differentiator affecting dosing, frequency of administration and thereby potentially patient compliance. Here, we report on an Fc-engineered variant with three amino acid substitutions Q311R/M428E/N434W (REW), that enhances plasma half-life and mucosal distribution, as well as allows for needle-free delivery across respiratory epithelial barriers in human FcRn transgenic mice. In addition, the Fc-engineered variant improves on-target complement-mediated killing of cancer cells as well as both gram-positive and gram-negative bacteria. Hence, this versatile Fc technology should be broadly applicable in antibody design aiming for long-acting prophylactic or therapeutic interventions.
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Affiliation(s)
- Stian Foss
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Siri A Sakya
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Leire Aguinagalde
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Marta Lustig
- Section for Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jutamas Shaughnessy
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ana Rita Cruz
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lisette Scheepmaker
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Line Mathiesen
- Department of Public Health, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fulgencio Ruso-Julve
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Aina Karen Anthi
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Torleif Tollefsrud Gjølberg
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Simone Mester
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Malin Bern
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway
| | - Mitchell Evers
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Diane B Bratlie
- Infection Immunology, Norwegian Institute of Public Health, Oslo, Norway
| | - Terje E Michaelsen
- Infection Immunology, Norwegian Institute of Public Health, Oslo, Norway
- Department of Chemical Pharmacy, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Tilman Schlothauer
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Munich, Germany
| | - Devin Sok
- International AIDS Vaccine Initiative (IAVI), New York, NY, USA
| | - Jayanta Bhattacharya
- Antibody Translational Research Program, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Jeanette Leusen
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Thomas Valerius
- Section for Stem Cell Transplantation and Immunotherapy, Department of Medicine II, Christian-Albrechts University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Sanjay Ram
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Suzan H M Rooijakkers
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Inger Sandlie
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jan Terje Andersen
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway.
- Precision Immunotherapy Alliance (PRIMA), University of Oslo, Oslo, Norway.
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7
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Saurabh S, Zhang Q, Seddon JM, Lu JR, Kalonia C, Bresme F. Unraveling the Microscopic Mechanism of Molecular Ion Interaction with Monoclonal Antibodies: Impact on Protein Aggregation. Mol Pharm 2024; 21:1285-1299. [PMID: 38345400 PMCID: PMC10915798 DOI: 10.1021/acs.molpharmaceut.3c00963] [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: 10/17/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 03/05/2024]
Abstract
Understanding and predicting protein aggregation represents one of the major challenges in accelerating the pharmaceutical development of protein therapeutics. In addition to maintaining the solution pH, buffers influence both monoclonal antibody (mAb) aggregation in solution and the aggregation mechanisms since the latter depend on the protein charge. Molecular-level insight is necessary to understand the relationship between the buffer-mAb interaction and mAb aggregation. Here, we use all-atom molecular dynamics simulations to investigate the interaction of phosphate (Phos) and citrate (Cit) buffer ions with the Fab and Fc domains of mAb COE3. We demonstrate that Phos and Cit ions feature binding mechanisms, with the protein that are very different from those reported previously for histidine (His). These differences are reflected in distinctive ion-protein binding modes and adsorption/desorption kinetics of the buffer molecules from the mAb surface and result in dissimilar effects of these buffer species on mAb aggregation. While His shows significant affinity toward hydrophobic amino acids on the protein surface, Phos and Cit ions preferentially bind to charged amino acids. We also show that Phos and Cit anions provide bridging contacts between basic amino acids in neighboring proteins. The implications of such contacts and their connection to mAb aggregation in therapeutic formulations are discussed.
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Affiliation(s)
- Suman Saurabh
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College, London W12 0BZ, U.K.
| | - Qinkun Zhang
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College, London W12 0BZ, U.K.
| | - John M. Seddon
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College, London W12 0BZ, U.K.
| | - Jian R. Lu
- Biological
Physics Group, School of Physics and Astronomy, Faculty of Science
and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Cavan Kalonia
- Dosage
Form Design and Development, BioPharmaceutical Development, BioPharmaceuticals
R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Fernando Bresme
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College, London W12 0BZ, U.K.
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8
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Park SA, Lee Y, Hwang H, Lee JH, Kang YJ, Kim Y, Jin C, An HJ, Oh YJ, Hinterdorfer P, Kim E, Choi S, Ko K. Fc engineered anti-virus therapeutic human IgG 1 expressed in plants with altered binding to the neonatal Fc receptor. Biotechnol J 2024; 19:e2300552. [PMID: 38528347 DOI: 10.1002/biot.202300552] [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: 10/11/2023] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 03/27/2024]
Abstract
Production of therapeutic monoclonal antibody (mAb) in transgenic plants has several advantages such as large-scale production and the absence of pathogenic animal contaminants. However, mAb with high mannose (HM) type glycans has shown a faster clearance compared to antibodies produced in animal cells. The neonatal Fc receptor (FcRn) regulates the persistence of immunoglobulin G (IgG) by the FcRn-mediated recycling pathway, which salvages IgG from lysosomal degradation within cells. In this study, Fc-engineering of antirabies virus therapeutic mAb SO57 with the endoplasmic reticulum (ER)-retention peptide signal (Lys-Asp-Glu-Leu; KDEL) (mAbpK SO57) in plant cell was conducted to enhance its binding activity to human neonatal Fc receptor (hFcRn), consequently improve its serum half-life. Enzyme-linked immunosorbent assay (ELISA) and Surface plasmon resonance assay showed altered binding affinity of the Fc region of three different mAbpK SO57 variants [M252Y/S254T/T256E (MST), M428L/N434S (MN), H433K/N434F (HN)] to hFcRn compared to wild type (WT) of mAbpK SO57. Molecular modeling data visualized the structural alterations in these mAbpK SO57. All of the mAbpK SO57 variants had HM type glycan structures similar to the WT mAbpK SO57. In addition, the neutralizing activity of the three variants against the rabies virus CVS-11 was effective as the WT mAbpK SO57. These results indicate that the binding affinity of mAbpK SO57 variants to hFcRn can be modified without alteration of N-glycan structure and neutralization activity. Taken together, this study suggests that Fc-engineering of antirabies virus mAb can be applied to enhance the efficacy of therapeutic mAbs in plant expression systems.
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Affiliation(s)
- Sol-Ah Park
- Department of Medicine, BioSystems Design Lab, College of Medicine, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - Yoonji Lee
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Hyunjoo Hwang
- Department of Medicine, BioSystems Design Lab, College of Medicine, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - Jeong Hwan Lee
- Department of Medicine, BioSystems Design Lab, College of Medicine, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - Yang Joo Kang
- Department of Medicine, BioSystems Design Lab, College of Medicine, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - Yerin Kim
- Department of Medicine, BioSystems Design Lab, College of Medicine, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - Caiquan Jin
- Department of Medicine, BioSystems Design Lab, College of Medicine, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Yoo Jin Oh
- Department of Applied Experimental Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Peter Hinterdorfer
- Department of Applied Experimental Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Eunhye Kim
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Sun Choi
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Kisung Ko
- Department of Medicine, BioSystems Design Lab, College of Medicine, Chung-Ang University, Dongjak-gu, Seoul, Republic of Korea
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9
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Saurabh S, Zhang Q, Li Z, Seddon JM, Kalonia C, Lu JR, Bresme F. Mechanistic Insights into the Adsorption of Monoclonal Antibodies at the Water/Vapor Interface. Mol Pharm 2024; 21:704-717. [PMID: 38194618 PMCID: PMC10848294 DOI: 10.1021/acs.molpharmaceut.3c00821] [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: 09/07/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 01/11/2024]
Abstract
Monoclonal antibodies (mAbs) are active components of therapeutic formulations that interact with the water-vapor interface during manufacturing, storage, and administration. Surface adsorption has been demonstrated to mediate antibody aggregation, which leads to a loss of therapeutic efficacy. Controlling mAb adsorption at interfaces requires a deep understanding of the microscopic processes that lead to adsorption and identification of the protein regions that drive mAb surface activity. Here, we report all-atom molecular dynamics (MD) simulations of the adsorption behavior of a full IgG1-type antibody at the water/vapor interface. We demonstrate that small local changes in the protein structure play a crucial role in promoting adsorption. Also, interfacial adsorption triggers structural changes in the antibody, potentially contributing to the further enhancement of surface activity. Moreover, we identify key amino acid sequences that determine the adsorption of antibodies at the water-air interface and outline strategies to control the surface activity of these important therapeutic proteins.
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Affiliation(s)
- Suman Saurabh
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
| | - Qinkun Zhang
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
| | - Zongyi Li
- Biological
Physics Group, School of Physics and Astronomy, Faculty of Science
and Engineering, the University of Manchester, Manchester M13 9PL, U.K.
| | - John M. Seddon
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
| | - Cavan Kalonia
- Dosage
Form Design and Development, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Jian R. Lu
- Biological
Physics Group, School of Physics and Astronomy, Faculty of Science
and Engineering, the University of Manchester, Manchester M13 9PL, U.K.
| | - Fernando Bresme
- Department
of Chemistry, Molecular Sciences Research
Hub Imperial College, London W12 0BZ, U.K.
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10
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Guo D, De Sciscio ML, Chi-Fung Ng J, Fraternali F. Modelling the assembly and flexibility of antibody structures. Curr Opin Struct Biol 2024; 84:102757. [PMID: 38118364 DOI: 10.1016/j.sbi.2023.102757] [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: 10/13/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023]
Abstract
Antibodies are large protein assemblies capable of both specifically recognising antigens and engaging with other proteins and receptors to coordinate immune action. Traditionally, structural studies have been dedicated to antibody variable regions, but efforts to determine and model full-length antibody structures are emerging. Here we review the current knowledge on modelling the structures of antibody assemblies, focusing on their conformational flexibility and the challenge this poses to obtaining and evaluating structural models. Integrative modelling approaches, combining experiments (cryo-electron microscopy, mass spectrometry, etc.) and computational methods (molecular dynamics simulations, deep-learning based approaches, etc.), hold the promise to map the complex conformational landscape of full-length antibody structures.
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Affiliation(s)
- Dongjun Guo
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom; Randall Centre for Cell & Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, United Kingdom
| | - Maria Laura De Sciscio
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom; Department of Chemistry, Sapienza University of Rome, P.le A. Moro 5, Rome, 00185, Italy
| | - Joseph Chi-Fung Ng
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Franca Fraternali
- Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, United Kingdom.
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11
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Li M, Wang Y, Tao F, Xu P, Zhang S. QTY code designed antibodies for aggregation prevention: A structural bioinformatic and computational study. Proteins 2024; 92:206-218. [PMID: 37795805 DOI: 10.1002/prot.26603] [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: 05/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023]
Abstract
Therapeutic monoclonal antibodies are the most rapidly growing class of molecular medicine, and they are beneficial to the treatment of a broad spectrum of human diseases. However, the aggregation of antibodies during the process of manufacture, distribution, and storage poses significant challenges, potentially compromising efficacy and inducing adverse immune responses. We previously conceived a QTY (glutamine, threonine, tyrosine) code, a simple tool for enhancing protein water-solubility by systematically pairwise replacing hydrophobic residues L (leucine), V (valine)/I (isoleucine), and F (phenylalanine). The QTY code offers a promising alternative to traditional methods of controlling aggregation in integral transmembrane proteins. In this study, we designed variants of four antibodies applying the QTY code, changing only the β-sheets. Through the structure-based aggregation analysis, we found that these QTY antibody variants demonstrated significantly decreased aggregation propensity compared to their wild-type counter parts. Our results of molecular dynamics simulations showed that the design by QTY code is capable of maintaining the antigen-binding affinity and structural stability. Our structural informatic and computational study suggests that the QTY code offers a significant potential in mitigating antibody aggregation.
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Affiliation(s)
- Mengke Li
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yanze Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ping Xu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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12
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Lee H. Separation of protein corona from nanoparticles under intracellular acidic conditions: effect of protonation on nanoparticle-protein and protein-protein interactions. Phys Chem Chem Phys 2024; 26:4000-4010. [PMID: 38224098 DOI: 10.1039/d3cp04887j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Protein coronas separate from nanoparticles under intracellular acidic conditions however, competitive adsorption of multiple proteins and their protein network formation under different pH conditions have not yet been systematically studied at the atomic scale. Herein, we report all-atom molecular dynamics simulations of plasma proteins (human serum albumin and immunoglobulin gamma-1 chain C) adsorbed to 10 nm-sized carboxyl-terminated polystyrene (PS) nanoparticles at different protonation states that mimic extracellular and intracellular pH conditions of 7, 6-5, and 4.5. Binding free energies are calculated from umbrella sampling simulations, showing the significantly weakened binding between PS particles and proteins at the protonation state at pH 4.5, in agreement with experiments showing the separation of protein corona from nanoparticles at pH 4.5. Mixtures of multiple proteins and PS particles are also simulated, showing much less protein adsorption and protein cluster formation at the protonation state at pH 4.5 than that at higher pH values, which are further confirmed by calculating the diffusivities and hydrodynamic radii of individual proteins. In particular, electrostatic particle-protein and protein-protein interactions are significantly weakened by a combination of particle and protein protonation rather than by particle protonation alone, to an extent dependent on different proteins. These findings help explain the experimental observations regarding separation of protein corona from nanoparticles under intracellular acidic conditions at pH 4.5 but not at higher pH, supporting that acidification cannot be the only reason for this separation during the process of endosome maturation.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin-si, 16890, South Korea.
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13
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Gozzo TA, Bush MF. Quantitatively Differentiating Antibodies Using Charge-State Manipulation, Collisional Activation, and Ion Mobility-Mass Spectrometry. Anal Chem 2024; 96:505-513. [PMID: 38146701 DOI: 10.1021/acs.analchem.3c04638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Antibody-based therapeutics continue to expand both in the number of products and in their use in patients. These heterogeneous proteins challenge traditional drug characterization strategies, but ion mobility (IM) and mass spectrometry (MS) approaches have eased the challenge of higher-order structural characterization. Energy-dependent IM-MS, e.g., collision-induced unfolding (CIU), has been demonstrated to be sensitive to subtle differences in structure. In this study, we combine a charge-reduction method, cation-to-anion proton-transfer reactions (CAPTR), with energy-dependent IM-MS and varied solution conditions to probe their combined effects on the gas-phase structures of IgG1κ and IgG4κ from human myeloma. CAPTR paired with MS-only analysis improves the confidence of charge-state assignments and the resolution of the interfering protein species. Collision cross-section distributions were determined for each of the charge-reduced products. Similarity scoring was used to quantitatively compare distributions determined from matched experiments analyzing samples of the two antibodies. Relative to workflows using energy-dependent IM-MS without charge-state manipulation, combining CAPTR and energy-dependent IM-MS enhanced the differentiation of these antibodies. Combined, these results indicate that CAPTR can benefit many aspects of antibody characterization and differentiation.
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Affiliation(s)
- Theresa A Gozzo
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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14
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Natesan R, Dykstra AB, Banerjee A, Agrawal NJ. Heterogeneity in Disulfide Bond Reduction in IgG1 Antibodies Is Governed by Solvent Accessibility of the Cysteines. Antibodies (Basel) 2023; 12:83. [PMID: 38131805 PMCID: PMC10741012 DOI: 10.3390/antib12040083] [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: 10/06/2023] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
We studied unpaired cysteine levels and disulfide bond susceptibility in four different γ-immunoglobulin antibodies using liquid chromatography-mass spectrometry. Our choice of differential alkylating agents ensures that the differential peaks are non-overlapping, thus allowing us to accurately quantify free cysteine levels. For each cysteine residue, we observed no more than 5% to be unpaired, and the free cysteine levels across antibodies were slightly higher in those containing lambda light chains. Interchain and hinge residues were highly susceptible to reducing stresses and showed a 100-1000-fold higher rate of reduction compared to intrachain cysteines. Estimations of the solvent-accessible surface for individual cysteines in IgG1, using an implicit all-atom molecular dynamics simulation, show that interchain and hinge cysteines have >1000-fold higher solvent accessibility compared to intrachain cysteines. Further analyses show that solvent accessibility and the rate of reduction are linearly correlated. Our work clearly establishes the fact that a cysteine's accessibility to the surrounding solvent is one of the primary determinants of its disulfide bond stability.
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Affiliation(s)
- Ramakrishnan Natesan
- Amgen Inc., Process Development, 360 Binney St., Cambridge, MA 02141, USA; (R.N.); (A.B.)
| | | | - Akash Banerjee
- Amgen Inc., Process Development, 360 Binney St., Cambridge, MA 02141, USA; (R.N.); (A.B.)
| | - Neeraj J. Agrawal
- Amgen Inc., Process Development, 360 Binney St., Cambridge, MA 02141, USA; (R.N.); (A.B.)
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15
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Hess R, Faessler J, Yun D, Saleh D, Grosch JH, Schwab T, Hubbuch J. Antibody sequence-based prediction of pH gradient elution in multimodal chromatography. J Chromatogr A 2023; 1711:464437. [PMID: 37865026 DOI: 10.1016/j.chroma.2023.464437] [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: 07/11/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/23/2023]
Abstract
Multimodal chromatography has emerged as a promising technique for antibody purification, owing to its capacity to selectively capture and separate target molecules. However, the optimization of chromatography parameters remains a challenge due to the intricate nature of protein-ligand interactions. To tackle this issue, efficient predictive tools are essential for the development and optimization of multimodal chromatography processes. In this study, we introduce a methodology that predicts the elution behavior of antibodies in multimodal chromatography based on their amino acid sequences. We analyzed a total of 64 full-length antibodies, including IgG1, IgG4, and IgG-like multispecific formats, which were eluted using linear pH gradients from pH 9.0 to 4.0 on the anionic mixed-mode resin Capto adhere. Homology models were constructed, and 1312 antibody-specific physicochemical descriptors were calculated for each molecule. Our analysis identified six key structural features of the multimodal antibody interaction, which were correlated with the elution behavior, emphasizing the antibody variable region. The results show that our methodology can predict pH gradient elution for a diverse range of antibodies and antibody formats, with a test set R² of 0.898. The developed model can inform process development by predicting initial conditions for multimodal elution, thereby reducing trial and error during process optimization. Furthermore, the model holds the potential to enable an in silico manufacturability assessment by screening target antibodies that adhere to standardized purification conditions. In conclusion, this study highlights the feasibility of using structure-based prediction to enhance antibody purification in the biopharmaceutical industry. This approach can lead to more efficient and cost-effective process development while increasing process understanding.
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Affiliation(s)
- Rudger Hess
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany; DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jan Faessler
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Doil Yun
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - David Saleh
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jan-Hendrik Grosch
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Thomas Schwab
- DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
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16
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Sela T, Mansø M, Siegel M, Marban-Doran C, Ducret A, Niewöhner J, Ravn J, Martin RE, Sommer A, Lohmann S, Krippendorff BF, Ladefoged M, Indlekofer A, Quaiser T, Bueddefeld F, Koller E, Mohamed MY, Oelschlaegel T, Gothelf KV, Hofer K, Schumacher FF. Diligent Design Enables Antibody-ASO Conjugates with Optimal Pharmacokinetic Properties. Bioconjug Chem 2023; 34:2096-2111. [PMID: 37916986 DOI: 10.1021/acs.bioconjchem.3c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Antisense-oligonucleotides (ASOs) are a promising drug modality for the treatment of neurological disorders, but the currently established route of administration via intrathecal delivery is a major limitation to its broader clinical application. An attractive alternative is the conjugation of the ASO to an antibody that facilitates access to the central nervous system (CNS) after peripheral application and target engagement at the blood-brain barrier, followed by transcytosis. Here, we show that the diligent conjugate design of Brainshuttle-ASO conjugates is the key to generating promising delivery vehicles and thereby establishing design principles to create optimized molecules with drug-like properties. An innovative site-specific transglutaminase-based conjugation technology was chosen and optimized in a stepwise process to identify the best-suited conjugation site, tags, reaction conditions, and linker design. The overall conjugation performance was found to be specifically governed by the choice of buffer conditions and the structure of the linker. The combination of the peptide tags YRYRQ and RYESK was chosen, showing high conjugation fidelity. Elaborate conjugate analysis revealed that one leading differentiating factor was hydrophobicity. The increase of hydrophobicity by the ASO payload could be mitigated by the appropriate choice of conjugation site and the heavy chain position 297 proved to be the most optimal. Evaluating the properties of the linker suggested a short bicyclo[6.1.0]nonyne (BCN) unit as best suited with regards to conjugation performance and potency. Promising in vitro activity and in vivo pharmacokinetic behavior of optimized Brainshuttle-ASO conjugates, based on a microtubule-associated protein tau (MAPT) targeting oligonucleotide, suggest that such designs have the potential to serve as a blueprint for peripherally delivered ASO-based drugs for the CNS in the future.
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Affiliation(s)
- Tatjana Sela
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg 82377, Germany
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich 80539, Germany
| | - Mads Mansø
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Copenhagen, F. Hoffmann-La Roche Ltd., Fremtidsvej 3, Hørsholm 2970, Denmark
| | - Michel Siegel
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Céline Marban-Doran
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Axel Ducret
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Jens Niewöhner
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg 82377, Germany
| | - Jacob Ravn
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Copenhagen, F. Hoffmann-La Roche Ltd., Fremtidsvej 3, Hørsholm 2970, Denmark
| | - Rainer E Martin
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Annika Sommer
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg 82377, Germany
| | - Sabine Lohmann
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg 82377, Germany
| | - Ben-Fillippo Krippendorff
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Mette Ladefoged
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Copenhagen, F. Hoffmann-La Roche Ltd., Fremtidsvej 3, Hørsholm 2970, Denmark
| | - Annette Indlekofer
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg 82377, Germany
| | - Tom Quaiser
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg 82377, Germany
| | - Florian Bueddefeld
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg 82377, Germany
| | - Erich Koller
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel 4070, Switzerland
| | | | | | - Kurt V Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus 8000, Central Denmark Region, Denmark
| | - Kerstin Hofer
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, Penzberg 82377, Germany
| | - Felix F Schumacher
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, Basel 4070, Switzerland
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17
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Martin TM, Robinson ST, Huang Y. Discovery medicine - the HVTN's iterative approach to developing an HIV-1 broadly neutralizing vaccine. Curr Opin HIV AIDS 2023; 18:290-299. [PMID: 37712873 PMCID: PMC10552837 DOI: 10.1097/coh.0000000000000821] [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] [Indexed: 09/16/2023]
Abstract
PURPOSE OF REVIEW In the past two decades, there has been an explosion in the discovery of HIV-1 broadly neutralizing antibodies (bnAbs) and associated vaccine strategies to induce them. This abundance of approaches necessitates a system that accurately and expeditiously identifies the most promising regimens. We herein briefly review the background science of bnAbs, provide a description of the first round of phase 1 discovery medicine studies, and suggest an approach to integrate these into a comprehensive HIV-1-neutralizing vaccine. RECENT FINDINGS With recent preclinical success including induction of early stage bnAbs in mouse knockin models and rhesus macaques, successful priming of VRC01-class bnAbs with eOD-GT8 in a recent study in humans, and proof-of-concept that intravenous infusion of VRC01 prevents sexual transmission of virus in humans, the stage is set for a broad and comprehensive bnAb vaccine program. Leveraging significant advances in protein nanoparticle science, mRNA technology, adjuvant development, and B-cell and antibody analyses, the HVTN has reconfigured its HIV-1 vaccine strategy by developing the Discovery Medicine Program to test promising vaccine candidates targeting six key epitopes. SUMMARY The HVTN Discovery Medicine program is testing multiple HIV-1-neutralizing vaccine candidates.
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Affiliation(s)
- Troy M Martin
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
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18
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Lee SM, Min SW, Kwon HS, Bae GD, Jung JH, Park HI, Lee SH, Lim CS, Ko BJ, Lee JC, Jung ST. Effective clearance of rituximab-resistant tumor cells by breaking the mirror-symmetry of immunoglobulin G and simultaneous binding to CD55 and CD20. Sci Rep 2023; 13:18275. [PMID: 37880350 PMCID: PMC10600224 DOI: 10.1038/s41598-023-45491-8] [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: 05/11/2023] [Accepted: 10/19/2023] [Indexed: 10/27/2023] Open
Abstract
Complement-dependent cytotoxicity (CDC), which eliminates aberrant target cells through the assembly and complex formation of serum complement molecules, is one of the major effector functions of anticancer therapeutic antibodies. In this study, we discovered that breaking the symmetry of natural immunoglobulin G (IgG) antibodies significantly increased the CDC activity of anti-CD20 antibodies. In addition, the expression of CD55 (a checkpoint inhibitor in the CDC cascade) was significantly increased in a rituximab-resistant cell line generated in-house, suggesting that CD55 overexpression might be a mechanism by which cancer cells acquire rituximab resistance. Based on these findings, we developed an asymmetric bispecific antibody (SBU-CD55 × CD20) that simultaneously targets both CD55 and CD20 to effectively eliminate rituximab-resistant cancer cells. In various cancer cell lines, including rituximab-resistant lymphoma cells, the SBU-CD55 × CD20 antibody showed significantly higher CDC activity than either anti-CD20 IgG antibody alone or a combination of anti-CD20 IgG antibody and anti-CD55 IgG antibody. Furthermore, the asymmetric bispecific antibody (SBU-CD55 × CD20) exhibited significantly higher CDC activity against rituximab-resistant cancer cells compared to other bispecific antibodies with symmetric features. These results demonstrate that enhancing CDC with an asymmetric CD55-binding bispecific antibody could be a new strategy for developing therapeutics to treat patients with relapsed or refractory cancers.
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Affiliation(s)
- Sang Min Lee
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, 73 Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
- Department of Applied Chemistry, Kookmin University, 77, Jeongneung-ro, Seongbuk-gu, Seoul, 02707, Republic of Korea
| | - Sung-Won Min
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea
| | - Hyeong Sun Kwon
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea
| | - Gong-Deuk Bae
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea
| | - Ji Hae Jung
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea
| | - Hye In Park
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea
| | - Seung Hyeon Lee
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, 73 Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Chung Su Lim
- New Drug Development Center, Osong Medical Innovation Foundation 123, Cheongju, Chungcheongbuk-do, 28160, Republic of Korea
| | - Byoung Joon Ko
- School of Biopharmaceutical and Medical Science, Sungshin Women's University, 55, Dobonng-Ro 76ga-gil, Gangbuk, Seoul, 01133, Republic of Korea
| | - Ji Chul Lee
- SG Medical, 3-11, Ogeum-ro 13-gil, Songpa-gu, Seoul, 05548, Republic of Korea.
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, 73 Goryeodae-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.
- Institute of Human Genetics, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
- Biomedical Research Center, Korea University Anam Hospital, Seoul, 02841, Republic of Korea.
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19
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Rakotoarinoro N, Dyck YFK, Krebs SK, Assi MK, Parr MK, Stech M. A disruptive clickable antibody design for the generation of antibody-drug conjugates. Antib Ther 2023; 6:298-310. [PMID: 38107665 PMCID: PMC10720948 DOI: 10.1093/abt/tbad023] [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: 07/20/2023] [Revised: 10/05/2023] [Accepted: 10/14/2023] [Indexed: 12/19/2023] Open
Abstract
Background Antibody-drug conjugates are cancer therapeutics that combine specificity and toxicity. A highly cytotoxic drug is covalently attached to an antibody that directs it to cancer cells. The conjugation of the drug-linker to the antibody is a key point in research and development as well as in industrial production. The consensus is to conjugate the drug to a surface-exposed part of the antibody to ensure maximum conjugation efficiency. However, the hydrophobic nature of the majority of drugs used in antibody-drug conjugates leads to an increased hydrophobicity of the generated antibody-drug conjugates, resulting in higher liver clearance and decreased stability. Methods In contrast, we describe a non-conventional approach in which the drug is conjugated in a buried part of the antibody. To achieve this, a ready-to-click antibody design was created in which an azido-based non-canonical amino acid is introduced within the Fab cavity during antibody synthesis using nonsense suppression technology. The Fab cavity was preferred over the Fc cavity to circumvent issues related to cleavage of the IgG1 lower hinge region in the tumor microenvironment. Results This antibody design significantly increased the hydrophilicity of the generated antibody-drug conjugates compared to the current best-in-class designs based on non-canonical amino acids, while conjugation efficiency and functionality were maintained. The robustness of this native shielding effect and the versatility of this approach were also investigated. Conclusions This pioneer design may become a starting point for the improvement of antibody-drug conjugates and an option to consider for protecting drugs and linkers from unspecific interactions.
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Affiliation(s)
- Nathanaël Rakotoarinoro
- Institute for Cell Therapy and Immunology branch Bioanalytics and Bioprocesses, Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung e.V., 14476 Potsdam-Golm, Germany
- Institute of Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Yan F K Dyck
- Institute of Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Simon K Krebs
- Institute for Cell Therapy and Immunology branch Bioanalytics and Bioprocesses, Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung e.V., 14476 Potsdam-Golm, Germany
- Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Miriam-Kousso Assi
- Institute for Cell Therapy and Immunology branch Bioanalytics and Bioprocesses, Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung e.V., 14476 Potsdam-Golm, Germany
- Department of Biotechnology, Hamburg University of Applied Sciences, 21033 Hamburg, Germany
| | - Maria K Parr
- Institute of Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Marlitt Stech
- Institute for Cell Therapy and Immunology branch Bioanalytics and Bioprocesses, Fraunhofer-Gesellschaft zur Förderung der angewandten Forschung e.V., 14476 Potsdam-Golm, Germany
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20
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Ratswohl C, Vázquez García C, Ahmad AUW, Gonschior H, Lebedin M, Silvis CE, Spatt L, Gerhard C, Lehmann M, Sander LE, Kurth F, Olsson S, de la Rosa K. A design strategy to generate a SARS-CoV-2 RBD vaccine that abrogates ACE2 binding and improves neutralizing antibody responses. Eur J Immunol 2023; 53:e2350408. [PMID: 37435628 DOI: 10.1002/eji.202350408] [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: 01/27/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023]
Abstract
The structure-based design of antigens holds promise for developing vaccines with higher efficacy and improved safety profiles. We postulate that abrogation of host receptor interaction bears potential for the improvement of vaccines by preventing antigen-induced modification of receptor function as well as the displacement or masking of the immunogen. Antigen modifications may yet destroy epitopes crucial for antibody neutralization. Here, we present a methodology that integrates deep mutational scans to identify and score SARS-CoV-2 receptor binding domain variants that maintain immunogenicity, but lack interaction with the widely expressed host receptor. Single point mutations were scored in silico, validated in vitro, and applied in vivo. Our top-scoring variant receptor binding domain-G502E prevented spike-induced cell-to-cell fusion, receptor internalization, and improved neutralizing antibody responses by 3.3-fold in rabbit immunizations. We name our strategy BIBAX for body-inert, B-cell-activating vaccines, which in the future may be applied beyond SARS-CoV-2 for the improvement of vaccines by design.
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Affiliation(s)
- Christoph Ratswohl
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
| | - Clara Vázquez García
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Ata Ul Wakeel Ahmad
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Hannes Gonschior
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Mikhail Lebedin
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Casper Ewijn Silvis
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité - Universitätsmedizin, Berlin, Germany
| | - Lisa Spatt
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Cathrin Gerhard
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Leif E Sander
- Charité - Universitätsmedizin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Berlin, Germany
| | | | - Simon Olsson
- Department of Computer Science and Engineering, Chalmers University of Technology, Göteborg, Västra Götalands län, Sweden
| | - Kathrin de la Rosa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Berlin, Germany
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21
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Mosca I, Pounot K, Beck C, Colin L, Matsarskaia O, Grapentin C, Seydel T, Schreiber F. Biophysical Determinants for the Viscosity of Concentrated Monoclonal Antibody Solutions. Mol Pharm 2023; 20:4698-4713. [PMID: 37549226 DOI: 10.1021/acs.molpharmaceut.3c00440] [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: 08/09/2023]
Abstract
Monoclonal antibodies (mAbs) are particularly relevant for therapeutics due to their high specificity and versatility, and mAb-based drugs are hence used to treat numerous diseases. The increased patient compliance of self-administration motivates the formulation of products for subcutaneous (SC) administration. The associated challenge is to formulate highly concentrated antibody solutions to achieve a significant therapeutic effect, while limiting their viscosity and preserving their physicochemical stability. Protein-protein interactions (PPIs) are in fact the root cause of several potential problems concerning the stability, manufacturability, and delivery of a drug product. The understanding of macroscopic viscosity requires an in-depth knowledge on protein diffusion, PPIs, and self-association/aggregation. Here, we study the self-diffusion of different mAbs of the IgG1 subtype in aqueous solution as a function of the concentration and temperature by quasi-elastic neutron scattering (QENS). QENS allows us to probe the short-time self-diffusion of the molecules and therefore to determine the hydrodynamic mAb cluster size and to gain information on the internal mAb dynamics. Small-angle neutron scattering (SANS) is jointly employed to probe structural details and to understand the nature and intensity of PPIs. Complementary information is provided by molecular dynamics (MD) simulations and viscometry, thus obtaining a comprehensive picture of mAb diffusion.
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Affiliation(s)
- Ilaria Mosca
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen 72076, Germany
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | - Kévin Pounot
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen 72076, Germany
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | - Christian Beck
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen 72076, Germany
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | - Louise Colin
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen 72076, Germany
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | - Olga Matsarskaia
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | | | - Tilo Seydel
- Institut Max von Laue - Paul Langevin, 71 Av. des Martyrs, Grenoble 38042, France
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, Tübingen 72076, Germany
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22
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Słyk E, Skóra T, Kondrat S. Minimal Coarse-Grained Model for Immunoglobulin G: Diffusion and Binding under Crowding. J Phys Chem B 2023; 127:7442-7448. [PMID: 37591305 PMCID: PMC10476189 DOI: 10.1021/acs.jpcb.3c02383] [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: 04/10/2023] [Revised: 07/25/2023] [Indexed: 08/19/2023]
Abstract
Immunoglobulin G (IgG) is the most common type of antibody found in blood and extracellular fluids and plays an essential role in our immune response. However, studies of the dynamics and reaction kinetics of IgG-antigen binding under physiological crowding conditions are scarce. Herein, we develop a coarse-grained model of IgG consisting of only six beads that we find minimal for a coarse representation of IgG's shape and a decent reproduction of its flexibility and diffusion properties measured experimentally. Using this model in Brownian dynamics simulations, we find that macromolecular crowding affects only slightly the IgG's flexibility, as described by the distribution of angles between the IgG's arms and stem. Our simulations indicate that, contrary to expectations, crowders slow down the translational diffusion of an IgG less strongly than they do for a smaller Ficoll 70, which we relate to the IgG's conformational size changes induced by crowding. We also find that crowders affect the binding kinetics by decreasing the rate of the first binding step and enhancing the second binding step.
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Affiliation(s)
- Edyta Słyk
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Warsaw 01-224, Poland
- Department
of Theoretical Chemistry, Institute of Chemical Sciences, Faculty
of Chemistry, Maria Curie-Skłodowska
University in Lublin, Lublin 20-031, Poland
| | - Tomasz Skóra
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Warsaw 01-224, Poland
| | - Svyatoslav Kondrat
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Warsaw 01-224, Poland
- Institute
for Computational Physics, University of
Stuttgart, Stuttgart 70569, Germany
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23
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Abendstein L, Dijkstra DJ, Tjokrodirijo RTN, van Veelen PA, Trouw LA, Hensbergen PJ, Sharp TH. Complement is activated by elevated IgG3 hexameric platforms and deposits C4b onto distinct antibody domains. Nat Commun 2023; 14:4027. [PMID: 37419978 PMCID: PMC10328927 DOI: 10.1038/s41467-023-39788-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/29/2023] [Indexed: 07/09/2023] Open
Abstract
IgG3 is unique among the IgG subclasses due to its extended hinge, allotypic diversity and enhanced effector functions, including highly efficient pathogen neutralisation and complement activation. It is also underrepresented as an immunotherapeutic candidate, partly due to a lack of structural information. Here, we use cryoEM to solve structures of antigen-bound IgG3 alone and in complex with complement components. These structures reveal a propensity for IgG3-Fab clustering, which is possible due to the IgG3-specific flexible upper hinge region and may maximise pathogen neutralisation by forming high-density antibody arrays. IgG3 forms elevated hexameric Fc platforms that extend above the protein corona to maximise binding to receptors and the complement C1 complex, which here adopts a unique protease conformation that may precede C1 activation. Mass spectrometry reveals that C1 deposits C4b directly onto specific IgG3 residues proximal to the Fab domains. Structural analysis shows this to be caused by the height of the C1-IgG3 complex. Together, these data provide structural insights into the role of the unique IgG3 extended hinge, which will aid the development and design of upcoming immunotherapeutics based on IgG3.
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Affiliation(s)
- Leoni Abendstein
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Douwe J Dijkstra
- Department of Immunology, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Rayman T N Tjokrodirijo
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Leendert A Trouw
- Department of Immunology, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Paul J Hensbergen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
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24
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Skóra T, Janssen M, Carlson A, Kondrat S. Crowding-Regulated Binding of Divalent Biomolecules. PHYSICAL REVIEW LETTERS 2023; 130:258401. [PMID: 37418731 DOI: 10.1103/physrevlett.130.258401] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 05/08/2023] [Indexed: 07/09/2023]
Abstract
Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding. Herein, we use scaled particle theory and develop a molecular simulation method to investigate the binding of monovalent to divalent biomolecules. We find that crowding can increase or reduce cooperativity-the extent to which the binding of a second molecule is enhanced after binding a first molecule-by orders of magnitude, depending on the sizes of the involved molecular complexes. Cooperativity generally increases when a divalent molecule swells and then shrinks upon binding two ligands. Our calculations also reveal that, in some cases, crowding enables binding that does not occur otherwise. As an immunological example, we consider immunoglobulin G-antigen binding and show that crowding enhances its cooperativity in bulk but reduces it when an immunoglobulin G binds antigens on a surface.
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Affiliation(s)
- Tomasz Skóra
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Mathijs Janssen
- Department of Mathematics, Mechanics Division, University of Oslo, N-0851 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway
- Norwegian University of Life Sciences, Faculty of Science and Technology, Pb 5003, 1433 Ås, Norway
| | - Andreas Carlson
- Department of Mathematics, Mechanics Division, University of Oslo, N-0851 Oslo, Norway
| | - Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Institute for Computational Physics, University of Stuttgart, Stuttgart 70569, Germany
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25
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Davies AM, Beavil RL, Barbolov M, Sandhar BS, Gould HJ, Beavil AJ, Sutton BJ, McDonnell JM. Crystal structures of the human IgD Fab reveal insights into C H1 domain diversity. Mol Immunol 2023; 159:28-37. [PMID: 37267832 DOI: 10.1016/j.molimm.2023.05.006] [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: 03/29/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/04/2023]
Abstract
Antibodies of the IgD isotype remain the least well characterized of the mammalian immunoglobulin isotypes. Here we report three-dimensional structures for the Fab region of IgD, based on four different crystal structures, at resolutions of 1.45-2.75 Å. These IgD Fab crystals provide the first high-resolution views of the unique Cδ1 domain. Structural comparisons identify regions of conformational diversity within the Cδ1 domain, as well as among the homologous domains of Cα1, Cγ1 and Cμ1. The IgD Fab structure also possesses a unique conformation of the upper hinge region, which may contribute to the overall disposition of the very long linker sequence between the Fab and Fc regions found in human IgD. Structural similarities observed between IgD and IgG, and differences with IgA and IgM, are consistent with predicted evolutionary relationships for the mammalian antibody isotypes.
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Affiliation(s)
- Anna M Davies
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Rebecca L Beavil
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Momchil Barbolov
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Balraj S Sandhar
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Hannah J Gould
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Andrew J Beavil
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Brian J Sutton
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - James M McDonnell
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom.
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26
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Natesan R, Agrawal NJ. IgG1 and IgG4 antibodies sample initial structure dependent local conformational states and exhibit non-identical Fab dynamics. Sci Rep 2023; 13:4791. [PMID: 36959284 PMCID: PMC10036467 DOI: 10.1038/s41598-023-32067-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/22/2023] [Indexed: 03/25/2023] Open
Abstract
We have investigated the dynamics of two [Formula: see text]-immunoglobulin molecules, IgG1 and IgG4, using long all atom molecular dynamics simulations. We first show that the de novo structures of IgG1 and IgG4 predicted using AlphaFold, with no interactions between the fragment crystallizable (Fc) domain and the antigen fragment binding domain (Fab), eventually relaxes to a state with persistent Fc-Fab interactions that mirrors experimentally resolved structures. We quantified the conformational space sampled by antibody trajectories spawned from six different initial structures and show that the individual trajectories only sample states bound by a local minimum and display very little mixing in their conformational states. Furthermore, the dynamics of the individual Fab domains are strongly dependent on the initial crystal structure and isotype. In all conditions, we observe non-identical dynamics between the Fab arms in an antibody. For a six-bead coarse grained model, we show that non-covalent Fc-Fab interactions can modulate the stiffnesses associated with Fc-Fab distances, angles, and dihedral angles by up to three orders of magnitude. Our results clearly illustrate the inherent complexities in studying antibody dynamics and highlight the need to include non-identical Fab dynamics as an inherent feature in computational models of therapeutic antibodies.
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Affiliation(s)
| | - Neeraj J Agrawal
- Process Development, Amgen Inc., 360 Binney St, Cambridge, MA, 02141, USA.
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27
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Aguinagalde Salazar L, den Boer MA, Castenmiller SM, Zwarthoff SA, de Haas C, Aerts PC, Beurskens FJ, Schuurman J, Heck AJR, van Kessel K, Rooijakkers SHM. Promoting Fc-Fc interactions between anti-capsular antibodies provides strong immune protection against Streptococcus pneumoniae. eLife 2023; 12:80669. [PMID: 36947116 PMCID: PMC10032657 DOI: 10.7554/elife.80669] [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: 05/30/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
Streptococcus pneumoniae is the leading cause of community-acquired pneumonia and an important cause of childhood mortality. Despite the introduction of successful vaccines, the global spread of both non-vaccine serotypes and antibiotic-resistant strains reinforces the development of alternative therapies against this pathogen. One possible route is the development of monoclonal antibodies (mAbs) that induce killing of bacteria via the immune system. Here, we investigate whether mAbs can be used to induce killing of pneumococcal serotypes for which the current vaccines show unsuccessful protection. Our study demonstrates that when human mAbs against pneumococcal capsule polysaccharides (CPS) have a poor capacity to induce complement activation, a critical process for immune protection against pneumococci, their activity can be strongly improved by hexamerization-enhancing mutations. Our data indicate that anti-capsular antibodies may have a low capacity to form higher-order oligomers (IgG hexamers) that are needed to recruit complement component C1. Indeed, specific point mutations in the IgG-Fc domain that strengthen hexamerization strongly enhance C1 recruitment and downstream complement activation on encapsulated pneumococci. Specifically, hexamerization-enhancing mutations E430G or E345K in CPS6-IgG strongly potentiate complement activation on S. pneumoniae strains that express capsular serotype 6 (CPS6), and the highly invasive serotype 19A strain. Furthermore, these mutations improve complement activation via mAbs recognizing CPS3 and CPS8 strains. Importantly, hexamer-enhancing mutations enable mAbs to induce strong opsonophagocytic killing by human neutrophils. Finally, passive immunization with CPS6-IgG1-E345K protected mice from developing severe pneumonia. Altogether, this work provides an important proof of concept for future optimization of antibody therapies against encapsulated bacteria.
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Affiliation(s)
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
- Netherlands Proteomics Center, Utrecht, Netherlands
| | - Suzanne M Castenmiller
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Seline A Zwarthoff
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Carla de Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Piet C Aerts
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | | | | | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
- Netherlands Proteomics Center, Utrecht, Netherlands
| | - Kok van Kessel
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Suzan H M Rooijakkers
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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28
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Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
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Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
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29
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Lee H. Differences in protein distribution, conformation, and dynamics in hard and soft coronas: dependence on protein and particle electrostatics. Phys Chem Chem Phys 2023; 25:7496-7507. [PMID: 36853334 DOI: 10.1039/d2cp05936c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
We perform all-atom molecular dynamics simulations of a 9 nm-thick protein layer, which consists of serum albumin (SA) or a mixture of SA and immunoglobulin gamma-1, formed on 10 nm-sized cationic, anionic, and neutral polystyrene particles. More than half of the proteins are densely concentrated within a distance of ∼3 nm from the particle surface, while fewer proteins are broadly distributed in the range of 3-9 nm from the particle. This compares favorably with the experimental observations of a hard corona as the first layer adjacent to the particle and a soft corona as a loose protein-network. The conformation and diffusivity of the proteins vary in different positions of the layer, and are to an extent dependent on the protein and particle electrostatics. These, combined with free energy calculations, show that the protein and particle charges do not significantly modify the strength of protein-particle binding but do influence the distribution of proteins in the layer. In particular, a free protein more strongly binds to the complex of a protein and particle than to either one, showing the synergistic effect of already adsorbed proteins and a particle. This helps explain the experimental observation regarding the formation of a denser protein layer and the stronger protein-protein interaction in the hard corona than the soft corona.
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Affiliation(s)
- Hwankyu Lee
- Department of Chemical Engineering, Dankook University, Yongin-si, 16890, South Korea.
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30
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Saporiti S, Laurenzi T, Guerrini U, Coppa C, Palinsky W, Benigno G, Palazzolo L, Ben Mariem O, Montavoci L, Rossi M, Centola F, Eberini I. Effect of Fc core fucosylation and light chain isotype on IgG1 flexibility. Commun Biol 2023; 6:237. [PMID: 36869088 PMCID: PMC9982779 DOI: 10.1038/s42003-023-04622-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
N-glycosylation plays a key role in modulating the bioactivity of monoclonal antibodies (mAbs), as well as the light chain (LC) isotype can influence their physicochemical properties. However, investigating the impact of such features on mAbs conformational behavior is a big challenge, due to the very high flexibility of these biomolecules. In this work we investigate, by accelerated molecular dynamics (aMD), the conformational behavior of two commercial immunoglobulins G1 (IgG1), representative of κ and λ LCs antibodies, in both their fucosylated and afucosylated forms. Our results show, through the identification of a stable conformation, how the combination of fucosylation and LC isotype modulates the hinge behavior, the Fc conformation and the position of the glycan chains, all factors potentially affecting the binding to the FcγRs. This work also represents a technological enhancement in the conformational exploration of mAbs, making aMD a suitable approach to clarify experimental results.
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Affiliation(s)
- Simona Saporiti
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Tommaso Laurenzi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Crescenzo Coppa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Sezione di Chimica Generale e Organica "A. Marchesini", Via Venezian, 21, 20133, Milano, Italy
| | - Wolf Palinsky
- Biotech Development Programme, Merck Biopharma, Aubonne, Switzerland
| | - Giulia Benigno
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Omar Ben Mariem
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Linda Montavoci
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Mara Rossi
- Global Analytical Pharmaceutical Science and Innovation, Merck Serono S.p.A., Rome, Italy
| | - Fabio Centola
- Global Analytical Pharmaceutical Science and Innovation, Merck Serono S.p.A., Rome, Italy.
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari & DSRC, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
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Deslignière E, Ollivier S, Beck A, Ropartz D, Rogniaux H, Cianférani S. Benefits and Limitations of High-Resolution Cyclic IM-MS for Conformational Characterization of Native Therapeutic Monoclonal Antibodies. Anal Chem 2023; 95:4162-4171. [PMID: 36780376 DOI: 10.1021/acs.analchem.2c05265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Monoclonal antibodies (mAbs) currently represent the main class of therapeutic proteins. mAbs approved by regulatory agencies are selected from IgG1, IgG2, and IgG4 subclasses, which possess different interchain disulfide connectivities. Ion mobility coupled to native mass spectrometry (IM-MS) has emerged as a valuable approach to tackle the challenging characterization of mAbs' higher order structures. However, due to the limited resolution of first-generation IM-MS instruments, subtle conformational differences on large proteins have long been hard to capture. Recent technological developments have aimed at increasing available IM resolving powers and acquisition mode capabilities, namely, through the release of high-resolution IM-MS (HR-IM-MS) instruments, like cyclic IM-MS (cIM-MS). Here, we outline the advantages and drawbacks of cIM-MS for better conformational characterization of intact mAbs (∼150 kDa) in native conditions compared to first-generation instruments. We first assessed the extent to which multipass cIM-MS experiments could improve the separation of mAbs' conformers. These initial results evidenced some limitations of HR-IM-MS for large native biomolecules which possess rich conformational landscapes that remain challenging to decipher even with higher IM resolving powers. Conversely, for collision-induced unfolding (CIU) approaches, higher resolution proved to be particularly useful (i) to reveal new unfolding states and (ii) to enhance the separation of coexisting activated states, thus allowing one to apprehend gas-phase CIU behaviors of mAbs directly at the intact level. Altogether, this study offers a first panoramic overview of the capabilities of cIM-MS for therapeutic mAbs, paving the way for more widespread HR-IM-MS/CIU characterization of mAb-derived formats.
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Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67000, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg 67087, France
| | - Simon Ollivier
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Alain Beck
- IRPF Centre d'Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois 74160, France
| | - David Ropartz
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Hélène Rogniaux
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67000, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg 67087, France
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32
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Colombo S, Alonso A, Real R, Goswami R, Suarez MC, Ogueta S, Almeida M, Adhikary L, Malmierca MG, de Melo IS. Improvement of monoclonal antibody stability by modulating trace metal iron concentration in cell culture media: A case study. Process Biochem 2023. [DOI: 10.1016/j.procbio.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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33
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Rubio-Pérez L, Lázaro-Gorines R, Harwood SL, Compte M, Navarro R, Tapia-Galisteo A, Bonet J, Blanco B, Lykkemark S, Ramírez-Fernández Á, Ferreras-Gutiérrez M, Domínguez-Alonso C, Díez-Alonso L, Segura-Tudela A, Hangiu O, Erce-Llamazares A, Blanco FJ, Santos C, Rodríguez-Peralto JL, Sanz L, Álvarez-Vallina L. A PD-L1/EGFR bispecific antibody combines immune checkpoint blockade and direct anti-cancer action for an enhanced anti-tumor response. Oncoimmunology 2023; 12:2205336. [PMID: 37114242 PMCID: PMC10128431 DOI: 10.1080/2162402x.2023.2205336] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Immune checkpoint blockade (ICB) with antibodies has shown durable clinical responses in a wide range of cancer types, but the overall response rate is still limited. Other effective therapeutic modalities to increase the ICB response rates are urgently needed. New bispecific antibody (bsAb) formats combining the ICB effect and a direct action on cancer cells could improve the efficacy of current immunotherapies. Here, we report the development of a PD-L1/EGFR symmetric bsAb by fusing a dual-targeting tandem trimmer body with the human IgG1 hinge and Fc regions. The bsAb was characterized in vitro and the antitumor efficacy was evaluated in humanized mice bearing xenografts of aggressive triple-negative breast cancer and lung cancer. The IgG-like hexavalent bsAb, designated IgTT-1E, was able to simultaneously bind both EGFR and PD-L1 antigens, inhibit EGF-mediated proliferation, effectively block PD-1/PD-L1 interaction, and induce strong antigen-specific antibody-dependent cellular cytotoxicity activity in vitro. Potent therapeutic efficacies of IgTT-1E in two different humanized mouse models were observed, where tumor growth control was associated with a significantly increased proportion of CD8+ T cells. These results support the development of IgTT-1E for the treatment of EGFR+ cancers.
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Affiliation(s)
- Laura Rubio-Pérez
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Chair for Immunology UFV/Merck, Universidad Francisco de Vitoria (UFV), Madrid, Spain
| | - Rodrigo Lázaro-Gorines
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Seandean L. Harwood
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Marta Compte
- Department of Antibody Engineering, Leadartis SL, QUBE Technology Park, Madrid, Spain
| | - Rocío Navarro
- Department of Antibody Engineering, Leadartis SL, QUBE Technology Park, Madrid, Spain
| | - Antonio Tapia-Galisteo
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jaume Bonet
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Belén Blanco
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Simon Lykkemark
- Immunotherapy and Cell Engineering Laboratory, Department of Engineering, Aarhus University, Aarhus C, Denmark
| | - Ángel Ramírez-Fernández
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Carmen Domínguez-Alonso
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Laura Díez-Alonso
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Alejandro Segura-Tudela
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Oana Hangiu
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- Department of Antibody Engineering, Leadartis SL, QUBE Technology Park, Madrid, Spain
| | - Ainhoa Erce-Llamazares
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- Department of Antibody Engineering, Leadartis SL, QUBE Technology Park, Madrid, Spain
| | - Francisco J. Blanco
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Cruz Santos
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria (UFV), Madrid, Spain
| | - José L. Rodríguez-Peralto
- Department of Pathology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Department of Pathology, Universidad Complutense, Madrid, Spain
- Cutaneous Oncology Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Madrid, Spain
| | - Laura Sanz
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Madrid, Spain
- Molecular Immunology Unit, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain
| | - Luis Álvarez-Vallina
- Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Madrid, Spain
- Immuno-Oncology and Immunotherapy Group, Instituto de Investigación Sanitaria 12 de Octubre (imas12), Madrid, Spain
- H12O-CNIO Cancer Immunotherapy Clinical Research Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Chair for Immunology UFV/Merck, Universidad Francisco de Vitoria (UFV), Madrid, Spain
- CONTACT Luis Álvarez-Vallina Cancer Immunotherapy Unit (UNICA), Department of Immunology, Hospital Universitario 12 de Octubre, Avda. Cordoba s/n, Madrid28041, Spain
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Saleh D, Hess R, Ahlers-Hesse M, Rischawy F, Wang G, Grosch JH, Schwab T, Kluters S, Studts J, Hubbuch J. A multiscale modeling method for therapeutic antibodies in ion exchange chromatography. Biotechnol Bioeng 2023; 120:125-138. [PMID: 36226467 DOI: 10.1002/bit.28258] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/09/2022] [Accepted: 10/08/2022] [Indexed: 11/10/2022]
Abstract
The development of biopharmaceutical downstream processes relies on exhaustive experimental studies. The root cause is the poorly understood relationship between the protein structure of monoclonal antibodies (mAbs) and their macroscopic process behavior. Especially the development of preparative chromatography processes is challenged by the increasing structural complexity of novel antibody formats and accelerated development timelines. This study introduces a multiscale in silico model consisting of homology modeling, quantitative structure-property relationships (QSPR), and mechanistic chromatography modeling leading from the amino acid sequence of a mAb to the digital representation of its cation exchange chromatography (CEX) process. The model leverages the mAbs' structural characteristics and experimental data of a diverse set of 21 therapeutic antibodies to predict elution profiles of two mAbs that were removed from the training data set. QSPR modeling identified mAb-specific protein descriptors relevant for the prediction of the thermodynamic equilibrium and the stoichiometric coefficient of the adsorption reaction. The consideration of two discrete conformational states of IgG4 mAbs enabled prediction of split-peak elution profiles. Starting from the sequence, the presented multiscale model allows in silico development of chromatography processes before protein material is available for experimental studies.
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Affiliation(s)
- David Saleh
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Rudger Hess
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Michelle Ahlers-Hesse
- Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Federico Rischawy
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Gang Wang
- Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Jan-Hendrik Grosch
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Thomas Schwab
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Simon Kluters
- Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Joey Studts
- Late Stage DSP Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Jürgen Hubbuch
- Institute of Process Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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Atsumi Y, Yamada A, Kojima Y, Yagi Y, Nishimura K, Wakamatsu K. Clip Formation in the Complementarity Determining Region of Bevacizumab Lowers Monomer Stability and Affinity for Both FcRn and FcγR: A Comprehensive Characterization of the Clipped Variant Including its Higher Order Structure. J Pharm Sci 2022; 111:3243-3250. [PMID: 36007559 DOI: 10.1016/j.xphs.2022.08.024] [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: 06/19/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 01/05/2023]
Abstract
The presence of monoclonal antibody (mAb) fragments in pharmaceutical mAb products is a critical quality attribute and should be controlled for safety. Several mAb fragments derived from clip formation in the complementarity determining regions (CDRs), as well as from cleavage in the hinge region, have been reported. However, the properties of CDR-clipped variants are not fully understood because of difficulties in separating them from intact mAbs under non-denaturing conditions due to similarities in size. We have established a method for separating CDR-clipped variants under non-denaturing conditions using an appropriate size exclusion chromatography column.1 In this report, we provide a comprehensive characterization of a CDR-clipped variant from bevacizumab. The variant exhibited a lower pI, a higher tendency to form dimers, and a lower affinity for both neonatal Fc receptor (FcRn) and Fcγ receptor (FcγR). The effects of clip formation in CDR H3 on the higher order structure were analyzed by hydrogen/deuterium exchange mass spectrometry, and the observed changes in the structures of the VH, CH2, and VL domains were in agreement with the lowered affinity for antigen, FcRn, and FcγR. These findings suggest that clip formation in the CDR may affect the efficacy, safety, and pharmacokinetics of pharmaceutical mAbs.
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Affiliation(s)
- Yuriko Atsumi
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin, Kiryu, Gunma 376-8515, Japan; Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co., Ltd., 100-1, Hagiwara-machi, Takasaki, Gunma 370-0013, Japan.
| | - Ayumi Yamada
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co., Ltd., 100-1, Hagiwara-machi, Takasaki, Gunma 370-0013, Japan
| | - Yuka Kojima
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co., Ltd., 100-1, Hagiwara-machi, Takasaki, Gunma 370-0013, Japan
| | - Yuki Yagi
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co., Ltd., 100-1, Hagiwara-machi, Takasaki, Gunma 370-0013, Japan
| | - Koichiro Nishimura
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co., Ltd., 100-1, Hagiwara-machi, Takasaki, Gunma 370-0013, Japan
| | - Kaori Wakamatsu
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin, Kiryu, Gunma 376-8515, Japan
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Bizeau J, Adam A, Nadal C, Francius G, Siniscalco D, Pauly M, Bégin-Colin S, Mertz D. Protein sustained release from isobutyramide-grafted stellate mesoporous silica nanoparticles. Int J Pharm X 2022; 4:100130. [PMID: 36156982 PMCID: PMC9494245 DOI: 10.1016/j.ijpx.2022.100130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 10/31/2022] Open
Abstract
Proteins are great therapeutic candidates as endogenous biomolecules providing a wide range of applications. However, their delivery suffers from some limitations and specifically designed delivery systems having an efficient protein anchoring and delivery strategy are still needed. In this work, we propose to combine large pore stellate mesoporous silica (STMS) with isobutyramide (IBAM), as a “glue” molecule which has been shown promising for immobilization of various biomacromolecules at silica surface. We address here for the first time the ability of such IBAM-modified NPs to sustainably deliver proteins over a prolonged time. In this work, a quantitative loading study of proteins (serum albumin (HSA), peroxidase (HRP), immunoglobulin (IgG) and polylysine (PLL)) on STMS@IBAM is first presented using three complementary detection techniques to ensure precision and avoid protein quantification issues. The results demonstrated a high loading capacity for HSA and HRP (≥ ca. 350 μg.mg−1) but a moderate one for IgG and PLL. After evaluating the physicochemical properties of the loaded particles and their stability over scaling-up and washings, the ability of STMS@IBAM to release proteins over prolonged time was evaluated in equilibrium (static) and flow mimicking (dynamic) conditions and at different temperatures (25, 37, 45 °C). Results show not only the potential of such “glue” functionalized STMS to release proteins in a sustained way, but also the retention of the biological activity of immobilized and released HRP, used as an enzyme model. Finally, an AFM-force spectroscopy study was conducted to decipher the interactions between IBAM and proteins, showing the involvement of different interactions in the adsorption and release processes. Isobutyramide bound stellate mesoporous silica allow the immobilization of various proteins. Protein release was achieved from the nanoparticles in a sustained way in buffer. Peroxidase activity was retained whether in immobilized or released conditions. Choice of protein detection techniques was shown to be crucial. AFM-spectroscopy was used to investigate IBAM-protein intermolecular bonding.
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The Fab region of IgG impairs the internalization pathway of FcRn upon Fc engagement. Nat Commun 2022; 13:6073. [PMID: 36241613 PMCID: PMC9568614 DOI: 10.1038/s41467-022-33764-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Binding to the neonatal Fc receptor (FcRn) extends serum half-life of IgG, and antagonizing this interaction is a promising therapeutic approach in IgG-mediated autoimmune diseases. Fc-MST-HN, designed for enhanced FcRn binding capacity, has not been evaluated in the context of a full-length antibody, and the structural properties of the attached Fab regions might affect the FcRn-mediated intracellular trafficking pathway. Here we present a comprehensive comparative analysis of the IgG salvage pathway between two full-size IgG1 variants, containing wild type and MST-HN Fc fragments, and their Fc-only counterparts. We find no evidence of Fab-regions affecting FcRn binding in cell-free assays, however, cellular assays show impaired binding of full-size IgG to FcRn, which translates into improved intracellular FcRn occupancy and intracellular accumulation of Fc-MST-HN compared to full size IgG1-MST-HN. The crystal structure of Fc-MST-HN in complex with FcRn provides a plausible explanation why the Fab disrupts the interaction only in the context of membrane-associated FcRn. Importantly, we find that Fc-MST-HN outperforms full-size IgG1-MST-HN in reducing IgG levels in cynomolgus monkeys. Collectively, our findings identify the cellular membrane context as a critical factor in FcRn biology and therapeutic targeting.
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Oostindie SC, Rinaldi DA, Zom GG, Wester MJ, Paulet D, Al-Tamimi K, van der Meijden E, Scheick JR, Wilpshaar T, de Jong B, Hoff-van den Broek M, Grattan RM, Oosterhoff JJ, Vignau J, Verploegen S, Boross P, Beurskens FJ, Lidke DS, Schuurman J, de Jong RN. Logic-gated antibody pairs that selectively act on cells co-expressing two antigens. Nat Biotechnol 2022; 40:1509-1519. [PMID: 35879362 PMCID: PMC9546771 DOI: 10.1038/s41587-022-01384-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/02/2022] [Indexed: 01/11/2023]
Abstract
The use of therapeutic monoclonal antibodies is constrained because single antigen targets often do not provide sufficient selectivity to distinguish diseased from healthy tissues. We present HexElect®, an approach to enhance the functional selectivity of therapeutic antibodies by making their activity dependent on clustering after binding to two different antigens expressed on the same target cell. lmmunoglobulin G (lgG)-mediated clustering of membrane receptors naturally occurs on cell surfaces to trigger complement- or cell-mediated effector functions or to initiate intracellular signaling. We engineer the Fc domains of two different lgG antibodies to suppress their individual homo-oligomerization while promoting their pairwise hetero-oligomerization after binding co-expressed antigens. We show that recruitment of complement component C1q to these hetero-oligomers leads to clustering-dependent activation of effector functions such as complement mediated killing of target cells or activation of cell surface receptors. HexElect allows selective antibody activity on target cells expressing unique, potentially unexplored combinations of surface antigens.
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Affiliation(s)
- Simone C Oostindie
- Genmab, Utrecht, the Netherlands
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Derek A Rinaldi
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | | | - Michael J Wester
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | | | | | | | | | | | | | | | - Rachel M Grattan
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | | | | | | | | | | | - Diane S Lidke
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, USA
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
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39
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Zhang J, Jiang X, Gao H, Zhang F, Zhang X, Zhou A, Xu T, Cai H. Structural Basis of a Novel Agonistic Anti-OX40 Antibody. Biomolecules 2022; 12:biom12091209. [PMID: 36139048 PMCID: PMC9496217 DOI: 10.3390/biom12091209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/24/2022] Open
Abstract
Agonistic antibodies targeting co-stimulating receptor OX40 on T cells are considered as important as (or complementary to) the immune checkpoint blockers in cancer treatment. However, none of these agonistic antibodies have reached the late stage of clinical development partially due to the lack of intrinsic potency with the correlation between binding epitope and activity of the antibody not well understood. Here, we identified a novel anti-OX40 agonistic antibody DF004, which stimulated the proliferation of human CD4+ T cells in vitro and inhibited tumor growth in a mouse model. Our crystallography structural studies showed that DF004 binds to the CRD2 region of OX40 while RG7888, an OX40 agonist antibody developed by Roche, binds to CRD3 of OX40 to the diametrically opposite position of DF004. This suggests that the agonistic activities of the antibodies are not necessarily epitope dependent. As their agonistic activities critically depend on clustering or cross-linking, our structural modeling indicates that the agonistic activity requires the optimal positioning of three Fc receptor/antibody/OX40 complexes on the cell membrane to facilitate the formation of one intracellular hexameric TRAF complex for downstream signal transduction, which is relatively inefficient. This may explain the lack of sufficient potency of these OX40 antibodies in a therapeutic setting and sheds light on the development of cross-linking-independent agonistic antibodies.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Xiaoyong Jiang
- Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Han Gao
- Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Fei Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Xin Zhang
- Dingfu Biotarget Co., Ltd., Suzhou 215126, China
| | - Aiwu Zhou
- Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
- Correspondence: (A.Z.); (T.X.); (H.C.)
| | - Ting Xu
- Dingfu Biotarget Co., Ltd., Suzhou 215126, China
- Correspondence: (A.Z.); (T.X.); (H.C.)
| | - Haiyan Cai
- Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
- Correspondence: (A.Z.); (T.X.); (H.C.)
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40
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Ma X, Zhu Y, Dong D, Chen Y, Wang S, Yang D, Ma Z, Zhang A, Zhang F, Guo C, Huang Z. Cryo-EM structures of two human B cell receptor isotypes. Science 2022; 377:880-885. [PMID: 35981028 DOI: 10.1126/science.abo3828] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The B cell receptor (BCR) complex plays a critical role in B cell development and immune responses. The assembly mechanisms underlying the BCR complex remain unknown. We determined the cryo-electron microscopy (cryo-EM) structures of human IgG-BCR and IgM-BCR, which consist of membrane-bound immunoglobulin molecules (mIg) and Igα/β subunits at a 1:1 stoichiometry. Assembly of both BCR complexes involves their extracellular domains, membrane-proximal connection peptides, and transmembrane (TM) helices. The TM helices of mIgG and mIgM share a conserved set of hydrophobic and polar interactions with Igα/β TM helices. By contrast, the IgG-Cγ3 and IgM-Cμ4 domains interact with extracellular Ig-like domains of Igα/β through head-to-tail and side-by-side modes, respectively. This work reveals the structural basis for BCR assembly and provides insights into BCR triggering.
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Affiliation(s)
- Xinyu Ma
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - De Dong
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Yan Chen
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Shubo Wang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Dehui Yang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Zhuo Ma
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Anqi Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Fan Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Changyou Guo
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
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41
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Su Q, Chen M, Shi Y, Zhang X, Huang G, Huang B, Liu D, Liu Z, Shi Y. Cryo-EM structure of the human IgM B cell receptor. Science 2022; 377:875-880. [PMID: 35981043 DOI: 10.1126/science.abo3923] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The B cell receptor (BCR) initiates immune responses through antigen recognition. We report a 3.3-angstrom cryo-electron microscopy structure of human immunoglobulin M (IgM)-BCR in the resting state. IgM-BCR comprises two heavy chains, two light chains, and the Igα/Igβ heterodimer. The ectodomains of the heavy chains closely stack against those of Igα/Igβ, with one heavy chain locked between Igα and Igβ in the juxtamembrane region. Extracellular interactions may determine isotype specificity of the BCR. The transmembrane helices of IgM-BCR form a four-helix bundle that appears to be conserved among all BCR isotypes. This structure contains 14 glycosylation sites on the IgM-BCR ectodomains and reveals three potential surface binding sites. Our work reveals the organizational principles of the BCR and may facilitate the design of antibody-based therapeutics.
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Affiliation(s)
- Qiang Su
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Mengying Chen
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yan Shi
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Department of Integrated Traditional and Western Nephrology, First Affiliated Hospital of Zhengzhou University, Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P. R. China
| | - Xiaofeng Zhang
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Gaoxingyu Huang
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Bangdong Huang
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Dongwei Liu
- Department of Integrated Traditional and Western Nephrology, First Affiliated Hospital of Zhengzhou University, Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P. R. China
| | - Zhangsuo Liu
- Department of Integrated Traditional and Western Nephrology, First Affiliated Hospital of Zhengzhou University, Henan Province Research Center for Kidney Disease, Zhengzhou 450052, P. R. China
| | - Yigong Shi
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
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42
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Saurabh S, Kalonia C, Li Z, Hollowell P, Waigh T, Li P, Webster J, Seddon JM, Lu JR, Bresme F. Understanding the Stabilizing Effect of Histidine on mAb Aggregation: A Molecular Dynamics Study. Mol Pharm 2022; 19:3288-3303. [PMID: 35946408 PMCID: PMC9449975 DOI: 10.1021/acs.molpharmaceut.2c00453] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Histidine, a widely used buffer in monoclonal antibody
(mAb) formulations,
is known to reduce antibody aggregation. While experimental studies
suggest a nonelectrostatic, nonstructural (relating to secondary structure
preservation) origin of the phenomenon, the underlying microscopic
mechanism behind the histidine action is still unknown. Understanding
this mechanism will help evaluate and predict the stabilizing effect
of this buffer under different experimental conditions and for different
mAbs. We have used all-atom molecular dynamics simulations and contact-based
free energy calculations to investigate molecular-level interactions
between the histidine buffer and mAbs, which lead to the observed
stability of therapeutic formulations in the presence of histidine.
We reformulate the Spatial Aggregation Propensity index by including
the buffer–protein interactions. The buffer adsorption on the
protein surface leads to lower exposure of the hydrophobic regions
to water. Our analysis indicates that the mechanism behind the stabilizing
action of histidine is connected to the shielding of the solvent-exposed
hydrophobic regions on the protein surface by the buffer molecules.
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Affiliation(s)
- Suman Saurabh
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London W12 0BZ, United Kingdom
| | - Cavan Kalonia
- Dosage Form Design and Development, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg 20878, Maryland, United States
| | - Zongyi Li
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, Oxford Road, The University of Manchester, Manchester M13 9PL, U.K
| | - Peter Hollowell
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, Oxford Road, The University of Manchester, Manchester M13 9PL, U.K
| | - Thomas Waigh
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, Oxford Road, The University of Manchester, Manchester M13 9PL, U.K.,Photon Science Institute, The University of Manchester, Manchester M13 9PL, U.K
| | - Peixun Li
- STFC ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX, U.K
| | - John Webster
- STFC ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX, U.K
| | - John M Seddon
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London W12 0BZ, United Kingdom
| | - Jian R Lu
- Biological Physics Group, School of Physics and Astronomy, Faculty of Science and Engineering, Oxford Road, The University of Manchester, Manchester M13 9PL, U.K
| | - Fernando Bresme
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London W12 0BZ, United Kingdom
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43
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Sand KMK, Gruber MM, Sandlie I, Mathiesen L, Andersen JT, Wadsack C. Contribution of the ex vivo placental perfusion model in understanding transplacental immunoglobulin G transfer. Placenta 2022; 127:77-87. [PMID: 35981406 DOI: 10.1016/j.placenta.2022.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/07/2022] [Accepted: 07/28/2022] [Indexed: 11/24/2022]
Abstract
INTRODUCTION The acquisition of humoral immunity in utero is essential for the fetus. The crucial protein, which is responsible for this part of immunity, is immunoglobulin-G (IgG). Immune functions of IgGs are mediated via the interaction of the crystallizable fragment (Fc) region of IgG with specific Fc γ receptors (FcγRs). However, an atypical FcγR, the neonatal Fc receptor (FcRn), is a key regulator of IgG transfer across the human placenta. During the last four decades ex vivo placental perfusion studies have contributed significantly to the study of mechanisms of IgG transfer across the multicellular placental barrier. METHOD A PubMed search was conducted by using specific keywords: placenta, perfusion and IgG to review manuscripts using human placental perfusion to study the transplacental transfer of IgG. Relevant studies found in reference lists of these manuscripts were also added to the review, and references were included that supported or gave nuance to the discussion of the mechanisms of IgG kinetics in the placenta. RESULTS AND DISCUSSION We found twenty publications on the study of transplacental transfer of IgG using human ex vivo placental perfusion, by research groups with partly different settings. This review summarizes knowledge about placental IgG transfer, with a strong focus on the contributions from ex vivo placental perfusion studies.
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Affiliation(s)
- Kine Marita Knudsen Sand
- Department of Biosciences, University of Oslo, 0371, Oslo, Norway; Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, 0424, Oslo, Norway; Department of Pharmacology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, 0424, Oslo, Norway
| | - Michael M Gruber
- Department of Obstetrics and Gynaecology, Medical University of Graz, 8036, Graz, Austria
| | - Inger Sandlie
- Department of Biosciences, University of Oslo, 0371, Oslo, Norway; Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, 0424, Oslo, Norway; Department of Pharmacology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, 0424, Oslo, Norway
| | - Line Mathiesen
- Section of Environmental Health, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Jan Terje Andersen
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, 0424, Oslo, Norway; Department of Pharmacology, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, 0424, Oslo, Norway
| | - Christian Wadsack
- Department of Obstetrics and Gynaecology, Medical University of Graz, 8036, Graz, Austria; BioTechMed-Graz, Austria
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44
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Dannheim FM, Walsh SJ, Orozco CT, Hansen AH, Bargh JD, Jackson SE, Bond NJ, Parker JS, Carroll JS, Spring DR. All-in-one disulfide bridging enables the generation of antibody conjugates with modular cargo loading. Chem Sci 2022; 13:8781-8790. [PMID: 35975158 PMCID: PMC9350601 DOI: 10.1039/d2sc02198f] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/10/2022] [Indexed: 12/30/2022] Open
Abstract
Antibody-drug conjugates (ADCs) are valuable therapeutic entities which leverage the specificity of antibodies to selectively deliver cytotoxins to antigen-expressing targets such as cancer cells. However, current methods for their construction still suffer from a number of shortcomings. For instance, using a single modification technology to modulate the drug-to-antibody ratio (DAR) in integer increments while maintaining homogeneity and stability remains exceptionally challenging. Herein, we report a novel method for the generation of antibody conjugates with modular cargo loading from native antibodies. Our approach relies on a new class of disulfide rebridging linkers, which can react with eight cysteine residues, thereby effecting all-in-one bridging of all four interchain disulfides in an IgG1 antibody with a single linker molecule. Modification of the antibody with the linker in a 1 : 1 ratio enabled the modulation of cargo loading in a quick and selective manner through derivatization of the linker with varying numbers of payload attachment handles to allow for attachment of either 1, 2, 3 or 4 payloads (fluorescent dyes or cytotoxins). Assessment of the biological activity of these conjugates demonstrated their exceptional stability in human plasma and utility for cell-selective cytotoxin delivery or imaging/diagnostic applications.
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Affiliation(s)
| | - Stephen J Walsh
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
- Cancer Research UK Cambridge Institute, University of Cambridge Cambridge CB2 0RE UK
| | - Carolina T Orozco
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Anders Højgaard Hansen
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
- Department of Chemistry, Technical University of Denmark (DTU) 2800 Kgs. Lyngby Denmark
| | - Jonathan D Bargh
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Nicholas J Bond
- Analytical Sciences, Biopharmaceutical Development, R&D, AstraZeneca Granta Park Cambridge CB21 6GH UK
| | - Jeremy S Parker
- Early Chemical Development, Pharmaceutical Development, R&D, AstraZeneca Macclesfield SK10 2NA UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge Cambridge CB2 0RE UK
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
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45
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Conner CG, McAndrew J, Menegatti S, Velev OD. An accelerated antibody aggregation test based on time sequenced dynamic light scattering. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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46
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Yin Y, Romei MG, Sankar K, Pal LR, Hon Hoi K, Yang Y, Leonard B, De Leon Boenig G, Kumar N, Matsumoto M, Payandeh J, Harris SF, Moult J, Lazar GA. Antibody Interfaces Revealed Through Structural Mining. Comput Struct Biotechnol J 2022; 20:4952-4968. [PMID: 36147680 PMCID: PMC9474289 DOI: 10.1016/j.csbj.2022.08.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 11/15/2022] Open
Abstract
Antibodies are fundamental effectors of humoral immunity, and have become a highly successful class of therapeutics. There is increasing evidence that antibodies utilize transient homotypic interactions to enhance function, and elucidation of such interactions can provide insights into their biology and new opportunities for their optimization as drugs. Yet the transitory nature of weak interactions makes them difficult to investigate. Capitalizing on their rich structural data and high conservation, we have characterized all the ways that antibody fragment antigen-binding (Fab) regions interact crystallographically. This approach led to the discovery of previously unrealized interfaces between antibodies. While diverse interactions exist, β-sheet dimers and variable-constant elbow dimers are recurrent motifs. Disulfide engineering enabled interactions to be trapped and investigated structurally and functionally, providing experimental validation of the interfaces and illustrating their potential for optimization. This work provides first insight into previously undiscovered oligomeric interactions between antibodies, and enables new opportunities for their biotherapeutic optimization.
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47
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Gonzalez JC, Chakraborty S, Thulin NK, Wang TT. Heterogeneity in IgG-CD16 signaling in infectious disease outcomes. Immunol Rev 2022; 309:64-74. [PMID: 35781671 PMCID: PMC9539944 DOI: 10.1111/imr.13109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In this review, we discuss how IgG antibodies can modulate inflammatory signaling during viral infections with a focus on CD16a-mediated functions. We describe the structural heterogeneity of IgG antibody ligands, including subclass and glycosylation that impact binding by and downstream activity of CD16a, as well as the heterogeneity of CD16a itself, including allele and expression density. While inflammation is a mechanism required for immune homeostasis and resolution of acute infections, we focus here on two infectious diseases that are driven by pathogenic inflammatory responses during infection. Specifically, we review and discuss the evolving body of literature showing that afucosylated IgG immune complex signaling through CD16a contributes to the overwhelming inflammatory response that is central to the pathogenesis of severe forms of dengue disease and coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Joseph C. Gonzalez
- Department of Medicine, Division of Infectious DiseasesStanford University School of MedicineStanfordCaliforniaUSA,Program in ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Saborni Chakraborty
- Department of Medicine, Division of Infectious DiseasesStanford University School of MedicineStanfordCaliforniaUSA
| | - Natalie K. Thulin
- Department of ImmunologyUniversity of WashingtonSeattleWashingtonUSA
| | - Taia T. Wang
- Department of Medicine, Division of Infectious DiseasesStanford University School of MedicineStanfordCaliforniaUSA,Program in ImmunologyStanford University School of MedicineStanfordCaliforniaUSA,Department of Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
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48
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Non-covalent Fc-Fab interactions significantly alter internal dynamics of an IgG1 antibody. Sci Rep 2022; 12:9321. [PMID: 35661134 PMCID: PMC9167292 DOI: 10.1038/s41598-022-13370-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
The fragment-antigen-binding arms (Fab1 and Fab2) in a canonical immunoglobulin G (IgG) molecule have identical sequences and hence are always expected to exhibit symmetric conformations and dynamics. Using long all atom molecular simulations of a human IgG1 crystal structure 1HZH, we demonstrate that the translational and rotational dynamics of Fab1 and Fab2 also strongly depend on their interactions with each other and with the fragment-crystallizable (Fc) region. We show that the Fab2 arm in the 1HZH structure is non-covalently bound to the Fc region via long-lived hydrogen bonds, involving its light chain and both heavy chains of the Fc region. These highly stable interactions stabilize non-trivial conformer states with constrained fluctuations. We observe subtle modifications in Fab1 dynamics in response to Fab2-Fc interactions that points to novel allosteric interactions between the Fab arms. These results yield novel insights into the inter- and intra-fragment motions of immunoglobulins which could help us better understand the relation between their structure and function.
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49
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Li T, Zhou B, Li Y, Huang S, Luo Z, Zhou Y, Lai Y, Gautam A, Bourgeau S, Wang S, Bao J, Tan J, Lavillette D, Li D. Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2. Int J Biol Macromol 2022; 209:1379-1388. [PMID: 35460753 PMCID: PMC9020654 DOI: 10.1016/j.ijbiomac.2022.04.096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/29/2022]
Abstract
SARS-CoV-2 engages with human cells through the binding of its Spike receptor-binding domain (S-RBD) to the receptor ACE2. Molecular blocking of this engagement represents a proven strategy to treat COVID-19. Here, we report a single-chain antibody (nanobody, DL4) isolated from immunized alpaca with picomolar affinity to RBD. DL4 neutralizes SARS-CoV-2 pseudoviruses with an IC50 of 0.101 μg mL-1 (6.2 nM). A crystal structure of the DL4-RBD complex at 1.75-Å resolution unveils the interaction detail and reveals a direct competition mechanism for DL4's ACE2-blocking and hence neutralizing activity. The structural information allows us to rationally design a mutant with higher potency. Our work adds diversity of neutralizing nanobodies against SARS-CoV-2 and should encourage protein engineering to improve antibody affinities in general.
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Affiliation(s)
- Tingting Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China
| | - Bingjie Zhou
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China
| | - Yaning Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China,University of CAS, Beijing 101408, China
| | - Suqiong Huang
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China,College of Pharmacy, Chongqing Medical University, China
| | - Zhipu Luo
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Yuanze Zhou
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Yanling Lai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China,University of CAS, Beijing 101408, China
| | - Anupriya Gautam
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China
| | - Salome Bourgeau
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China,Institut National de la Santé et de la Recherche Médicale, École des Hautes Etudes en Santé Publique, Institut de Recherche en Santé, Environnement et Travail, Université de Rennes, F-35000 Rennes, France
| | - Shurui Wang
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China
| | - Jingquan Tan
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Dimitri Lavillette
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China; Pasteurien College, Soochow University, Jiangsu, China.
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China.
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Martí D, Martín-Martínez E, Torras J, Betran O, Turon P, Alemán C. In silico study of substrate chemistry effect on the tethering of engineered antibodies for SARS-CoV-2 detection: Amorphous silica vs gold. Colloids Surf B Biointerfaces 2022; 213:112400. [PMID: 35158221 PMCID: PMC8820101 DOI: 10.1016/j.colsurfb.2022.112400] [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: 01/10/2022] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 11/26/2022]
Abstract
The influence of the properties of different solid substrates on the tethering of two antibodies, IgG1-CR3022 and IgG1-S309, which were specifically engineered for the detection of SARS-CoV-2, has been examined at the molecular level using conventional and accelerated Molecular Dynamics (cMD and aMD, respectively). Two surfaces with very different properties and widely used in immunosensors for diagnosis, amorphous silica and the most stable facet of the face-centered cubic gold structure, have been considered. The effects of such surfaces on the structure and orientation of the immobilized antibodies have been determined by quantifying the tilt and hinge angles that describe the orientation and shape of the antibody, respectively, and the dihedrals that measure the relative position of the antibody arms with respect to the surface. Results show that the interactions with amorphous silica, which are mainly electrostatic due to the charged nature of the surface, help to preserve the orientation and structure of the antibodies, especially of the IgG1-CR3022, indicating that the primary sequence of those antibodies also plays some role. Instead, short-range van der Waals interactions with the inert gold surface cause a higher degree tilting and fraying of the antibodies with respect to amorphous silica. The interactions between the antibodies and the surface also affect the correlation among the different angles and dihedrals, which increases with their strength. Overall, results explain why amorphous silica substrates are frequently used to immobilize antibodies in immunosensors.
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Affiliation(s)
- Didac Martí
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain
| | - Eduard Martín-Martínez
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
| | - Juan Torras
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain.
| | - Oscar Betran
- Departament de Física, EETAC, Universitat Politècnica de Catalunya (UPC), c/ Esteve Terrades, 7, 08860 Castelldefels, Spain
| | - Pau Turon
- B. Braun Surgical, S.A.U. Carretera de Terrasa 121, Rubí, 08191 Barcelona, Spain.
| | - Carlos Alemán
- Departament d'Enginyeria Química (DEQ), EEBE, Universitat Politècnica de Catalunya (UPC), C/ Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain; Barcelona Research Center in Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/ Eduard Maristany, 10-14, 08019 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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