1
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Tagawa H, Saeki R, Yamamoto C, Tanito K, Tanaka C, Munekawa S, Nii T, Kishimura A, Murakami H, Mori T, Katayama Y. The effect of Fc region affinity of protein-based antibody-recruiting molecules on antibody-dependent cellular cytotoxicity. RSC Adv 2024; 14:22860-22866. [PMID: 39040702 PMCID: PMC11262565 DOI: 10.1039/d4ra03391d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 07/06/2024] [Indexed: 07/24/2024] Open
Abstract
Previously, we reported anticancer molecules, Fc-binding antibody-recruiting molecules (Fc-ARMs), which crosslink proteins on cancer cells with endogenous immunoglobulin Gs (IgGs) via their Fc region. The mobilized IgGs on cancer cells can accommodate natural killer cells to induce antibody-dependent cellular cytotoxicity (ADCC). Because previous Fc-ARMs utilized Fc-binding peptides, their affinity to IgGs is weak, which resulted in the limited induction capability of ADCC. Previous Fc-ARMs also unitized small molecular ligands to cancer cells, which limited their universal applicability to any cancer cells. A recent study reported that protein-based Fc-ARMs might overcome the issues associated with non-proteinous Fc-ARMs. Here, we examined the universality of a protein-based Fc-ARM by replacing its tumor-binding domain with a human epidermal growth factor receptor 2 (HER2)-specific affibody (ZHER2:342). We also examined the requirement of its Fc-binding domain affinity. We found that the Fc-ARMs accepted an affibody as a tumor-binding domain to induce ADCC. Furthermore, the required residence time of the complex between Fc-ARM and IgG was ∼102 min, which was comparable to that when monoclonal antibodies bind to their specific antigens. However, we found that the extent of ADCC induced by Fc-ARM was lower than that of conventional IgG-mediated ADCC, indicating that further enhancement of the affinity of the antibody-binding terminus and tumor-binding terminus of Fc-ARM may be needed to achieve ADCC equivalent to that of conventional IgG-mediated ADCC.
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Affiliation(s)
- Hiroshi Tagawa
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Riku Saeki
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Chihaya Yamamoto
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Kenta Tanito
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Chihiro Tanaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Shoki Munekawa
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Teruki Nii
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Akihiro Kishimura
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Future Chemistry, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- International Research Center for Molecular Systems, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Takeshi Mori
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Future Chemistry, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Yoshiki Katayama
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Future Chemistry, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
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2
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Fernando A, Sparkes A, Matus EI, Patel A, Foster FS, Goertz D, Lee P, Gariépy J. Broadly Applicable Bispecific Linker Approach to Noncovalently Target Therapeutic Nanoparticles to Tumor Cells Expressing Carcinoembryonic Antigen. ACS Pharmacol Transl Sci 2024; 7:1864-1873. [PMID: 38898951 PMCID: PMC11184605 DOI: 10.1021/acsptsci.4c00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
Design strategies that lead to a more focused in vivo delivery of functionalized nanoparticles (NPs) and their cargo can potentially maximize their therapeutic efficiency while reducing systemic effects, broadening their clinical applications. Here, we report the development of a noncovalent labeling approach where immunoglobulin G (IgG)-decorated NPs can be directed to a cancer cell using a simple, linear bispecific protein adaptor, termed MFE23-ZZ. MFE23-ZZ was created by fusing a single-chain fragment variable domain, termed MFE23, recognizing carcinoembryonic antigen (CEA) expressed on tumor cells, to a small protein ZZ module, which binds to the Fc fragment of IgG. As a proof of concept, monoclonal antibodies (mAbs) were generated against a NP coat protein, namely, gas vesicle protein A (GvpA) of Halobacterium salinarum gas vesicles (GVs). The surface of each GV was therapeutically derivatized with the photoreactive agent chlorin e6 (Ce6GVs) and anti-GvpA mAbs were subsequently bound to GvpA on the surface of each Ce6GV. The bispecific ligand MFE23-ZZ was then bound to mAb-decorated Ce6GVs via their Fc domain, resulting in a noncovalent tripartite complex, namely, MFE23.ZZ-2B10-Ce6GV. This complex enhanced the intracellular uptake of Ce6GVs into human CEA-expressing murine MC38 colon carcinoma cells (MC38.CEA) relative to the CEA-negative parental cell line MC38 in vitro, making them more sensitive to light-induced cell killing. These results suggest that the surface of NP can be rapidly and noncovalently functionalized to target tumor-associated antigen-expressing tumor cells using simple bispecific linkers and any IgG-labeled cargo. This noncovalent approach is readily applicable to other types of functionalized NPs.
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Affiliation(s)
- Ann Fernando
- Physical
Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Amanda Sparkes
- Physical
Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
| | - Esther I. Matus
- Physical
Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ayushi Patel
- Physical
Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
| | - F. Stuart Foster
- Physical
Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - David Goertz
- Physical
Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Peter Lee
- Physical
Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
| | - Jean Gariépy
- Physical
Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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3
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Cleary SJ, Seo Y, Tian JJ, Kwaan N, Bulkley DP, Bentlage AE, Vidarsson G, Boilard É, Spirig R, Zimring JC, Looney MR. IgG hexamers initiate complement-dependent acute lung injury. J Clin Invest 2024; 134:e178351. [PMID: 38530369 PMCID: PMC11142733 DOI: 10.1172/jci178351] [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: 12/15/2023] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
Antibodies can initiate lung injury in a variety of disease states such as autoimmunity, in reactions to transfusions, or after organ transplantation, but the key factors determining in vivo pathogenicity of injury-inducing antibodies are unclear. Harmful antibodies often activate the complement cascade. A model for how IgG antibodies trigger complement activation involves interactions between IgG Fc domains driving the assembly of IgG hexamer structures that activate C1 complexes. The importance of IgG hexamers in initiating injury responses was not clear, so we tested their relevance in a mouse model of alloantibody- and complement-mediated acute lung injury. We used 3 approaches to block alloantibody hexamerization (antibody carbamylation, the K439E Fc mutation, or treatment with domain B from staphylococcal protein A), all of which reduced acute lung injury. Conversely, Fc mutations promoting spontaneous hexamerization made a harmful alloantibody into a more potent inducer of acute lung injury and rendered an innocuous alloantibody pathogenic. Treatment with a recombinant Fc hexamer "decoy" therapeutic protected mice from lung injury, including in a model with transgenic human FCGR2A expression that exacerbated pathology. These results indicate an in vivo role of IgG hexamerization in initiating acute lung injury and the potential for therapeutics that inhibit or mimic hexamerization to treat antibody-mediated diseases.
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Affiliation(s)
| | | | | | | | - David P. Bulkley
- Department of Biochemistry and Biophysics, UCSF, San Francisco, California, USA
| | | | | | - Éric Boilard
- Centre de Recherche du Centre Hospitalier Universitaire de Québec – Université Laval, Québec, Quebec, Canada
| | - Rolf Spirig
- CSL Behring, Research, CSL Behring Biologics Research Center, Bern, Switzerland
| | - James C. Zimring
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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4
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Cleary SJ, Seo Y, Tian JJ, Kwaan N, Bulkley DP, Bentlage AEH, Vidarsson G, Boilard É, Spirig R, Zimring JC, Looney MR. IgG hexamers initiate acute lung injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577129. [PMID: 38328049 PMCID: PMC10849723 DOI: 10.1101/2024.01.24.577129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Antibodies can initiate lung injury in a variety of disease states such as autoimmunity, transfusion reactions, or after organ transplantation, but the key factors determining in vivo pathogenicity of injury-inducing antibodies are unclear. A previously overlooked step in complement activation by IgG antibodies has been elucidated involving interactions between IgG Fc domains that enable assembly of IgG hexamers, which can optimally activate the complement cascade. Here, we tested the in vivo relevance of IgG hexamers in a complement-dependent alloantibody model of acute lung injury. We used three approaches to block alloantibody hexamerization (antibody carbamylation, the K439E Fc mutation, or treatment with domain B from Staphylococcal protein A), all of which reduced acute lung injury. Conversely, Fc mutations promoting spontaneous hexamerization made a harmful alloantibody into a more potent inducer of acute lung injury and rendered an innocuous alloantibody pathogenic. Treatment with a recombinant Fc hexamer 'decoy' therapeutic protected mice from lung injury, including in a model with transgenic human FCGR2A expression that exacerbated pathology. These results indicate a direct in vivo role of IgG hexamerization in initiating acute lung injury and the potential for therapeutics that inhibit or mimic hexamerization to treat antibody-mediated diseases.
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Affiliation(s)
- Simon J. Cleary
- Department of Medicine, University of California, San Francisco (UCSF), CA, USA
| | - Yurim Seo
- Department of Medicine, University of California, San Francisco (UCSF), CA, USA
| | - Jennifer J. Tian
- Department of Medicine, University of California, San Francisco (UCSF), CA, USA
| | - Nicholas Kwaan
- Department of Medicine, University of California, San Francisco (UCSF), CA, USA
| | - David P. Bulkley
- Department of Biochemistry and Biophysics, University of California, San Francisco (UCSF), CA, USA
| | | | | | - Éric Boilard
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada
| | - Rolf Spirig
- CSL Behring, Research, CSL Behring Biologics Research Center, Bern, Switzerland
| | - James C. Zimring
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Mark R. Looney
- Department of Medicine, University of California, San Francisco (UCSF), CA, USA
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5
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Kim S, Kim S, Kim S, Kim N, Lee SW, Yi H, Lee S, Sim T, Kwon Y, Lee HS. Affinity-Directed Site-Specific Protein Labeling and Its Application to Antibody-Drug Conjugates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306401. [PMID: 38032124 PMCID: PMC10811483 DOI: 10.1002/advs.202306401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/05/2023] [Indexed: 12/01/2023]
Abstract
Chemically modified proteins have diverse applications; however, conventional chemo-selective methods often yield heterogeneously labeled products. To address this limitation, site-specific protein labeling holds significant potential, driving extensive research in this area. Nevertheless, site-specific modification of native proteins remains challenging owing to the complexity of their functional groups. Therefore, a method for site-selective labeling of intact proteins is aimed to design. In this study, a novel approach to traceless affinity-directed intact protein labeling is established, which leverages small binding proteins and genetic code expansion technology. By applying this method, a site-specific antibody labeling with a drug, which leads to the production of highly effective antibody-drug conjugates specifically targeting breast cancer cell lines is achieved. This approach enables traceless conjugation of intact target proteins, which is a critical advantage in pharmaceutical applications. Furthermore, small helical binding proteins can be easily engineered for various target proteins, thereby expanding their potential applications in diverse fields. This innovative approach represents a significant advancement in site-specific modification of native proteins, including antibodies. It also bears immense potential for facilitating the development of therapeutic agents for various diseases.
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Affiliation(s)
- Sooin Kim
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Sanggil Kim
- New Drug Development CenterOsong Medical Innovation Foundation123 Osongsaengmyeong‐ro, Heungdeok‐guCheongjuChungbuk28160Republic of Korea
| | - Sangji Kim
- School of PharmacySungkyunkwan University2066 Seobu‐ro, Jangan‐guSuwon16419Republic of Korea
| | - Namkyoung Kim
- Department of Biomedical SciencesGraduate School of Medical ScienceBrain Korea 21 ProjectYonsei University College of Medicine50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Sang Won Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Hanbin Yi
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Seungeun Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Taebo Sim
- Department of Biomedical SciencesGraduate School of Medical ScienceBrain Korea 21 ProjectYonsei University College of Medicine50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Yongseok Kwon
- School of PharmacySungkyunkwan University2066 Seobu‐ro, Jangan‐guSuwon16419Republic of Korea
| | - Hyun Soo Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
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6
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Delaney S, Nagy Á, Karlström AE, Zeglis BM. Site-Specific Photoaffinity Bioconjugation for the Creation of 89Zr-Labeled Radioimmunoconjugates. Mol Imaging Biol 2023; 25:1104-1114. [PMID: 37052759 PMCID: PMC10570397 DOI: 10.1007/s11307-023-01818-5] [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: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/23/2023] [Indexed: 04/14/2023]
Abstract
PURPOSE Site-specific approaches to bioconjugation produce well-defined and homogeneous immunoconjugates with potential for superior in vivo behavior compared to analogs synthesized using traditional, stochastic methods. The possibility of incorporating photoaffinity chemistry into a site-specific bioconjugation strategy is particularly enticing, as it could simplify and accelerate the preparation of homogeneous immunoconjugates for the clinic. In this investigation, we report the synthesis, in vitro characterization, and in vivo evaluation of a site-specifically modified, 89Zr-labeled radioimmunoconjugate created via the reaction between an mAb and an Fc-binding protein bearing a photoactivatable 4-benzoylphenylalanine residue. PROCEDURES A variant of the Fc-binding Z domain of protein A containing a photoactivatable, 4-benzoylphenylalanine residue - Z(35BPA) - was modified with desferrioxamine (DFO), combined with the A33 antigen-targeting mAb huA33, and irradiated with UV light. The resulting immunoconjugate - DFOZ(35BPA)-huA33 - was purified and characterized via SDS-PAGE, MALDI-ToF mass spectrometry, surface plasmon resonance, and flow cytometry. The radiolabeling of DFOZ(35BPA)-huA33 was optimized to produce [89Zr]Zr-DFOZ(35BPA)-huA33, and the immunoreactivity of the radioimmunoconjugate was determined with SW1222 human colorectal cancer cells. Finally, the in vivo performance of [89Zr]Zr-DFOZ(35BPA)-huA33 in mice bearing subcutaneous SW1222 xenografts was interrogated via PET imaging and biodistribution experiments and compared to that of a stochastically labeled control radioimmunoconjugate, [89Zr]Zr-DFO-huA33. RESULTS HuA33 was site-specifically modified with Z(35BPA)-DFO, producing an immunoconjugate with on average 1 DFO/mAb, high in vitro stability, and high affinity for its target. [89Zr]Zr-DFOZ(35BPA)-huA33 was synthesized in 95% radiochemical yield and exhibited a specific activity of 2 mCi/mg and an immunoreactive fraction of ~ 0.85. PET imaging and biodistribution experiments revealed that high concentrations of the radioimmunoconjugate accumulated in tumor tissue (i.e., ~ 40%ID/g at 120 h p.i.) but also that the Z(35BPA)-bearing immunoPET probe produced higher uptake in the liver, spleen, and kidneys than its stochastically modified cousin, [89Zr]Zr-DFO-huA33. CONCLUSIONS Photoaffinity chemistry and an Fc-binding variant of the Z domain were successfully leveraged to create a novel site-specific strategy for the synthesis of radioimmunoconjugates. The probe synthesized using this method - DFOZ(35BPA)-huA33 - was well-defined and homogeneous, and the resulting radioimmunoconjugate ([89Zr]Zr-DFOZ(35BPA)-huA33) boasted high specific activity, stability, and immunoreactivity. While the site-specifically modified radioimmunoconjugate produced high activity concentrations in tumor tissue, it also yielded higher uptake in healthy organs than a stochastically modified analog, suggesting that optimization of this system is necessary prior to clinical translation.
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Affiliation(s)
- Samantha Delaney
- Department of Chemistry, Hunter College, City University of New York, New York, NY, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ábel Nagy
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Amelie Eriksson Karlström
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Brian M Zeglis
- Department of Chemistry, Hunter College, City University of New York, New York, NY, USA.
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA.
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, USA.
- Department of Radiology, Weill Cornell Medical College, New York, NY, USA.
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7
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Jukič M, Kralj S, Kolarič A, Bren U. Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening. Pharmaceuticals (Basel) 2023; 16:1170. [PMID: 37631085 PMCID: PMC10459493 DOI: 10.3390/ph16081170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Peptides, or short chains of amino-acid residues, are becoming increasingly important as active ingredients of drugs and as crucial probes and/or tools in medical, biotechnological, and pharmaceutical research. Situated at the interface between small molecules and larger macromolecular systems, they pose a difficult challenge for computational methods. We report an in silico peptide library generation and prioritization workflow using CmDock for identifying tetrapeptide ligands that bind to Fc regions of antibodies that is analogous to known in vitro recombinant peptide libraries' display and expression systems. The results of our in silico study are in accordance with existing scientific literature on in vitro peptides that bind to antibody Fc regions. In addition, we postulate an evolving in silico library design workflow that will help circumvent the combinatorial problem of in vitro comprehensive peptide libraries by focusing on peptide subunits that exhibit favorable interaction profiles in initial in silico peptide generation and testing.
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Affiliation(s)
- Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, SI-6000 Koper, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000 Maribor, Slovenia
| | - Sebastjan Kralj
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
| | - Anja Kolarič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000 Maribor, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, SI-6000 Koper, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000 Maribor, Slovenia
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8
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Herman CE, Min L, Choe LH, Maurer RW, Xu X, Ghose S, Lee KH, Lenhoff AM. Analytical characterization of host-cell-protein-rich aggregates in monoclonal antibody solutions. Biotechnol Prog 2023; 39:e3343. [PMID: 37020359 DOI: 10.1002/btpr.3343] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/07/2023]
Abstract
Host-cell proteins (HCPs) and high molecular weight (HMW) species have historically been treated as independent classes of impurities in the downstream processing of monoclonal antibodies (mAbs), but recent indications suggest that they may be partially linked. We have explored this connection with a shotgun proteomic analysis of HMW impurities that were isolated from harvest cell culture fluid (HCCF) and protein A eluate using size-exclusion chromatography (SEC). As part of the proteomic analysis, a cross-digest study was performed in which samples were analyzed using both the standard and native digest techniques to enable a fair comparison between bioprocess pools. This comparison reveals that the HCP profiles of HCCF and protein A eluate overlap substantially more than previous work has suggested, because hundreds of HCPs are conserved in aggregates that may be up to ~50 nm in hydrodynamic radius and that persist through the protein A capture step. Quantitative SWATH proteomics suggests that the majority of the protein A eluate's HCP mass is found in such aggregates, and this is corroborated by ELISA measurements on SEC fractions. The SWATH data also show that intra-aggregate concentrations of individual HCPs are positively correlated between aggregates that were isolated from HCCF and protein A eluate, and species that have generally been considered difficult to remove tend to be more concentrated than their counterparts. These observations support prior hypotheses regarding aggregate-mediated HCP persistence through protein A chromatography and highlight the importance of this persistence mechanism.
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Affiliation(s)
- Chase E Herman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716, USA
| | - Lie Min
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716, USA
| | - Leila H Choe
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716, USA
| | - Ronald W Maurer
- Biologics Process Development, Bristol Myers Squibb, Massachusetts, 01434, Devens, USA
| | - Xuankuo Xu
- Biologics Process Development, Bristol Myers Squibb, Massachusetts, 01434, Devens, USA
| | - Sanchayita Ghose
- Biologics Process Development, Bristol Myers Squibb, Massachusetts, 01434, Devens, USA
| | - Kelvin H Lee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716, USA
| | - Abraham M Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716, USA
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9
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Nandy S, Crum M, Wasden K, Strych U, Goyal A, Maranholkar V, Mo W, Vu B, Kourentzi K, Willson RC. Protein A-Nanoluciferase fusion protein for generalized, sensitive detection of immunoglobulin G. Anal Biochem 2023; 660:114929. [PMID: 36270332 PMCID: PMC9826736 DOI: 10.1016/j.ab.2022.114929] [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: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Abstract
Detection and quantification of antibodies, especially immunoglobulin G (IgG), is a cornerstone of ELISAs, many diagnostics, and the development of antibody-based drugs. Current state-of-the-art immunoassay techniques for antibody detection require species-specific secondary antibodies and carefully-controlled bioconjugations. Poor conjugation efficiency degrades assay performance and increases the risk of clinical false positives due to non-specific binding. We developed a generic, highly-sensitive platform for IgG quantification by fusing the IgG-Fc binding Z domain of Staphylococcal Protein A with the ultrabright bioluminescence reporter Nanoluc-luciferase (Nluc). We demonstrated the application of this fusion protein in a sandwich IgG detection immunoassay using surface-bound antigens to capture target IgG and protein A-Nanoluc fusion as the detector. We optimized the platform's sensitivity by incorporating multiple repeats of the Z domain into the fusion protein constructs. Using rabbit and mouse anti-SARS-CoV-2 Nucleoprotein IgGs as model analytes, we performed ELISAs in two different formats, either with SARS-CoV-2 Nucleoprotein as the capture antigen or with polyclonal chicken IgY as the capture antibody. Using standard laboratory equipment, the platform enabled the quantitation of antibody analytes at concentrations as low as 10 pg/mL (67 fM).
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Affiliation(s)
- Suman Nandy
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Mary Crum
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA,Present address: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Katherine Wasden
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA,Present address: Harvard Medical School, Boston, MA, USA
| | - Ulrich Strych
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA,Present address: Department of Paediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Atul Goyal
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA,Present address: Vaccine Research and Development, Pfizer, Pearl River, NY, USA
| | - Vijay Maranholkar
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - William Mo
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA,Present address: Department of Biomedical Engineering, The University of Texas at Austin, TX, USA
| | - Binh Vu
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Katerina Kourentzi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Richard C Willson
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA,Department of Biology and Biochemistry, University of Houston, Houston, TX, USA,Escuela de Medicina y Ciencias de Salud, Tecnológico de Monterrey, Monterrey, Nuevo León, Mexico,Corresponding author. (Richard C Willson)
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10
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In Silico Genome-Scale Analysis of Molecular Mechanisms Contributing to the Development of a Persistent Infection with Methicillin-Resistant Staphylococcus aureus (MRSA) ST239. Int J Mol Sci 2022; 23:ijms232416086. [PMID: 36555727 PMCID: PMC9781258 DOI: 10.3390/ijms232416086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/05/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
The increasing frequency of isolation of methicillin-resistant Staphylococcus aureus (MRSA) limits the chances for the effective antibacterial therapy of staphylococcal diseases and results in the development of persistent infection such as bacteremia and osteomyelitis. The aim of this study was to identify features of the MRSAST239 0943-1505-2016 (SA943) genome that contribute to the formation of both acute and chronic musculoskeletal infections. The analysis was performed using comparative genomics data of the dominant epidemic S. aureus lineages, namely ST1, ST8, ST30, ST36, and ST239. The SA943 genome encodes proteins that provide resistance to the host's immune system, suppress immunological memory, and form biofilms. The molecular mechanisms of adaptation responsible for the development of persistent infection were as follows: amino acid substitution in PBP2 and PBP2a, providing resistance to ceftaroline; loss of a large part of prophage DNA and restoration of the nucleotide sequence of beta-hemolysin, that greatly facilitates the escape of phagocytosed bacteria from the phagosome and formation of biofilms; dysfunction of the AgrA system due to the presence of psm-mec and several amino acid substitutions in the AgrC; partial deletion of the nucleotide sequence in genomic island vSAβ resulting in the loss of two proteases of Spl-operon; and deletion of SD repeats in the SdrE amino acid sequence.
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11
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Hsu YP, Verma D, Sun S, McGregor C, Mangion I, Mann BF. Successive remodeling of IgG glycans using a solid-phase enzymatic platform. Commun Biol 2022; 5:328. [PMID: 35393560 PMCID: PMC8990068 DOI: 10.1038/s42003-022-03257-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
The success of glycoprotein-based drugs in various disease treatments has become widespread. Frequently, therapeutic glycoproteins exhibit a heterogeneous array of glycans that are intended to mimic human glycopatterns. While immunogenic responses to biologic drugs are uncommon, enabling exquisite control of glycosylation with minimized microheterogeneity would improve their safety, efficacy and bioavailability. Therefore, close attention has been drawn to the development of glycoengineering strategies to control the glycan structures. With the accumulation of knowledge about the glycan biosynthesis enzymes, enzymatic glycan remodeling provides a potential strategy to construct highly ordered glycans with improved efficiency and biocompatibility. In this study, we quantitatively evaluate more than 30 enzymes for glycoengineering immobilized immunoglobulin G, an impactful glycoprotein class in the pharmaceutical field. We demonstrate successive glycan remodeling in a solid-phase platform, which enabled IgG glycan harmonization into a series of complex-type N-glycoforms with high yield and efficiency while retaining native IgG binding affinity. A solid-phase glycan remodeling (SPGR) platform is presented. Over thirty enzymes were evaluated for successive glycoengineering of immobilized antibodies with outstanding performance in several SPGR reactions.
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Affiliation(s)
- Yen-Pang Hsu
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, 07065, USA.,Exploratory Science Center, Merck & Co., Inc, Cambridge, MA, 02141, USA
| | - Deeptak Verma
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc, Rahway, NJ, 07065, USA
| | - Shuwen Sun
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, 07065, USA
| | - Caroline McGregor
- Process Research & Development, Merck & Co., Inc, Rahway, NJ, 07065, USA
| | - Ian Mangion
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, 07065, USA
| | - Benjamin F Mann
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, 07065, USA.
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12
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Chu H, Zhao Q, Liu J, Yang K, Wang Y, Liu J, Zhang K, Zhao B, He H, Zheng Y, Zhong S, Liang Z, Zhang L, Zhang Y. Ionic Liquid-Based Extraction System for In-Depth Analysis of Membrane Protein Complexes. Anal Chem 2021; 94:758-767. [PMID: 34932315 DOI: 10.1021/acs.analchem.1c03195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Limited by the rare efficient extraction system in extracting hydrophobic membrane protein complexes (MPCs) without compromising the stability of protein-protein interactions (PPIs), the in-depth functional study of MPCs has lagged far behind. In this study, the first systematic screening of ionic liquids (ILs) was performed and showed that triethylammonium acetate (TEAA) IL exhibited excellent performance in stabilizing PPIs, which was further confirmed by molecular docking simulations. By combining TEAA with the conventional detergent Nonidet P-40 (NP-40), a novel IL-based extraction system, i-TAN (TEAA IL with 1% NP-40), was proposed, which demonstrated superior performance in extracting and stabilizing MPCs, attributed to its larger size, more uniform distribution, and closer-to-neutral microenvironment of micelles. Extraction of MPCs with i-TAN allowed the confident identification of more hydrophobic EGFR-interacting proteins that are easily dissociated during the extraction process. Quantitative analysis of the difference in EGFR complexes between trastuzumab-sensitive and trastuzumab-resistant breast cancer cells provided comprehensive insights to understand the drug resistance mechanism, suggesting that i-TAN has great potential in interactomics and functional analysis of MPCs. This study provides a novel strategy for MPC extraction and downstream processing.
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Affiliation(s)
- Hongwei Chu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,Dalian University of Technology, Dalian 116024, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Ju Liu
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yanlei Wang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianhui Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Kun Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Hongyan He
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Yong Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Shijun Zhong
- Dalian University of Technology, Dalian 116024, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China.,Dalian University of Technology, Dalian 116024, China
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13
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Gil-Garcia M, Ventura S. Multifunctional antibody-conjugated coiled-coil protein nanoparticles for selective cell targeting. Acta Biomater 2021; 131:472-482. [PMID: 34192568 DOI: 10.1016/j.actbio.2021.06.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 12/22/2022]
Abstract
Nanostructures decorated with antibodies (Abs) are applied in bioimaging and therapeutics. However, most covalent conjugation strategies affect Abs functionality. In this study, we aimed to create protein-based nanoparticles to which intact Abs can be attached through tight, specific, and noncovalent interactions. Initially considered waste products, bacterial inclusion bodies (IBs) have been used in biotechnology and biomedicine. However, the amyloid-like nature of IBs limits their functionality and raises safety concerns. To bypass these obstacles, we have recently developed highly functional α-helix-rich IBs exploiting the natural self-assembly capacity of coiled-coil domains. We used this approach to create spherical, submicrometric, biocompatible and fluorescent protein nanoparticles capable of capturing Abs with high affinity. We showed that these IBs can be exploited for Ab-directed cell targeting. Simultaneous decoration of the nanoparticles with two different Abs in a controllable ratio enabled the construction of a bispecific antibody mimic that redirected T lymphocytes specifically to cancer cells. Overall, we describe an easy and cost-effective strategy to produce multivalent, traceable protein nanostructures with the potential to be used for biomedical applications. STATEMENT OF SIGNIFICANCE: Functional inclusion bodies (IBs) are promising platforms for biomedical and biotechnological applications. These nanoparticles are usually sustained by amyloid-like interactions, which imposes some limitations on their use. In this work, we exploit the natural coiled-coil self-assembly properties to create highly functional, nonamyloid, and fluorescent IBs capable of capturing antibodies. These protein-based nanoparticles are successfully used to specifically and simultaneously target two unrelated cell types and bring them close together, becoming a technology with potential application in bioimaging and immunotherapy.
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14
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Shibasaki S, Karasaki M, Matsui K, Iwasaki T. Functional Evaluation of Anti-TNF-α Affibody Molecules in Biochemical Detection and Inhibition to Signalling Pathways of a Synovial Cell. Curr Pharm Biotechnol 2021; 22:1228-1234. [PMID: 33069194 DOI: 10.2174/1389201021666201016143730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND An affibody molecule obtained from a bioengineered staphylococcal protein was previously shown to act as an affinity binder for a wide range of targets and develop Tumour Necrosis Factor α (TNF-α)-binding clones. METHODS In this study, we demonstrated that affibody molecules against TNF-α could bind to recombinant TNF-α on the membrane for biochemical detection. In addition, we examined whether the affibody molecules could block binding between recombinant TNF-α and its receptor on MH7A synovial cells. RESULTS When a TNF-α-binding affibody was added, the production level of inflammatory mediators IL-6 and MMP-3 in MH7A were found to decrease up to 44%. Additionally, proliferation of synovial cells was also inhibited by the addition of TNF-α to cultivation media. CONCLUSION These results suggest that affibody molecules against TNF-α could be candidate molecules for the detection of TNF-α during biochemical analysis and pharmacotherapy for rheumatoid arthritis.
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Affiliation(s)
- Seiji Shibasaki
- Department of Internal Medicine, Hyogo College of Medicine, Mukogawa-cho, Nishinomiya, 663-8501, Japan
| | - Miki Karasaki
- General Education Center, Hyogo University of Health Sciences, Minatojima 1-3-6, Kobe, 650-8530, Japan
| | - Kiyoshi Matsui
- Department of Internal Medicine, Hyogo College of Medicine, Mukogawa-cho, Nishinomiya, 663-8501, Japan
| | - Tsuyoshi Iwasaki
- Department of Internal Medicine, Hyogo College of Medicine, Mukogawa-cho, Nishinomiya, 663-8501, Japan
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15
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Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota. Nat Med 2021; 27:1442-1450. [PMID: 34282338 DOI: 10.1038/s41591-021-01409-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022]
Abstract
Serum antibodies can recognize both pathogens and commensal gut microbiota. However, our current understanding of antibody repertoires is largely based on DNA sequencing of the corresponding B-cell receptor genes, and actual bacterial antigen targets remain incompletely characterized. Here we have profiled the serum antibody responses of 997 healthy individuals against 244,000 rationally selected peptide antigens derived from gut microbiota and pathogenic and probiotic bacteria. Leveraging phage immunoprecipitation sequencing (PhIP-Seq) based on phage-displayed synthetic oligo libraries, we detect a wide breadth of individual-specific as well as shared antibody responses against microbiota that associate with age and gender. We also demonstrate that these antibody epitope repertoires are more longitudinally stable than gut microbiome species abundances. Serum samples of more than 200 individuals collected five years apart could be accurately matched and could serve as an immunologic fingerprint. Overall, our results suggest that systemic antibody responses provide a non-redundant layer of information about microbiota beyond gut microbial species composition.
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16
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Lee HG, Kang S, Lee JS. Binding characteristics of staphylococcal protein A and streptococcal protein G for fragment crystallizable portion of human immunoglobulin G. Comput Struct Biotechnol J 2021; 19:3372-3383. [PMID: 34194664 PMCID: PMC8217638 DOI: 10.1016/j.csbj.2021.05.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/29/2021] [Accepted: 05/30/2021] [Indexed: 12/03/2022] Open
Abstract
In the wide array of physiological processes, protein-protein interactions and their binding are the most basal activities for achieving adequate biological metabolism. Among the studies on binding proteins, the examination of interactions between immunoglobulin G (IgG) and natural immunoglobulin-binding ligands, such as staphylococcal protein A (spA) and streptococcal protein G (spG), is essential in the development of pharmaceutical science, biotechnology, and affinity chromatography. The widespread utilization of IgG-spA/spG binding characteristics has allowed researchers to investigate these molecular interactions. However, the detailed binding strength of each ligand and the corresponding binding mechanisms have yet to be fully investigated. In this study, the authors analyzed the binding strengths of IgG-spA and IgG-spG complexes and identified the mechanisms enabling these bindings using molecular dynamics simulation, steered molecular dynamics, and advanced Poisson-Boltzmann Solver simulations. Based on the presented data, the binding strength of the spA ligand was found to significantly exceed that of the spG ligand. To find out which non-covalent interactions or amino acid sites have a dominant role in the tight binding of these ligands, further detailed analyses of electrostatic interactions, hydrophobic bonding, and binding free energies have been performed. In investigating their binding affinity, a relatively independent and different unbinding mechanism was found in each ligand. These distinctly different mechanisms were observed to be highly correlated to the protein secondary and tertiary structures of spA and spG ligands, as explicated from the perspective of hydrogen bonding.
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Key Words
- AFM, Atomic Force Microscopy
- APBS, Advanced Poisson–Boltzmann Solver
- Affinity chromatography
- BIR, Between Protein–Protein Interface Residues
- ELISA, Enzyme-linked Immunosorbent Assays
- Fc, Fragment Crystallizable
- IgG, Immunoglobulin G
- Immunoglobulin G
- MD, Molecular Dynamics
- MM/PBSA, Molecular Mechanics Poisson–Boltzmann Surface Area
- Molecular dynamics
- Protein A
- Protein G
- Protein docking
- RMSD, Root Mean Square Deviation
- SASA, Solvent Accessible Surface Area
- SMD, Steered Molecular Dynamics
- spA, Staphylococcal Protein A
- spG, Streptococcal Protein G
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Affiliation(s)
- Hae Gon Lee
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, South Korea
| | - Shinill Kang
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, South Korea
| | - Joon Sang Lee
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, South Korea
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17
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Rincon Pabon JP, Kochert BA, Liu YH, Richardson DD, Weis DD. Protein A does not induce allosteric structural changes in an IgG1 antibody during binding. J Pharm Sci 2021; 110:2355-2361. [PMID: 33640336 DOI: 10.1016/j.xphs.2021.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 10/22/2022]
Abstract
Affinity chromatography is widely used for antibody purification in biopharmaceutical production. Although there is evidence suggesting that affinity chromatography might induce structural changes in antibodies, allosteric changes in structure have not been well-explored. Here, we used hydrogen exchange-mass spectrometry (HX-MS) to reveal conformational changes in the NIST mAb upon binding with a protein A (ProA) matrix. HX-MS measurements of NIST mAb bound to in-solution and resin forms of ProA revealed regions of the CH2 and CH3 domains with increased protection from HX upon ProA binding, consistent with the known ProA binding region. In-solution ProA experiments revealed regions in the Fab with increased HX uptake when the ProA:mAb molar ratio was increased to 2:1, suggesting an allosterically induced increase in backbone flexibility. Such effects were not observed with lower ProA concentration (1:1 molar ratio) or when ProA resin was used, suggesting some kind of change in binding mode. Since all pharmaceutical processes use ProA bound to resin, our results rule out reversible allosteric effects on the NIST mAb during interaction with resin ProA. However, irreversible effects cannot be ruled out since the NIST mAb was previously exposed to ProA during its original purification.
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Affiliation(s)
- Juan P Rincon Pabon
- Department of Chemistry and the Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, United States
| | - Brent A Kochert
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Yan-Hui Liu
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Douglas D Richardson
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - David D Weis
- Department of Chemistry and the Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, United States.
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18
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19
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Electrokinetic sandwich assay and DNA mediated charge amplification for enhanced sensitivity and specificity. Biosens Bioelectron 2020; 176:112917. [PMID: 33421763 DOI: 10.1016/j.bios.2020.112917] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/27/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022]
Abstract
An electrical immuno-sandwich assay utilizing an electrokinetic-based streaming current method for signal transduction is proposed. The method records the changes in streaming current, first when a target molecule binds to the capture probes immobilized on the inner surface of a silica micro-capillary, and then when the detection probes interact with the bound target molecules on the surface. The difference in signals in these two steps constitute the response of the assay, which offers better target selectivity and a linear concentration dependent response for a target concentration within the range 0.2-100 nM. The proof of concept is demonstrated by detecting different concentrations of Immunoglobulin G (IgG) in both phosphate buffered saline (PBS) and spiked in E. coli cell lysate. A superior target specificity for the sandwich assay compared to the corresponding direct assay is demonstrated along with a limit of detection of 90 pM in PBS. The prospect of improving the detection sensitivity was theoretically analysed, which indicated that the charge contrast between the target and the detection probe plays a crucial role in determining the signal. This aspect was then experimentally validated by modulating the zeta potential of the detection probe by conjugating negatively charged DNA oligonucleotides. The length of the conjugated DNA was varied from 5 to 30 nucleotides, altering the zeta potential of the detection probe from -9.3 ± 0.8 mV to -20.1 ± 0.9 mV. The measurements showed a clear and consistent enhancement of detection signal as a function of DNA lengths. The results presented here conclusively demonstrate the role of electric charge in detection sensitivity as well as the prospect for further improvement. The study therefore is a step forward in developing highly selective and sensitive electrokinetic assays for possible application in clinical investigations.
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20
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Abstract
The concept of engineering robust protein scaffolds for novel binding functions emerged 20 years ago, one decade after the advent of recombinant antibody technology. Early examples were the Affibody, Monobody (Adnectin), and Anticalin proteins, which were derived from fragments of streptococcal protein A, from the tenth type III domain of human fibronectin, and from natural lipocalin proteins, respectively. Since then, this concept has expanded considerably, including many other protein templates. In fact, engineered protein scaffolds with useful binding specificities, mostly directed against targets of biomedical relevance, constitute an area of active research today, which has yielded versatile reagents as laboratory tools. However, despite strong interest from basic science, only a handful of those protein scaffolds have undergone biopharmaceutical development up to the clinical stage. This includes the abovementioned pioneering examples as well as designed ankyrin repeat proteins (DARPins). Here we review the current state and clinical validation of these next-generation therapeutics.
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Affiliation(s)
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany;
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21
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Yageta S, Imamura H, Shibuya R, Honda S. C H2 domain orientation of human immunoglobulin G in solution: Structural comparison of glycosylated and aglycosylated Fc regions using small-angle X-ray scattering. MAbs 2019; 11:453-462. [PMID: 30513259 PMCID: PMC6512918 DOI: 10.1080/19420862.2018.1546086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/24/2018] [Accepted: 10/31/2018] [Indexed: 01/27/2023] Open
Abstract
The N-linked glycan in immunoglobulin G is critical for the stability and function of the crystallizable fragment (Fc) region. Alteration of these protein properties upon the removal of the N-linked glycan has often been explained by the alteration of the CH2 domain orientation in the Fc region. To confirm this hypothesis, we examined the small-angle X-ray scattering (SAXS) profile of the glycosylated Fc region (gFc) and aglycosylated Fc region (aFc) in solution. Conformational characteristics of the CH2 domain orientation were validated by comparison with SAXS profiles theoretically calculated from multiple crystal structures of the Fc region with different CH2 domain orientations. The reduced chi-square values from the fitting analyses of gFc and aFc associated with the degree of openness or closure of each crystal structure, as determined from the first principal component that partially governed the variation of the CH2 domain orientation extracted by a singular value decomposition analysis. For both gFc and aFc, the best-fitted SAXS profiles corresponded to ones calculated based on the crystal structure of gFc that formed a "semi-closed" CH2 domain orientation. Collectively, the data indicated that the removal of the N-linked glycan only negligibly affected the CH2 domain orientation in solution. These findings will guide the development of methodology for the production of highly refined functional Fc variants.
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Affiliation(s)
- Seiki Yageta
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
- Manufacturing Technology Association of Biologics, Tsukuba, Ibaraki, Japan
| | - Hiroshi Imamura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Risa Shibuya
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
| | - Shinya Honda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
- Manufacturing Technology Association of Biologics, Tsukuba, Ibaraki, Japan
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22
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Ali AM, Atmaj J, Van Oosterwijk N, Groves MR, Dömling A. Stapled Peptides Inhibitors: A New Window for Target Drug Discovery. Comput Struct Biotechnol J 2019; 17:263-281. [PMID: 30867891 PMCID: PMC6396041 DOI: 10.1016/j.csbj.2019.01.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
Protein-protein interaction (PPI) is a hot topic in clinical research as protein networking has a major impact in human disease. Such PPIs are potential drugs targets, leading to the need to inhibit/block specific PPIs. While small molecule inhibitors have had some success and reached clinical trials, they have generally failed to address the flat and large nature of PPI surfaces. As a result, larger biologics were developed for PPI surfaces and they have successfully targeted PPIs located outside the cell. However, biologics have low bioavailability and cannot reach intracellular targets. A novel class -hydrocarbon-stapled α-helical peptides that are synthetic mini-proteins locked into their bioactive structure through site-specific introduction of a chemical linker- has shown promise. Stapled peptides show an ability to inhibit intracellular PPIs that previously have been intractable with traditional small molecule or biologics, suggesting that they offer a novel therapeutic modality. In this review, we highlight what stapling adds to natural-mimicking peptides, describe the revolution of synthetic chemistry techniques and how current drug discovery approaches have been adapted to stabilize active peptide conformations, including ring-closing metathesis (RCM), lactamisation, cycloadditions and reversible reactions. We provide an overview on the available stapled peptide high-resolution structures in the protein data bank, with four selected structures discussed in details due to remarkable interactions of their staple with the target surface. We believe that stapled peptides are promising drug candidates and open the doors for peptide therapeutics to reach currently "undruggable" space.
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Affiliation(s)
| | | | | | | | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan1, 9700AD Groningen, the Netherlands
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23
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Vance N, Zacharias N, Ultsch M, Li G, Fourie A, Liu P, LaFrance-Vanasse J, Ernst JA, Sandoval W, Kozak KR, Phillips G, Wang W, Sadowsky J. Development, Optimization, and Structural Characterization of an Efficient Peptide-Based Photoaffinity Cross-Linking Reaction for Generation of Homogeneous Conjugates from Wild-Type Antibodies. Bioconjug Chem 2018; 30:148-160. [DOI: 10.1021/acs.bioconjchem.8b00809] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Nicholas Vance
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Neelie Zacharias
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Mark Ultsch
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Guangmin Li
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Aimee Fourie
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter Liu
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Julien LaFrance-Vanasse
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - James A. Ernst
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wendy Sandoval
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Katherine R. Kozak
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Gail Phillips
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Weiru Wang
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jack Sadowsky
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Yang XH, Huan LM, Chu XS, Sun Y, Shi QH. A comparative investigation of random and oriented immobilization of protein A ligands on the binding of immunoglobulin G. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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25
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Protein Engineering Allows for Mild Affinity-based Elution of Therapeutic Antibodies. J Mol Biol 2018; 430:3427-3438. [DOI: 10.1016/j.jmb.2018.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/25/2018] [Accepted: 06/04/2018] [Indexed: 01/08/2023]
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