1
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SureshKumar H, Appadurai R, Srivastava A. Glycans modulate lipid binding in Lili-Mip lipocalin protein: insights from molecular simulations and protein network analyses. Glycobiology 2024; 34:cwad094. [PMID: 38015986 DOI: 10.1093/glycob/cwad094] [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: 03/10/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023] Open
Abstract
The unique viviparous Pacific Beetle cockroaches provide nutrition to their embryo by secreting milk proteins Lili-Mip, a lipid-binding glycoprotein that crystallises in-vivo. The resolved in-vivo crystal structure of variably glycosylated Lili-Mip shows a classical Lipocalin fold with an eight-stranded antiparallel beta-barrel enclosing a fatty acid. The availability of physiologically unaltered glycoprotein structure makes Lili-Mip a very attractive model system to investigate the role of glycans on protein structure, dynamics, and function. Towards that end, we have employed all-atom molecular dynamics simulations on various glycosylated stages of a bound and free Lili-Mip protein and characterised the impact of glycans and the bound lipid on the dynamics of this glycoconjugate. Our work provides important molecular-level mechanistic insights into the role of glycans in the nutrient storage function of the Lili-Mip protein. Our analyses show that the glycans stabilise spatially proximal residues and regulate the low amplitude opening motions of the residues at the entrance of the binding pocket. Glycans also preserve the native orientation and conformational flexibility of the ligand. However, we find that either deglycosylation or glycosylation with high-mannose and paucimannose on the core glycans, which better mimic the natural insect glycosylation state, significantly affects the conformation and dynamics. A simple but effective distance- and correlation-based network analysis of the protein also reveals the key residues regulating the barrel's architecture and ligand binding characteristics in response to glycosylation.
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Affiliation(s)
- Harini SureshKumar
- Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Road, Bangalore, KA 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Road, Bangalore, KA 560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Road, Bangalore, KA 560012, India
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2
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Nador E, Xia C, Santangelo PJ, Whaley KJ, Costello CE, Anderson DJ. Platform-Specific Fc N-Glycan Profiles of an Antisperm Antibody. Antibodies (Basel) 2024; 13:17. [PMID: 38534207 PMCID: PMC10967333 DOI: 10.3390/antib13010017] [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: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 03/28/2024] Open
Abstract
IgG Fc N-glycosylation is necessary for effector functions and is an important component of quality control. The choice of antibody manufacturing platform has the potential to significantly influence the Fc glycans of an antibody and consequently alter their activity and clinical profile. The Human Contraception Antibody (HCA) is an IgG1 antisperm monoclonal antibody (mAb) currently in clinical development as a novel, non-hormonal contraceptive. Part of its development is selecting a suitable expression platform to manufacture HCA for use in the female reproductive tract. Here, we compared the Fc glycosylation of HCA produced in two novel mAb manufacturing platforms, namely transgenic tobacco plants (Nicotiana benthamiana; HCA-N) and mRNA-mediated expression in human vaginal cells (HCAmRNA). The Fc N-glycan profiles of the two HCA products were determined using mass spectrometry. Major differences in site occupancy, glycan types, and glycoform distributions were revealed. To address how these differences affect Fc function, antibody-dependent cellular phagocytosis (ADCP) assays were performed. The level of sperm phagocytosis was significantly lower in the presence of HCA-N than HCAmRNA. This study provides evidence that the two HCA manufacturing platforms produce functionally distinct HCAs; this information could be useful for the selection of an optimal platform for HCA clinical development and for mAbs in general.
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Affiliation(s)
- Ellena Nador
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Chaoshuang Xia
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Philip J. Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | | | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Deborah J. Anderson
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
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3
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Park W, Yoon T, Chang H, You J, Na S. An atomistic scale simulation study of structural properties in the silk-fibrohexamerin complex. NANOSCALE 2024; 16:821-832. [PMID: 38093650 DOI: 10.1039/d3nr04787c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
The use of Bombyx mori silk fibroin in composite materials has been extensively explored in many studies, owing to its remarkable mechanical properties. Recently, the N-glycan-engineered P25 protein was utilized to improve the mechanical properties of silk. However, the mechanism by which N-glycan-engineered P25 protein enhances the mechanical properties of silk remains unclear. This study analyzed the interaction between the P25 protein and silkworm silk using quantum mechanics/molecular mechanics multiscale simulations and discovered stronger hydrogen bonding between the amorphous domain and the P25 protein. The results confirmed that glycoengineering of the mannose molecule in N-glycan in orders of three, five, and seven increased the hydrogen bonding of the amorphous structures. However, P25 has fewer binding interactions with the crystalline domain. Silk amino acids and mannose molecules were analyzed using QM simulations, and hydroxyl and charged amino acids in the amorphous domains were found to have relatively higher reactivity with mannose molecules in N-glycans than basic and aliphatic amino acids in the crystalline domain. This study demonstrates how the N-glycan-engineered P25 protein can improve the mechanical properties of silk fibroin and identifies a key factor for N-glycan-engineered proteins.
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Affiliation(s)
- Wooboum Park
- Department of Mechanical Engineering, Korea University, 02841, Seoul, Republic of Korea.
| | - Taeyoung Yoon
- Department of Mechanical Engineering, Korea University, 02841, Seoul, Republic of Korea.
| | - Hyunjoon Chang
- HITS Inc., 124, Teheran-ro, Gangnam-gu, Seoul, 06234, Republic of Korea
| | - Juneseok You
- Department of Mechanical Engineering, Korea University, 02841, Seoul, Republic of Korea.
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, 02841, Seoul, Republic of Korea.
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4
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Bergonzo C, Hoopes JT, Kelman Z, Gallagher DT. Effects of glycans and hinge on dynamics in the IgG1 Fc. J Biomol Struct Dyn 2023:1-9. [PMID: 37897185 PMCID: PMC11055941 DOI: 10.1080/07391102.2023.2270749] [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: 07/11/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023]
Abstract
The crystallizable fragment (Fc) domain of immunoglobulin subclass IgG1 antibodies is engineered for a wide variety of pharmaceutical applications. Two important structural variables in Fc constructs are the hinge region connecting the Fc to the antigen binding fragments (Fab) and the glycans present in various glycoforms. These components affect receptor binding interactions that mediate immune activation. To design new antibody drugs, a robust in silico method for linking stability to structural changes is necessary. In this work, all-atom simulations were used to compare the dynamic behavior of the four structural variants arising from presence or absence of the hinge and glycans. We expressed the simplest of these constructs, the 'minimal Fc' with no hinge and no glycans, in Escherichia coli and report its crystal structure. The 'maximal Fc' that includes full hinge and G0F/G1F glycans is based on a previously reported structure, Protein Data Bank (PDB) ID: 5VGP. These, along with two intermediate structures (with only the glycans or with only the hinge) were used to independently measure the stability effects of the two structural variables using umbrella sampling simulations. Principal component analysis (PCA) was used to determine free energy effects along the Fc's dominant mode of motion. This work provides a comprehensive picture of the effects of hinge and glycans on Fc dynamics and stability.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Christina Bergonzo
- National Institute of Standards and Technology, 9600 Gudelsky Dr. Rockville, MD, 20850
- The Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Dr. Rockville, MD, 20850
| | - J. Todd Hoopes
- The Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Dr. Rockville, MD, 20850
- The Biomolecular Labeling Laboratory, 9600 Gudelsky Dr. Rockville, MD, 20850
| | - Zvi Kelman
- National Institute of Standards and Technology, 9600 Gudelsky Dr. Rockville, MD, 20850
- The Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Dr. Rockville, MD, 20850
- The Biomolecular Labeling Laboratory, 9600 Gudelsky Dr. Rockville, MD, 20850
| | - D. Travis Gallagher
- National Institute of Standards and Technology, 9600 Gudelsky Dr. Rockville, MD, 20850
- The Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Dr. Rockville, MD, 20850
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5
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Hiranyakorn M, Iwamoto S, Hoshinoo A, Tsumura R, Takashima H, Yasunaga M, Manabe S. Chromatographic Analysis of the N-Glycan Profile on Therapeutic Antibodies Using FcγRIIIa Affinity Column Chromatography. ACS OMEGA 2023; 8:16513-16518. [PMID: 37179638 PMCID: PMC10173337 DOI: 10.1021/acsomega.3c02374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023]
Abstract
N-Linked glycosylation on IgG has a profound impact on antibody functions. The relationship between the N-glycan structure and the binding affinity of FcγRIIIa, relating to antibody-dependent cell-mediated cytotoxicity (ADCC) activity, is important for the efficient development of a therapeutic antibody. Here, we report an influence of the N-glycan structure of IgGs, Fc fragments, and antibody-drug conjugates (ADCs) on FcγRIIIa affinity column chromatography. We compared the retention time of several IgGs with heterogeneous and homogeneous N-glycans. IgGs with a heterogeneous N-glycan structure provided several peaks in column chromatography. On the other hand, homogeneous IgGs and ADCs gave a single peak in column chromatography. The length of glycan on IgG also affected the retention time of the FcγRIIIa column, suggesting that the length of glycan is also impacted by binding affinity to FcγRIIIa, resulting in ADCC activity. This analytic methodology provides evaluation of the binding affinity of FcγRIIIa and ADCC activity, not only full-length IgG but also Fc fragments, which are difficult to measure in a cell-based assay. Furthermore, we showed that the glycan-remodeling strategy controls the ADCC activity of IgGs, Fc fragment, and ADCs.
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Affiliation(s)
- Methanee Hiranyakorn
- Laboratory
of Functional Molecule Chemistry, Pharmaceutical Department, Hoshi University, Ebara, Shinagawa, Tokyo 142-8501, Japan
| | - Shogo Iwamoto
- Fushimi
Pharmaceutical Co. Ltd., Nakatsu, Marugame, Kagawa 763-8605 Japan
| | - Asako Hoshinoo
- Fushimi
Pharmaceutical Co. Ltd., Nakatsu, Marugame, Kagawa 763-8605 Japan
| | - Ryo Tsumura
- Division
of Developmental Therapeutics, Exploratory
Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa City 277-8577, Japan
| | - Hiroki Takashima
- Division
of Developmental Therapeutics, Exploratory
Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa City 277-8577, Japan
| | - Masahiro Yasunaga
- Division
of Developmental Therapeutics, Exploratory
Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa City 277-8577, Japan
| | - Shino Manabe
- Laboratory
of Functional Molecule Chemistry, Pharmaceutical Department, Hoshi University, Ebara, Shinagawa, Tokyo 142-8501, Japan
- Institute
of Medicinal Chemistry, Hoshi University, Ebara, Shinagawa, Tokyo 142-8501, Japan
- Research
Center for Pharmaceutical Development Graduate School of Pharmaceutical
Sciences & Faculty of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
- ; . Tel.: + 81-3-5498-5770. Fax: +81-3-5498-5837
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6
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Crowley AR, Mehlenbacher MR, Sajadi MM, DeVico AL, Lewis GK, Ackerman ME. Evidence of variable human Fcγ receptor-Fc affinities across differentially-complexed IgG. MAbs 2023; 15:2231128. [PMID: 37405954 PMCID: PMC10324447 DOI: 10.1080/19420862.2023.2231128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/07/2023] Open
Abstract
Antibody-mediated effector functions are widely considered to unfold according to an associative model of IgG-Fcγ receptor (FcγR) interactions. The associative model presupposes that Fc receptors cannot discriminate antigen-bound IgG from free IgG in solution and have equivalent affinities for each. Therefore, the clustering of Fcγ receptors (FcγR) in the cell membrane, cross-activation of intracellular signaling domains, and the formation of the immune synapse are all the result of avid interactions between the Fc region of IgG and FcγRs that collectively overcome the individually weak, transient interactions between binding partners. Antibody allostery, specifically conformational allostery, is a competing model in which antigen-bound antibody molecules undergo a physical rearrangement that causes them to stand out from the background of free IgG by virtue of greater FcγR affinity. Various evidence exists in support of this model of antibody allostery, but it remains controversial. We report observations from multiplexed, label-free kinetic experiments in which the affinity values of FcγR were characterized for covalently immobilized, captured, and antigen-bound IgG. Across the strategies tested, receptors had greater affinity for the antigen-bound mode of IgG presentation. This phenomenon was observed across multiple FcγRs and generalized to multiple antigens, antibody specificities, and subclasses. Furthermore, the thermodynamic signatures of FcγR binding to free or immune-complexed IgG in solution differed when measured by an orthogonal label-free method, but the failure to recapitulate the trend in overall affinity leaves open questions as to what additional factors may be at play.
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Affiliation(s)
- Andrew R. Crowley
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | | | - Mohammad M. Sajadi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
- Baltimore VA Medical Center, VA Maryland Health Care System, Baltimore, USA
| | - Anthony L. DeVico
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - George K. Lewis
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Margaret E. Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
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7
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Sudol ASL, Butler J, Ivory DP, Tews I, Crispin M. Extensive substrate recognition by the streptococcal antibody-degrading enzymes IdeS and EndoS. Nat Commun 2022; 13:7801. [PMID: 36528711 PMCID: PMC9759587 DOI: 10.1038/s41467-022-35340-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Enzymatic cleavage of IgG antibodies is a common strategy used by pathogenic bacteria to ablate immune effector function. The Streptococcus pyogenes bacterium secretes the protease IdeS and the glycosidase EndoS, which specifically catalyse cleavage and deglycosylation of human IgG, respectively. IdeS has received clinical approval for kidney transplantation in hypersensitised individuals, while EndoS has found application in engineering antibody glycosylation. We present crystal structures of both enzymes in complex with their IgG1 Fc substrate, which was achieved using Fc engineering to disfavour preferential Fc crystallisation. The IdeS protease displays extensive Fc recognition and encases the antibody hinge. Conversely, the glycan hydrolase domain in EndoS traps the Fc glycan in a "flipped-out" conformation, while additional recognition of the Fc peptide is driven by the so-called carbohydrate binding module. In this work, we reveal the molecular basis of antibody recognition by bacterial enzymes, providing a template for the development of next-generation enzymes.
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Affiliation(s)
- Abigail S. L. Sudol
- grid.5491.90000 0004 1936 9297School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ UK
| | - John Butler
- grid.5491.90000 0004 1936 9297School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ UK
| | - Dylan P. Ivory
- grid.5491.90000 0004 1936 9297School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ UK
| | - Ivo Tews
- grid.5491.90000 0004 1936 9297School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ UK
| | - Max Crispin
- grid.5491.90000 0004 1936 9297School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ UK
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8
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Wei YL, Wegesser T, Kuhns S, Werner J, Lebrec H, Wang X. Strategies to evaluate potential effector function of glycan variants: a case study of ordesekimab (AMG 714 or PRV-015). J Immunotoxicol 2022; 19:109-116. [PMID: 36083248 DOI: 10.1080/1547691x.2022.2113841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The potential for effector functions of therapeutic antibodies, including antibody-dependent cell-mediated cytotoxicity (ADCC), is a biological activity of interest for characterization, regardless of if ADCC is an intended primary pharmacological effect. The composition of the conserved antibody Fc glycan can vary as a function of post-translational processing which may affect the binding affinity to Fc receptors, leading to a change of effector activity. Ordesekimab (AMG 714 or PRV-015), a fully human immunoglobulin G1-kappa anti-interleukin (IL)-15 monoclonal antibody, is in clinical development for celiac disease. The binding of ordesekimab to IL-15 inhibits the interaction of IL-15 with the IL-2Rβ and common γ chain of the IL-15 receptor complex, but not with the IL-15Rα chain. Therefore, the simultaneous binding of ordesekimab to the Fcγ receptor (R) IIIα expressed on natural killer (NK) cells and to the IL-15/IL-15Rα complex on cells such as monocytes may theoretically enable ADCC toward the IL-15Rα-expressing cells. The high mannose (HM) levels on the Fc glycan were found to vary in different lots of ordesekimab resulting from refinements to the manufacturing process, and the impact on ordesekimab-mediated ADCC activity was evaluated in in vivo and in vitro studies. A review of nonclinical and clinical data found no evidence of ordesekimab-induced depletion of monocytes, or cytotoxicity in organs with wide IL-15Rα expression, suggesting a lack of in vivo ADCC activity. In addition, in vitro peripheral blood mononuclear cells-based ADCC assay did not reveal any cytolytic effect of ordesekimab with various levels of HM content when cocultured with recombinant human IL-15. Taken together, these data demonstrate that ADCC is not a potential liability for ordesekimab and does not contribute to the reduction of IL-15-mediated inflammation, the intended pharmacological effect.
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Affiliation(s)
- Yu-Ling Wei
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Inc., South San Francisco, CA, USA
| | - Teresa Wegesser
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Scott Kuhns
- Process Development, Amgen Inc., Thousand Oaks, CA, USA
| | - Jonathan Werner
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Hervé Lebrec
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Inc., South San Francisco, CA, USA
| | - Xiaoting Wang
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Inc., South San Francisco, CA, USA
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9
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Definition of IgG Subclass-Specific Glycopatterns in Idiopathic Membranous Nephropathy: Aberrant IgG Glycoforms in Blood. Int J Mol Sci 2022; 23:ijms23094664. [PMID: 35563055 PMCID: PMC9101794 DOI: 10.3390/ijms23094664] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 11/18/2022] Open
Abstract
The podocyte injury, and consequent proteinuria, that characterize the pathology of idiopathic membranous nephropathy (IMN) is mediated by an autoimmune reaction against podocyte antigens. In particular, the activation of pathways leading to abundant renal deposits of complement is likely to involve the binding of mannose-binding lectin (MBL) to aberrant glycans on immunoglobulins. To obtain a landscape of circulatory IgG Fc glycosylation characterizing this disease, we conducted a systematic N-glycan profiling study of IgG1, 2, and 4 by mass spectrometry. The cohort included 57 IMN patients, a pathological control group with nephrotic syndrome (PN) (n = 20), and 88 healthy control subjects. The effect of sex and age was assessed in all groups and controlled by rigorous matching. Several IgG Fc glycan traits were found to be associated with IMN. Interestingly, among them, only IgG4-related results were specific for IMN and not for PN. Hypo-galactosylation of IgG4, already shown for IMN, was observed to occur in the absence of core fucose, in line with a probable increase of pro-inflammatory IgG. In addition, elevated levels of fucosylated IgG4, along with low levels of hybrid-type glycans, were detected. Some of these IgG4 alterations are likely to be more pronounced in high PLA2R (phospholipase A2 receptor) patients. IgG Fc glycosylation patterns associated with IMN warrant further studies of their role in disease mechanisms and may eventually enrich the diagnostic spectrum regarding patient stratification.
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10
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Lin T, Huang X, Guo L, Zhou S, Li X, Liu Y, Hu J, Chen X, Xiong Y. Boronate affinity-assisted oriented antibody conjugation on quantum dot nanobeads for improved detection performance in lateral flow immunoassay. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Füssl F, Barry CS, Pugh KM, Chooi KP, Vijayakrishnan B, Kang GD, von Bulow C, Howard PW, Bones J. Simultaneous monitoring of multiple attributes of pyrrolobenzodiazepine antibody-drug conjugates by size exclusion chromatography - high resolution mass spectrometry. J Pharm Biomed Anal 2021; 205:114287. [PMID: 34385015 DOI: 10.1016/j.jpba.2021.114287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/07/2021] [Accepted: 07/24/2021] [Indexed: 11/24/2022]
Abstract
Antibody-drug conjugates (ADCs) are an emerging class of oncology treatments combining the unique specificity of monoclonal antibodies with the highly cytotoxic properties of small molecule compounds. Pyrrolobenzodiazepines (PBDs) are highly potent agents capable of inhibiting cellular DNA replication which leads to apoptosis. To ensure efficacy and patient safety upon administration of such toxic and heterogeneous molecules, their structure and quality attributes must be closely monitored. Size exclusion chromatography (SEC) is a powerful, fast and robust tool for the separation of compounds varying in molecular weight. When using volatile components in the chromatographic mobile phase, SEC has also been shown to be amenable for interfacing to mass spectrometry, providing potential for reliable identification of protein isoforms across the size variants present. Here, we present a SEC-MS method developed for the characterisation of PBD-based ADCs on the intact molecular level. We demonstrate that information on ADC monomers such as the glycoform distribution and the average drug-antibody ratio (DAR) can be obtained in 15 minutes of analysis time. Qualitative and quantitative information on low and high molecular weight impurities such as aggregates and fragments, fundamental for critical quality attribute analysis of biopharmaceuticals, can be generated simultaneously. SEC-MS enables the characterisation of multiple product quality attributes of complex biotherapeutics at the same time.
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Affiliation(s)
- Florian Füssl
- NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
| | - Conor S Barry
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Kathryn M Pugh
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - K Phin Chooi
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Balakumar Vijayakrishnan
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Gyoung-Dong Kang
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Christina von Bulow
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Philip W Howard
- Spirogen, a Member of the AstraZeneca Group, QMB Innovation Centre, 42 New Road, London, E1 2AX, United Kingdom
| | - Jonathan Bones
- NIBRT - The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland; School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.
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12
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On the Use of Surface Plasmon Resonance Biosensing to Understand IgG-FcγR Interactions. Int J Mol Sci 2021; 22:ijms22126616. [PMID: 34205578 PMCID: PMC8235063 DOI: 10.3390/ijms22126616] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 01/01/2023] Open
Abstract
Surface plasmon resonance (SPR)-based optical biosensors offer real-time and label-free analysis of protein interactions, which has extensively contributed to the discovery and development of therapeutic monoclonal antibodies (mAbs). As the biopharmaceutical market for these biologics and their biosimilars is rapidly growing, the role of SPR biosensors in drug discovery and quality assessment is becoming increasingly prominent. One of the critical quality attributes of mAbs is the N-glycosylation of their Fc region. Other than providing stability to the antibody, the Fc N-glycosylation influences immunoglobulin G (IgG) interactions with the Fcγ receptors (FcγRs), modulating the immune response. Over the past two decades, several studies have relied on SPR-based assays to characterize the influence of N-glycosylation upon the IgG-FcγR interactions. While these studies have unveiled key information, many conclusions are still debated in the literature. These discrepancies can be, in part, attributed to the design of the reported SPR-based assays as well as the methodology applied to SPR data analysis. In fact, the SPR biosensor best practices have evolved over the years, and several biases have been pointed out in the development of experimental SPR protocols. In parallel, newly developed algorithms and data analysis methods now allow taking into consideration complex biomolecular kinetics. In this review, we detail the use of different SPR biosensing approaches for characterizing the IgG-FcγR interactions, highlighting their merit and inherent experimental complexity. Furthermore, we review the latest SPR-derived conclusions on the influence of the N-glycosylation upon the IgG-FcγR interactions and underline the differences and similarities across the literature. Finally, we explore new avenues taking advantage of novel computational analysis of SPR results as well as the latest strategies to control the glycoprofile of mAbs during production, which could lead to a better understanding and modelling of the IgG-FcγRs interactions.
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13
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Yamaguchi Y, Barb AW. A synopsis of recent developments defining how N-glycosylation impacts immunoglobulin G structure and function. Glycobiology 2020; 30:214-225. [PMID: 31822882 DOI: 10.1093/glycob/cwz068] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/26/2019] [Accepted: 08/21/2019] [Indexed: 12/21/2022] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) are the fastest growing group of drugs with 11 new antibodies or antibody-drug conjugates approved by the Food and Drug Administration in 2018. Many mAbs require effector function for efficacy, including antibody-dependent cell-mediated cytotoxicity triggered following contact of an immunoglobulin G (IgG)-coated particle with activating crystallizable fragment (Fc) γ receptors (FcγRs) expressed by leukocytes. Interactions between IgG1 and the FcγRs require post-translational modification of the Fc with an asparagine-linked carbohydrate (N-glycan). Though the structure of IgG1 Fc and the role of Fc N-glycan composition on disease were known for decades, the underlying mechanism of how the N-glycan affected FcγR binding was not defined until recently. This review will describe the current understanding of how N-glycosylation impacts the structure and function of the IgG1 Fc and describe new techniques that are poised to provide the next critical breakthroughs.
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Affiliation(s)
| | - Adam W Barb
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30602
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14
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Štambuk J, Nakić N, Vučković F, Pučić-Baković M, Razdorov G, Trbojević-Akmačić I, Novokmet M, Keser T, Vilaj M, Štambuk T, Gudelj I, Šimurina M, Song M, Wang H, Salihović MP, Campbell H, Rudan I, Kolčić I, Eller LA, McKeigue P, Robb ML, Halfvarson J, Kurtoglu M, Annese V, Škarić-Jurić T, Molokhia M, Polašek O, Hayward C, Kibuuka H, Thaqi K, Primorac D, Gieger C, Nitayaphan S, Spector T, Wang Y, Tillin T, Chaturvedi N, Wilson JF, Schanfield M, Filipenko M, Wang W, Lauc G. Global variability of the human IgG glycome. Aging (Albany NY) 2020; 12:15222-15259. [PMID: 32788422 PMCID: PMC7467356 DOI: 10.18632/aging.103884] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/25/2020] [Indexed: 12/20/2022]
Abstract
Immunoglobulin G (IgG) is the most abundant serum antibody which structural characteristics and effector functions are modulated through the attachment of various sugar moieties called glycans. Composition of the IgG N-glycome changes with age of an individual and in different diseases. Variability of IgG glycosylation within a population is well studied and is known to be affected by both genetic and environmental factors. However, global inter-population differences in IgG glycosylation have never been properly addressed. Here we present population-specific N-glycosylation patterns of IgG, analyzed in 5 different populations totaling 10,482 IgG glycomes, and of IgG’s fragment crystallizable region (Fc), analyzed in 2,579 samples from 27 populations sampled across the world. Country of residence associated with many N-glycan features and the strongest association was with monogalactosylation where it explained 38% of variability. IgG monogalactosylation strongly correlated with the development level of a country, defined by United Nations health and socioeconomic development indicators, and with the expected lifespan. Subjects from developing countries had low levels of IgG galactosylation, characteristic for inflammation and ageing. Our results suggest that citizens of developing countries may be exposed to environmental factors that can cause low-grade chronic inflammation and the apparent increase in biological age.
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Affiliation(s)
- Jerko Štambuk
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Natali Nakić
- Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | | | | | | | | | | | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Marija Vilaj
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Tamara Štambuk
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Ivan Gudelj
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Mirna Šimurina
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Manshu Song
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Hao Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | | | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ivana Kolčić
- School of Medicine, University of Split, Split, Croatia
| | - Leigh Anne Eller
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Paul McKeigue
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Merlin L Robb
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Metin Kurtoglu
- Department of Oncology, Koç University School of Medicine, Istanbul, Turkey
| | - Vito Annese
- Careggi University Hospital, Florence, Italy
| | | | - Mariam Molokhia
- School of Population Health and Environmental Sciences, King's College London, London, United Kingdom
| | - Ozren Polašek
- School of Medicine, University of Split, Split, Croatia
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Kujtim Thaqi
- Institute of Clinical Biochemistry, Priština, Kosovo
| | | | - Christian Gieger
- Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Therese Tillin
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, London, United Kingdom
| | - Nish Chaturvedi
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, London, United Kingdom
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom.,MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Moses Schanfield
- Department of Forensic Sciences, George Washington University, Washington, DC 20007, USA
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Wei Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.,School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
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15
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Yanaka S, Yogo R, Kato K. Biophysical characterization of dynamic structures of immunoglobulin G. Biophys Rev 2020; 12:637-645. [PMID: 32410186 PMCID: PMC7311591 DOI: 10.1007/s12551-020-00698-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/01/2020] [Indexed: 12/25/2022] Open
Abstract
Immunoglobulin G (IgG) is a major antibody and functions as a hub linking specific antigen binding and recruitment of effector molecules typified by Fcγ receptors (FcγRs). These activities are associated primarily with interactions involving its Fab and Fc sites, respectively. An IgG molecule is characterized by a multiple domain modular structure with conserved N-glycosylation in Fc. The molecule displays significant freedom in internal motion on various spatiotemporal scales. The consequent conformational flexibility and plasticity of IgG glycoproteins are functionally significant and potentially important factors for design and engineering of antibodies with enhanced functionality. In this article, experimental and computational approaches are outlined for characterizing the conformational dynamics of IgG molecules in solution. In particular, the importance of integration of these approaches is highlighted, as illustrated by dynamic intramolecular interactions between the pair of N-glycans and their proximal amino acid residues in Fc. These interactions can critically affect effector functions mediated by human IgG1 and FcγRIII. Further improvements in individual biophysical techniques and their integration will advance understanding of dynamic behaviors of antibodies in physiological and pathological conditions. Such understanding will provide opportunities for engineering antibodies through controlling allosteric networks in IgG molecules.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan.
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16
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Reprogramming the Constant Region of Immunoglobulin G Subclasses for Enhanced Therapeutic Potency against Cancer. Biomolecules 2020; 10:biom10030382. [PMID: 32121592 PMCID: PMC7175108 DOI: 10.3390/biom10030382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/18/2022] Open
Abstract
The constant region of immunoglobulin (Ig) G antibodies is responsible for their effector immune mechanism and prolongs serum half-life, while the fragment variable (Fv) region is responsible for cellular or tissue targeting. Therefore, antibody engineering for cancer therapeutics focuses on both functional efficacy of the constant region and tissue- or cell-specificity of the Fv region. In the functional aspect of therapeutic purposes, antibody engineers in both academia and industry have capitalized on the constant region of different IgG subclasses and engineered the constant region to enhance therapeutic efficacy against cancer, leading to a number of successes for cancer patients in clinical settings. In this article, we review IgG subclasses for cancer therapeutics, including (i) IgG1, (ii) IgG2, 3, and 4, (iii) recent findings on Fc receptor functions, and (iv) future directions of reprogramming the constant region of IgG to maximize the efficacy of antibody drug molecules in cancer patients.
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17
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Kang TH, Jung ST. Boosting therapeutic potency of antibodies by taming Fc domain functions. Exp Mol Med 2019; 51:1-9. [PMID: 31735912 PMCID: PMC6859160 DOI: 10.1038/s12276-019-0345-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 01/12/2023] Open
Abstract
Monoclonal antibodies (mAbs) are one of the most widely used drug platforms for infectious diseases or cancer therapeutics because they selectively target pathogens, infectious cells, cancerous cells, and even immune cells. In this way, they mediate the elimination of target molecules and cells with fewer side effects than other therapeutic modalities. In particular, cancer therapeutic mAbs can recognize cell-surface proteins on target cells and then kill the targeted cells by multiple mechanisms that are dependent upon a fragment crystallizable (Fc) domain interacting with effector Fc gamma receptors, including antibody-dependent cell-mediated cytotoxicity and antibody-dependent cell-mediated phagocytosis. Extensive engineering efforts have been made toward tuning Fc functions by either reinforcing (e.g. for targeted therapy) or disabling (e.g. for immune checkpoint blockade therapy) effector functions and prolonging the serum half-lives of antibodies, as necessary. In this report, we review Fc engineering efforts to improve therapeutic potency, and propose future antibody engineering directions that can fulfill unmet medical needs. Fine-tuning the function of monoclonal antibodies (mAbs) holds promise for developing new therapeutic agents. Antibodies bind to pathogens or cancer cells, flagging them with Fc (fragment crystallizable) domain for destruction by the immune system. mAbs attached only to specific target cells enable lower side effect than other conventional drugs. Sang Taek Jung at Korea University and Tae Hyun Kang at Kookmin University, both in Seoul, reviewed recent developments in engineering therapeutic potency of mAbs. They report that mAbs can be engineered to activate effective immune cell types to treat a particular disease. Engineering can also increase mAbs’ persistence in the blood, enabling less frequent administration. Antibodies engineered to bind to two different antigens at once can also improve therapeutic efficacy. Applying these techniques could help developing new treatments against cancer, and infectious and autoimmune diseases.
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Affiliation(s)
- Tae Hyun Kang
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seongbuk-gu, Seoul, 02707, Republic of Korea
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, Seoul, 02841, Republic of Korea.
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18
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Optimal combination of beneficial mutations for improved ADCC effector function of aglycosylated antibodies. Mol Immunol 2019; 114:62-71. [PMID: 31336250 DOI: 10.1016/j.molimm.2019.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 01/07/2023]
Abstract
The Fc region of IgG antibodies is crucial for binding to Fc receptors expressed on the surfaces of various immune leukocytes and eliciting therapeutic effector functions such as clearance of antibody-opsonized tumor cells. Despite abrogated Fc gamma receptor (FcγR) binding and therapeutic effector function in the absence of N-linked glycosylation at Asn297, the aglycosylated Fc region of IgG antibodies has bioprocessing advantages such as the absence of glycan heterogeneity and simple bacterial antibody production. Therefore, these antibodies have been comprehensively engineered as effector functional units for human therapy. In this work, we constructed a huge library of Fc variants with combinations of 25 beneficial mutations that were previously identified to improve binding of glycosylated or aglycosylated Fc regions to human FcγRs in previous studies. High-throughput screening of the resulting library led to the identification of an aglycosylated Fc variant that exhibited almost double the antibody-dependent cell-mediated cytotoxicity than wild-type glycosylated Fc. All mutations in this aglycosylated Fc variant were derived from previously identified beneficial mutations for engineered aglycosylated Fc variants as opposed to glycosylated variants, suggesting that significantly different sets of beneficial mutations are necessary to improve the effector function of aglycosylated Fc.
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19
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Yanaka S, Yogo R, Inoue R, Sugiyama M, Itoh SG, Okumura H, Miyanoiri Y, Yagi H, Satoh T, Yamaguchi T, Kato K. Dynamic Views of the Fc Region of Immunoglobulin G Provided by Experimental and Computational Observations. Antibodies (Basel) 2019; 8:antib8030039. [PMID: 31544845 PMCID: PMC6784063 DOI: 10.3390/antib8030039] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/08/2019] [Accepted: 06/12/2019] [Indexed: 01/08/2023] Open
Abstract
The Fc portion of immunoglobulin G (IgG) is a horseshoe-shaped homodimer, which interacts with various effector proteins, including Fcγ receptors (FcγRs). These interactions are critically dependent on the pair of N-glycans packed between the two CH2 domains. Fucosylation of these N-glycans negatively affects human IgG1-FcγRIIIa interaction. The IgG1-Fc crystal structures mostly exhibit asymmetric quaternary conformations with divergent orientations of CH2 with respect to CH3. We aimed to provide dynamic views of IgG1-Fc by performing long-timescale molecular dynamics (MD) simulations, which were experimentally validated by small-angle X-ray scattering and nuclear magnetic resonance spectroscopy. Our simulation results indicated that the dynamic conformational ensembles of Fc encompass most of the previously reported crystal structures determined in both free and complex forms, although the major Fc conformers in solution exhibited almost symmetric, stouter quaternary structures, unlike the crystal structures. Furthermore, the MD simulations suggested that the N-glycans restrict the motional freedom of CH2 and endow quaternary-structure plasticity through multiple intramolecular interaction networks. Moreover, the fucosylation of these N-glycans restricts the conformational freedom of the proximal tyrosine residue of functional importance, thereby precluding its interaction with FcγRIIIa. The dynamic views of Fc will provide opportunities to control the IgG interactions for developing therapeutic antibodies.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Satoru G Itoh
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hisashi Okumura
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Takumi Yamaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi 923-1292, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan.
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan.
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20
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Park SJ, Lee J, Qi Y, Kern NR, Lee HS, Jo S, Joung I, Joo K, Lee J, Im W. CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates. Glycobiology 2019; 29:320-331. [PMID: 30689864 DOI: 10.1093/glycob/cwz003] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/20/2019] [Accepted: 01/22/2019] [Indexed: 12/15/2022] Open
Abstract
Characterizing glycans and glycoconjugates in the context of three-dimensional structures is important in understanding their biological roles and developing efficient therapeutic agents. Computational modeling and molecular simulation have become an essential tool complementary to experimental methods. Here, we present a computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems. In our previous study, we developed Glycan Reader, a web-based tool for detecting carbohydrate molecules from a PDB structure and generation of simulation system and input files. As integrated into Glycan Reader in CHARMM-GUI, Glycan Modeler (Glycan Reader & Modeler) enables to generate the structures of glycans and glycoconjugates for given glycan sequences and glycosylation sites using PDB glycan template structures from Glycan Fragment Database (http://glycanstructure.org/fragment-db). Our benchmark tests demonstrate the universal applicability of Glycan Reader & Modeler to various glycan sequences and target proteins. We also investigated the structural properties of modeled glycan structures by running 2-μs molecular dynamics simulations of HIV envelope protein. The simulations show that the modeled glycan structures built by Glycan Reader & Modeler have the similar structural features compared to the ones solved by X-ray crystallography. We also describe the representative examples of glycoconjugate modeling with video demos to illustrate the practical applications of Glycan Reader & Modeler. Glycan Reader & Modeler is freely available at http://charmm-gui.org/input/glycan.
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Affiliation(s)
- Sang-Jun Park
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Jumin Lee
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Yifei Qi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Nathan R Kern
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Hui Sun Lee
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Sunhwan Jo
- Leadership Computing Facility, Argonne National Laboratory, Argonne, IL, USA
| | - InSuk Joung
- Center for Advanced Computation, Korea Institute for Advanced Study, Republic of Korea
| | - Keehyung Joo
- Center for Advanced Computation, Korea Institute for Advanced Study, Republic of Korea
| | - Jooyoung Lee
- Center for Advanced Computation, Korea Institute for Advanced Study, Republic of Korea
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA, USA
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21
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Zhao J, Nussinov R, Ma B. Antigen binding allosterically promotes Fc receptor recognition. MAbs 2019; 11:58-74. [PMID: 30212263 PMCID: PMC6343797 DOI: 10.1080/19420862.2018.1522178] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/10/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022] Open
Abstract
A key question in immunology is whether antigen recognition and Fc receptor (FcR) binding are allosterically linked. This question is also relevant for therapeutic antibody design. Antibody Fab and Fc domains are connected by flexible unstructured hinge region. Fc chains have conserved glycosylation sites at Asn297, with each conjugated to a core heptasaccharide and forming biantennary Fc glycan. The glycans modulate the Fc conformations and functions. It is well known that the antibody Fab and Fc domains and glycan affect antibody activity, but whether these elements act independently or synergistically is still uncertain. We simulated four antibody complexes: free antibody, antigen-bound antibody, FcR-bound antibody, and an antigen-antibody-FcR complex. We found that, in the antibody's "T/Y" conformation, the glycans, and the Fc domain all respond to antigen binding, with the antibody population shifting to two dominant clusters, both with the Fc-receptor binding site open. The simulations reveal that the Fc-glycan-receptor complexes also segregate into two conformational clusters, one corresponding to the antigen-free antibody-FcR baseline binding, and the other with an antigen-enhanced antibody-FcR interaction. Our study confirmed allosteric communications in antibody-antigen recognition and following FcR activation. Even though we observed allosteric communications through the IgG domains, the most important mechanism that we observed is the communication via population shift, stimulated by antigen binding and propagating to influence FcR recognition.
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Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
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22
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Sequence-to-structure dependence of isolated IgG Fc complex biantennaryN-glycans: a molecular dynamics study. Glycobiology 2018; 29:94-103. [DOI: 10.1093/glycob/cwy097] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/15/2018] [Indexed: 12/14/2022] Open
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23
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Subedi GP, Sinitskiy AV, Roberts JT, Patel KR, Pande VS, Barb AW. Intradomain Interactions in an NMDA Receptor Fragment Mediate N-Glycan Processing and Conformational Sampling. Structure 2018; 27:55-65.e3. [PMID: 30482728 DOI: 10.1016/j.str.2018.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/02/2018] [Accepted: 09/19/2018] [Indexed: 11/18/2022]
Abstract
The structural and functional roles of highly conserved asparagine-linked (N)-glycans on the extracellular ligand-binding domain (LBD) of the N-methyl-D-aspartate receptors are poorly understood. We applied solution- and computation-based methods that identified N-glycan-mediated intradomain and interglycan interactions. Nuclear magnetic resonance (NMR) spectra of the GluN1 LBD showed clear signals corresponding to each of the three N-glycans and indicated the reducing end of glycans at N440 and N771 potentially contacted nearby amino acids. Molecular dynamics simulations identified contacts between nearby amino acids and the N440- and N771-glycans that were consistent with the NMR spectra. The distal portions of the N771-glycan also contacted the core residues of the nearby N471-glycan. This result was consistent with mass spectrometry data indicating the limited N471-glycan core fucosylation and reduced branch processing of the N771-glycan could be explained by interglycan contacts. We discuss a potential role for the GluN1 LBD N-glycans in interdomain contacts formed in NMDA receptors.
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Affiliation(s)
- Ganesh P Subedi
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive Molecular Biology Building, Room 4210, Ames, IA 50011, USA
| | - Anton V Sinitskiy
- Department of Bioengineering, Stanford University, 318 Campus Drive, Room S295, Stanford, CA 94305, USA
| | - Jacob T Roberts
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive Molecular Biology Building, Room 4210, Ames, IA 50011, USA
| | - Kashyap R Patel
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive Molecular Biology Building, Room 4210, Ames, IA 50011, USA
| | - Vijay S Pande
- Department of Bioengineering, Stanford University, 318 Campus Drive, Room S295, Stanford, CA 94305, USA
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive Molecular Biology Building, Room 4210, Ames, IA 50011, USA.
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24
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Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
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Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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25
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Zhao J, Nussinov R, Wu WJ, Ma B. In Silico Methods in Antibody Design. Antibodies (Basel) 2018; 7:E22. [PMID: 31544874 PMCID: PMC6640671 DOI: 10.3390/antib7030022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/28/2018] [Accepted: 06/28/2018] [Indexed: 01/10/2023] Open
Abstract
Antibody therapies with high efficiency and low toxicity are becoming one of the major approaches in antibody therapeutics. Based on high-throughput sequencing and increasing experimental structures of antibodies/antibody-antigen complexes, computational approaches can predict antibody/antigen structures, engineering the function of antibodies and design antibody-antigen complexes with improved properties. This review summarizes recent progress in the field of in silico design of antibodies, including antibody structure modeling, antibody-antigen complex prediction, antibody stability evaluation, and allosteric effects in antibodies and functions. We listed the cases in which these methods have helped experimental studies to improve the affinities and physicochemical properties of antibodies. We emphasized how the molecular dynamics unveiled the allosteric effects during antibody-antigen recognition and antibody-effector recognition.
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Affiliation(s)
- Jun Zhao
- Division of Biotechnology Review and Research I, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
- Interagency Oncology Task Force (IOTF) Fellowship: Oncology Product Research/Review Fellow, National Cancer Institute, Bethesda, MD 20892, USA.
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Wen-Jin Wu
- Division of Biotechnology Review and Research I, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA.
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26
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More AS, Toth RT, Okbazghi SZ, Middaugh CR, Joshi SB, Tolbert TJ, Volkin DB, Weis DD. Impact of Glycosylation on the Local Backbone Flexibility of Well-Defined IgG1-Fc Glycoforms Using Hydrogen Exchange-Mass Spectrometry. J Pharm Sci 2018; 107:2315-2324. [PMID: 29751008 DOI: 10.1016/j.xphs.2018.04.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/31/2018] [Accepted: 04/27/2018] [Indexed: 10/17/2022]
Abstract
We have used hydrogen exchange-mass spectrometry to characterize local backbone flexibility of 4 well-defined IgG1-Fc glycoforms expressed and purified from Pichia pastoris, 2 of which were prepared using subsequent in vitro enzymatic treatments. Progressively decreasing the size of the N-linked N297 oligosaccharide from high mannose (Man8-Man12), to Man5, to GlcNAc, to nonglycosylated N297Q resulted in progressive increases in backbone flexibility. Comparison of these results with recently published physicochemical stability and Fcγ receptor binding data with the same set of glycoproteins provide improved insights into correlations between glycan structure and these pharmaceutical properties. Flexibility significantly increased upon glycan truncation in 2 potential aggregation-prone regions. In addition, a correlation was established between increased local backbone flexibility and increased deamidation at asparagine 315. Interestingly, the opposite trend was observed for oxidation of tryptophan 277 where faster oxidation correlated with decreased local backbone flexibility. Finally, a trend of increasing C'E glycopeptide loop flexibility with decreasing glycan size was observed that correlates with their FcγRIIIa receptor binding properties. These well-defined IgG1-Fc glycoforms serve as a useful model system to identify physicochemical stability and local backbone flexibility data sets potentially discriminating between various IgG glycoforms for potential applicability to future comparability or biosimilarity assessments.
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Affiliation(s)
- Apurva S More
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047
| | - Ronald T Toth
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047
| | - Solomon Z Okbazghi
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047
| | - C Russell Middaugh
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047
| | - Sangeeta B Joshi
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047
| | - Thomas J Tolbert
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047
| | - David B Volkin
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047; Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas 66047.
| | - David D Weis
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047; Department of Chemistry, University of Kansas, Lawrence, Kansas 66045.
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27
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Yang M, Aytenfisu AH, MacKerell AD. Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field. Carbohydr Res 2018; 457:41-50. [PMID: 29422120 DOI: 10.1016/j.carres.2018.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/02/2018] [Accepted: 01/15/2018] [Indexed: 01/22/2023]
Abstract
Motivated by underestimation of the diffusion constant of glucose in aqueous solution at high glucose concentrations we performed additional optimization of the Drude polarizable hexopyranose monosaccharide force field. This indicated aggregation of the glucose at higher concentrations, which is a concern for studies of complex glycan systems such as the HIV Envelope where high effective concentrations of sugars are present. High-level quantum mechanical calculations were undertaken on water monohydrate-glucose interactions, on water cluster-glucose interactions and on glucose-glucose dimers in stacked (parallel) and perpendicular orientations. Optimization of the nonbond and dihedral parameters targeting these data yielded a revised model that showed improved agreement with experimental aqueous diffusion data. However, limitations in the diffusion constants were still present. These were due to the SWM4-NDP inherently overestimating the diffusion constant of water, a problem that was validated by calculation of the aqueous diffusion constants using the SWM6-NDP water model. In addition, results show the water diffusion constant to be significantly overestimated at high glucose concentrations though the glucose diffusion is in satisfactory agreement with experiment. These results indicate the subtle balance of water-sugar, water-water and sugar-sugar interactions that needs to be properly modeled to account for the full range of aqueous behavior of sugars in aqueous solution.
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Affiliation(s)
- Mingjun Yang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201, USA; XtalPi Inc., Shennan Road 6025, Futian District, Shenzhen, China
| | - Asaminew H Aytenfisu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201, USA.
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