1
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Jiang Y, Lin Y, Tetlow AM, Pan R, Ji C, Kong XP, Congdon EE, Sigurdsson EM. Single-domain antibody-based protein degrader for synucleinopathies. Mol Neurodegener 2024; 19:44. [PMID: 38816762 PMCID: PMC11140919 DOI: 10.1186/s13024-024-00730-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/06/2024] [Indexed: 06/01/2024] Open
Abstract
Synucleinopathies are a group of neurodegenerative diseases characterized by the accumulation of α-synuclein (α-syn) in the brain, leading to motor and neuropsychiatric symptoms. Currently, there are no known cures for synucleinopathies, and treatments mainly focus on symptom management. In this study, we developed a single-domain antibody (sdAb)-based protein degrader with features designed to enhance proteasomal degradation of α-syn. This sdAb derivative targets both α-syn and Cereblon (CRBN), a substrate-receptor for the E3-ubiquitin ligase CRL4CRBN, and thereby induces α-syn ubiquitination and proteasomal degradation. Our results indicate that this therapeutic candidate enhances proteasomal degradation of α-syn, in addition to the endogenous lysosomal degradation machinery. By promoting proteasomal degradation of α-syn, we improved clearance of α-syn in primary culture and mouse models of synucleinopathy. These findings indicate that our sdAb-based protein degrader is a promising therapeutic candidate for synucleinopathies. Considering that only a small percentage of antibodies enter the brain, more potent sdAbs with greater brain entry than whole antibodies could enhance clinical benefits of antibody-based therapies.
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Affiliation(s)
- Yixiang Jiang
- Department of Neuroscience and Physiology, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Yan Lin
- Department of Neuroscience and Physiology, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Amber M Tetlow
- Department of Neuroscience and Physiology, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ruimin Pan
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Changyi Ji
- Department of Neuroscience and Physiology, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Erin E Congdon
- Department of Neuroscience and Physiology, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Einar M Sigurdsson
- Department of Neuroscience and Physiology, and Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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2
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Jiang Y, Lin Y, Tetlow AM, Pan R, Ji C, Kong XP, Congdon EE, Sigurdsson EM. Single-Domain Antibody-Based Protein Degrader for Synucleinopathies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584473. [PMID: 38558982 PMCID: PMC10979981 DOI: 10.1101/2024.03.11.584473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Synucleinopathies are a group of neurodegenerative diseases characterized by the accumulation of α-synuclein (α-syn) in the brain, leading to motor and neuropsychiatric symptoms. Currently, there are no known cures for synucleinopathies, and treatments mainly focus on symptom management. In this study, we developed a single-domain antibody (sdAb)-based protein degrader with features designed to enhance proteasomal degradation of α-syn. This sdAb derivative targets both α-syn and Cereblon (CRBN), a substrate-receptor for the E3-ubiquitin ligase CRL4CRBN, and thereby induces α-syn ubiquitination and proteasomal degradation. Our results indicate that this therapeutic candidate enhances proteasomal degradation of α-syn, in addition to the endogenous lysosomal degradation machinery. By promoting proteasomal degradation of α-syn, we improved clearance of α-syn in primary culture and mouse models of synucleinopathy. These findings indicate that our sdAb-based protein degrader is a promising therapeutic candidate for synucleinopathies. Considering that only a small percentage of antibodies enter the brain, more potent sdAbs with greater brain entry than whole antibodies could enhance clinical benefits of antibody-based therapies.
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Affiliation(s)
- Yixiang Jiang
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, 435 East 30 Street, New York NY 10016, USA
| | - Yan Lin
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, 435 East 30 Street, New York NY 10016, USA
| | - Amber M Tetlow
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, 435 East 30 Street, New York NY 10016, USA
| | - Ruimin Pan
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 435 East 30 Street, New York NY 10016, USA
| | - Changyi Ji
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, 435 East 30 Street, New York NY 10016, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, 435 East 30 Street, New York NY 10016, USA
| | - Erin E Congdon
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, 435 East 30 Street, New York NY 10016, USA
| | - Einar M Sigurdsson
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Grossman School of Medicine, 435 East 30 Street, New York NY 10016, USA
- Department of Psychiatry, New York University Grossman School of Medicine, 435 East 30 Street, New York NY 10016, USA
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3
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Matsunaga R, Ujiie K, Inagaki M, Fernández Pérez J, Yasuda Y, Mimasu S, Soga S, Tsumoto K. High-throughput analysis system of interaction kinetics for data-driven antibody design. Sci Rep 2023; 13:19417. [PMID: 37990030 PMCID: PMC10663500 DOI: 10.1038/s41598-023-46756-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023] Open
Abstract
Surface plasmon resonance (SPR) is widely used for antigen-antibody interaction kinetics analysis. However, it has not been used in the screening phase because of the low throughput of measurement and analysis. Herein, we proposed a high-throughput SPR analysis system named "BreviA" using the Brevibacillus expression system. Brevibacillus was transformed using a plasmid library containing various antibody sequences, and single colonies were cultured in 96-well plates. Sequence analysis was performed using bacterial cells, and recombinant antibodies secreted in the supernatant were immobilized on a sensor chip to analyze their interactions with antigens using high-throughput SPR. Using this system, the process from the transformation to 384 interaction analyses can be performed within a week. This system utility was tested using an interspecies specificity design of an anti-human programmed cell death protein 1 (PD-1) antibody. A plasmid library containing alanine and tyrosine mutants of all complementarity-determining region residues was generated. A high-throughput SPR analysis was performed against human and mouse PD-1, showing that the mutation in the specific region enhanced the affinity for mouse PD-1. Furthermore, deep mutational scanning of the region revealed two mutants with > 100-fold increased affinity for mouse PD-1, demonstrating the potential efficacy of antibody design using data-driven approach.
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Affiliation(s)
- Ryo Matsunaga
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Kan Ujiie
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Mayuko Inagaki
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Jorge Fernández Pérez
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Yoshiki Yasuda
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Shinya Mimasu
- Biologics Engineering, Discovery Intelligence, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi, Ibaraki, 305-8585, Japan
| | - Shinji Soga
- Biologics Engineering, Discovery Intelligence, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi, Ibaraki, 305-8585, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
- The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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4
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Li J, Kang G, Wang J, Yuan H, Wu Y, Meng S, Wang P, Zhang M, Wang Y, Feng Y, Huang H, de Marco A. Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization. Int J Biol Macromol 2023; 247:125733. [PMID: 37423452 DOI: 10.1016/j.ijbiomac.2023.125733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Routinely screened antibody fragments usually require further in vitro maturation to achieve the desired biophysical properties. Blind in vitro strategies can produce improved ligands by introducing random mutations into the original sequences and selecting the resulting clones under more and more stringent conditions. Rational approaches exploit an alternative perspective that aims first at identifying the specific residues potentially involved in the control of biophysical mechanisms, such as affinity or stability, and then to evaluate what mutations could improve those characteristics. The understanding of the antigen-antibody interactions is instrumental to develop this process the reliability of which, consequently, strongly depends on the quality and completeness of the structural information. Recently, methods based on deep learning approaches critically improved the speed and accuracy of model building and are promising tools for accelerating the docking step. Here, we review the features of the available bioinformatic instruments and analyze the reports illustrating the result obtained with their application to optimize antibody fragments, and nanobodies in particular. Finally, the emerging trends and open questions are summarized.
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Affiliation(s)
- Jiaqi Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Guangbo Kang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jiewen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Haibin Yuan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yili Wu
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and the Affiliated Kangning Hospital, Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Wenzhou Medical University, Oujiang Laboratory, Wenzhou, Zhejiang 325035, China
| | - Shuxian Meng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Ping Wang
- New Technology R&D Department, Tianjin Modern Innovative TCM Technology Company Limited, Tianjin 300392, China
| | - Miao Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; China Resources Biopharmaceutical Company Limited, Beijing 100029, China
| | - Yuli Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Tianjin Pharmaceutical Da Ren Tang Group Corporation Limited, Traditional Chinese Pharmacy Research Institute, Tianjin Key Laboratory of Quality Control in Chinese Medicine, Tianjin 300457, China; State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China
| | - Yuanhang Feng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - He Huang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia.
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5
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Rezhdo A, Lessard CT, Islam M, Van Deventer JA. Strategies for enriching and characterizing proteins with inhibitory properties on the yeast surface. Protein Eng Des Sel 2023; 36:gzac017. [PMID: 36648434 PMCID: PMC10365883 DOI: 10.1093/protein/gzac017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 10/20/2022] [Accepted: 11/07/2022] [Indexed: 01/18/2023] Open
Abstract
Display technologies are powerful tools for discovering binding proteins against a broad range of biological targets. However, it remains challenging to adapt display technologies for the discovery of proteins that inhibit the enzymatic activities of targets. Here, we investigate approaches for discovering and characterizing inhibitory antibodies in yeast display format using a well-defined series of constructs and the target matrix metalloproteinase-9. Three previously reported antibodies were used to create model libraries consisting of inhibitory, non-inhibitory, and non-binding constructs. Conditions that preferentially enrich for inhibitory clones were identified for both magnetic bead-based enrichments and fluorescence-activated cell sorting. Half maximal inhibitory concentration (IC50) was obtained through yeast titration assays. The IC50 of the inhibitory antibody obtained in yeast display format falls within the confidence interval of the IC50 value determined in soluble form. Overall, this study identifies strategies for the discovery and characterization of inhibitory clones directly in yeast display format.
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Affiliation(s)
- Arlinda Rezhdo
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Catherine T Lessard
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - Mariha Islam
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
| | - James A Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, MA 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, MA 02155, USA
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Yin M, Izadi M, Tenglin K, Viennet T, Zhai L, Zheng G, Arthanari H, Dassama LMK, Orkin SH. Evolution of nanobodies specific for BCL11A. Proc Natl Acad Sci U S A 2023; 120:e2218959120. [PMID: 36626555 PMCID: PMC9933118 DOI: 10.1073/pnas.2218959120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Transcription factors (TFs) control numerous genes that are directly relevant to many human disorders. However, developing specific reagents targeting TFs within intact cells is challenging due to the presence of highly disordered regions within these proteins. Intracellular antibodies offer opportunities to probe protein function and validate therapeutic targets. Here, we describe the optimization of nanobodies specific for BCL11A, a validated target for the treatment of hemoglobin disorders. We obtained first-generation nanobodies directed to a region of BCL11A comprising zinc fingers 4 to 6 (ZF456) from a synthetic yeast surface display library, and employed error-prone mutagenesis, structural determination, and molecular modeling to enhance binding affinity. Engineered nanobodies recognized ZF6 and mediated targeted protein degradation (TPD) of BCL11A protein in erythroid cells, leading to the anticipated reactivation of fetal hemoglobin (HbF) expression. Evolved nanobodies distinguished BCL11A from its close paralog BCL11B, which shares an identical DNA-binding specificity. Given the ease of manipulation of nanobodies and their exquisite specificity, nanobody-mediated TPD of TFs should be suitable for dissecting regulatory relationships of TFs and gene targets and validating therapeutic potential of proteins of interest.
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Affiliation(s)
- Maolu Yin
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Manizheh Izadi
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Karin Tenglin
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Thibault Viennet
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, MA02115
- Department of Cancer Biology, Dana-Farber Cancer Institute, MA02215
| | - Liting Zhai
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Ge Zheng
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, MA02115
- Department of Cancer Biology, Dana-Farber Cancer Institute, MA02215
| | - Laura M. K. Dassama
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Stuart H. Orkin
- Dana Farber Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA02115
- HHMI, Harvard Medical School, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
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7
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Modeling and affinity maturation of an anti-CD20 nanobody: a comprehensive in-silico investigation. Sci Rep 2023; 13:582. [PMID: 36631511 PMCID: PMC9834265 DOI: 10.1038/s41598-023-27926-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023] Open
Abstract
B-cell Non-Hodgkin lymphomas are the malignancies of lymphocytes. CD20 is a membrane protein, which is highly expressed on the cell surface of the B-cells in NHL. Treatments using monoclonal antibodies (mAbs) have resulted in failure in some cases. Nanobodies (NBs), single-domain antibodies with low molecular weights and a high specificity in antigen recognition, could be practical alternatives for traditional mAbs with superior characteristics. To design an optimized NB as a candidate CD20 inhibitor with raised binding affinity to CD20, the structure of anti-CD20 NB was optimized to selectively target CD20. The 3D structure of the NB was constructed based on the optimal templates (6C5W and 5JQH), and the key residues were determined by applying a molecular docking study. After identifying the key residues, some mutations were introduced using a rational protocol to improve the binding affinity of the NB to CD20. The rational mutations were conducted using the experimental design (Taguchi method). Six residues (Ser27, Thr28, Phe29, Ile31, Asp99, and Asn100) were selected as the key residues, and five residues were targeted for rational mutation (Trp, Phe, His, Asp, and Tyr). Based on the mutations suggested by the experimental design, two optimized NB structures were constructed. NB2 showed a remarkable binding affinity to CD20 in docking studies with a binding energy of - 853 kcal/mol. The optimized NB was further evaluated using molecular dynamics simulation. The results revealed that CDR1 (complementarity determining regions1) and CDR3 are essential loops for recognizing the antigen. NB2 could be considered as a potential inhibitor of CD20, though experimental evaluations are needed to confirm it.
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8
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Neamtu A, Mocci F, Laaksonen A, Barroso da Silva FL. Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants. Colloids Surf B Biointerfaces 2023; 221:112986. [PMID: 36375294 PMCID: PMC9617679 DOI: 10.1016/j.colsurfb.2022.112986] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/13/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022]
Abstract
A highly efficient and robust multiple scales in silico protocol, consisting of atomistic Molecular Dynamics (MD), coarse-grain (CG) MD, and constant-pH CG Monte Carlo (MC), has been developed and used to study the binding affinities of selected antigen-binding fragments of the monoclonal antibody (mAbs) CR3022 and several of its here optimized versions against 11 SARS-CoV-2 variants including the wild type. Totally 235,000 mAbs structures were initially generated using the RosettaAntibodyDesign software, resulting in top 10 scored CR3022-like-RBD complexes with critical mutations and compared to the native one, all having the potential to block virus-host cell interaction. Of these 10 finalists, two candidates were further identified in the CG simulations to be the best against all SARS-CoV-2 variants. Surprisingly, all 10 candidates and the native CR3022 exhibited a higher affinity for the Omicron variant despite its highest number of mutations. The multiscale protocol gives us a powerful rational tool to design efficient mAbs. The electrostatic interactions play a crucial role and appear to be controlling the affinity and complex building. Studied mAbs carrying a more negative total net charge show a higher affinity. Structural determinants could be identified in atomistic simulations and their roles are discussed in detail to further hint at a strategy for designing the best RBD binder. Although the SARS-CoV-2 was specifically targeted in this work, our approach is generally suitable for many diseases and viral and bacterial pathogens, leukemia, cancer, multiple sclerosis, rheumatoid, arthritis, lupus, and more.
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Affiliation(s)
- Andrei Neamtu
- Department of Physiology, "Grigore T. Popa" University of Medicine and Pharmacy of Iasi, Str. Universitatii nr. 16, 700051 Iasi, România; TRANSCEND Centre - Regional Institute of Oncology (IRO) Iasi, Str. General Henri Mathias Berthelot, Nr. 2-4 Iași, România
| | - Francesca Mocci
- University of Cagliari, Department of Chemical and Geological Sciences, Campus Monserrato, SS 554 bivio per Sestu, 09042 Monserrato, Italy
| | - Aatto Laaksonen
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, PetruPoni Institute of Macromolecular Chemistry Aleea Grigore Ghica-Voda, 41 A, 700487 Iasi, Romania; University of Cagliari, Department of Chemical and Geological Sciences, Campus Monserrato, SS 554 bivio per Sestu, 09042 Monserrato, Italy; Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden; State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing 210009, PR China; Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Fernando L Barroso da Silva
- Universidade de São Paulo, Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. café, s/no - campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.
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9
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Chiba S, Okuno Y, Ohta M. Structure-Based Affinity Maturation of Antibody Based on Double-Point Mutations. Methods Mol Biol 2023; 2552:323-331. [PMID: 36346601 DOI: 10.1007/978-1-0716-2609-2_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Structure-based site-directed affinity maturation of antibodies can be expanded by multiple-point mutations to obtain various mutants. However, selecting the appropriate number of promising mutants for experimental evaluation from the vast number of combinations of multiple-point mutations is challenging. In this report, we describe how to narrow candidate mutants using the so-called weak interaction analysis such as CH-π and CH-O in addition to widely recognized interactions such as hydrogen bonds.
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Affiliation(s)
- Shuntaro Chiba
- RIKEN Center for Computational Science, RIKEN, Yokohama, Japan
| | - Yasushi Okuno
- RIKEN Center for Computational Science, RIKEN, Yokohama, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masateru Ohta
- RIKEN Center for Computational Science, RIKEN, Yokohama, Japan.
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10
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Mahajan SP, Ruffolo JA, Frick R, Gray JJ. Hallucinating structure-conditioned antibody libraries for target-specific binders. Front Immunol 2022; 13:999034. [PMID: 36341416 PMCID: PMC9635398 DOI: 10.3389/fimmu.2022.999034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Antibodies are widely developed and used as therapeutics to treat cancer, infectious disease, and inflammation. During development, initial leads routinely undergo additional engineering to increase their target affinity. Experimental methods for affinity maturation are expensive, laborious, and time-consuming and rarely allow the efficient exploration of the relevant design space. Deep learning (DL) models are transforming the field of protein engineering and design. While several DL-based protein design methods have shown promise, the antibody design problem is distinct, and specialized models for antibody design are desirable. Inspired by hallucination frameworks that leverage accurate structure prediction DL models, we propose the FvHallucinator for designing antibody sequences, especially the CDR loops, conditioned on an antibody structure. Such a strategy generates targeted CDR libraries that retain the conformation of the binder and thereby the mode of binding to the epitope on the antigen. On a benchmark set of 60 antibodies, FvHallucinator generates sequences resembling natural CDRs and recapitulates perplexity of canonical CDR clusters. Furthermore, the FvHallucinator designs amino acid substitutions at the VH-VL interface that are enriched in human antibody repertoires and therapeutic antibodies. We propose a pipeline that screens FvHallucinator designs to obtain a library enriched in binders for an antigen of interest. We apply this pipeline to the CDR H3 of the Trastuzumab-HER2 complex to generate in silico designs predicted to improve upon the binding affinity and interfacial properties of the original antibody. Thus, the FvHallucinator pipeline enables generation of inexpensive, diverse, and targeted antibody libraries enriched in binders for antibody affinity maturation.
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Affiliation(s)
- Sai Pooja Mahajan
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Jeffrey A. Ruffolo
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Rahel Frick
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, United States
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
- *Correspondence: Jeffrey J. Gray,
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11
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In Silico Maturation of a Nanomolar Antibody against the Human CXCR2. Biomolecules 2022; 12:biom12091285. [PMID: 36139124 PMCID: PMC9496334 DOI: 10.3390/biom12091285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
The steady increase in computational power in the last 50 years is opening unprecedented opportunities in biology, as computer simulations of biological systems have become more accessible and can reproduce experimental results more accurately. Here, we wanted to test the ability of computer simulations to replace experiments in the limited but practically useful scope of improving the biochemical characteristics of the abN48 antibody, a nanomolar antagonist of the CXC chemokine receptor 2 (CXCR2) that was initially selected from a combinatorial antibody library. Our results showed a good correlation between the computed binding energies of the antibody to the peptide target and the experimental binding affinities. Moreover, we showed that it is possible to design new antibody sequences in silico with a higher affinity to the desired target using a Monte Carlo Metropolis algorithm. The newly designed sequences had an affinity comparable to the best ones obtained using in vitro affinity maturation and could be obtained within a similar timeframe. The methodology proposed here could represent a valid alternative for improving antibodies in cases in which experiments are too expensive or technically tricky and could open an opportunity for designing antibodies for targets that have been elusive so far.
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12
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Marino M, Zhou L, Rincon MY, Callaerts-Vegh Z, Verhaert J, Wahis J, Creemers E, Yshii L, Wierda K, Saito T, Marneffe C, Voytyuk I, Wouters Y, Dewilde M, Duqué SI, Vincke C, Levites Y, Golde TE, Saido TC, Muyldermans S, Liston A, De Strooper B, Holt MG. AAV-mediated delivery of an anti-BACE1 VHH alleviates pathology in an Alzheimer's disease model. EMBO Mol Med 2022; 14:e09824. [PMID: 35352880 PMCID: PMC8988209 DOI: 10.15252/emmm.201809824] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/18/2023] Open
Abstract
Single domain antibodies (VHHs) are potentially disruptive therapeutics, with important biological value for treatment of several diseases, including neurological disorders. However, VHHs have not been widely used in the central nervous system (CNS), largely because of their restricted blood-brain barrier (BBB) penetration. Here, we propose a gene transfer strategy based on BBB-crossing Adeno-associated virus (AAV)-based vectors to deliver VHH directly into the CNS. As a proof-of-concept, we explored the potential of AAV-delivered VHH to inhibit BACE1, a well-characterized target in Alzheimer's disease. First, we generated a panel of VHHs targeting BACE1, one of which, VHH-B9, shows high selectivity for BACE1 and efficacy in lowering BACE1 activity in vitro. We further demonstrate that a single systemic dose of AAV-VHH-B9 produces positive long-term (12 months plus) effects on amyloid load, neuroinflammation, synaptic function, and cognitive performance, in the AppNL-G-F Alzheimer's disease mouse model. These results constitute a novel therapeutic approach forneurodegenerative diseases, which is applicable to a range of CNS disease targets.
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Affiliation(s)
- Marika Marino
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Lujia Zhou
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Melvin Y Rincon
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | | | - Jens Verhaert
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Jérôme Wahis
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Eline Creemers
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,Electrophysiology Expertise Unit, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Lidia Yshii
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Keimpe Wierda
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,Electrophysiology Expertise Unit, VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Catherine Marneffe
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Iryna Voytyuk
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Yessica Wouters
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Maarten Dewilde
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Sandra I Duqué
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Cécile Vincke
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yona Levites
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Todd E Golde
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako-shi, Japan
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Adrian Liston
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.,Immunology Programme, The Babraham Institute, Cambridge, UK
| | - Bart De Strooper
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,UK Dementia Research institute at UCL, London, UK.,Leuven Brain Institute, Leuven, Belgium
| | - Matthew G Holt
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,Leuven Brain Institute, Leuven, Belgium.,Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
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13
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V HH Structural Modelling Approaches: A Critical Review. Int J Mol Sci 2022; 23:ijms23073721. [PMID: 35409081 PMCID: PMC8998791 DOI: 10.3390/ijms23073721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/20/2022] Open
Abstract
VHH, i.e., VH domains of camelid single-chain antibodies, are very promising therapeutic agents due to their significant physicochemical advantages compared to classical mammalian antibodies. The number of experimentally solved VHH structures has significantly improved recently, which is of great help, because it offers the ability to directly work on 3D structures to humanise or improve them. Unfortunately, most VHHs do not have 3D structures. Thus, it is essential to find alternative ways to get structural information. The methods of structure prediction from the primary amino acid sequence appear essential to bypass this limitation. This review presents the most extensive overview of structure prediction methods applied for the 3D modelling of a given VHH sequence (a total of 21). Besides the historical overview, it aims at showing how model software programs have been shaping the structural predictions of VHHs. A brief explanation of each methodology is supplied, and pertinent examples of their usage are provided. Finally, we present a structure prediction case study of a recently solved VHH structure. According to some recent studies and the present analysis, AlphaFold 2 and NanoNet appear to be the best tools to predict a structural model of VHH from its sequence.
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14
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Van Fossen EM, Grutzius S, Ruby CE, Mourich DV, Cebra C, Bracha S, Karplus PA, Cooley RB, Mehl RA. Creating a Selective Nanobody Against 3-Nitrotyrosine Containing Proteins. Front Chem 2022; 10:835229. [PMID: 35265586 PMCID: PMC8899190 DOI: 10.3389/fchem.2022.835229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
A critical step in developing therapeutics for oxidative stress-related pathologies is the ability to determine which specific modified protein species are innocuous by-products of pathology and which are causative agents. To achieve this goal, technologies are needed that can identify, characterize and quantify oxidative post translational modifications (oxPTMs). Nanobodies (Nbs) represent exquisite tools for intracellular tracking of molecules due to their small size, stability and engineerability. Here, we demonstrate that it is possible to develop a selective Nb against an oxPTM protein, with the key advance being the use of genetic code expansion (GCE) to provide an efficient source of the large quantities of high-quality, homogenous and site-specific oxPTM-containing protein needed for the Nb selection process. In this proof-of-concept study, we produce a Nb selective for a 3-nitrotyrosine (nitroTyr) modified form of the 14-3-3 signaling protein with a lesser recognition of nitroTyr in other protein contexts. This advance opens the door to the GCE-facilitated development of other anti-PTM Nbs.
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Affiliation(s)
- Elise M. Van Fossen
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Sonia Grutzius
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Carl E. Ruby
- Oregon State University, Department of Clinical Sciences, College of Veterinary Medicine, Corvallis, OR, United States
| | - Dan V. Mourich
- Oregon State University, Department of Clinical Sciences, College of Veterinary Medicine, Corvallis, OR, United States
| | - Chris Cebra
- Oregon State University, Department of Clinical Sciences, College of Veterinary Medicine, Corvallis, OR, United States
| | - Shay Bracha
- Department of Small Animal Clinical Sciences (VSCS), Texas A&M College of Veterinary Medicine and Biomedical Sciences, College Station, TX, United States
| | - P. Andrew Karplus
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Richard B. Cooley
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Ryan A. Mehl
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
- *Correspondence: Ryan A. Mehl,
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15
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Wang J, Kang G, Yuan H, Cao X, Huang H, de Marco A. Research Progress and Applications of Multivalent, Multispecific and Modified Nanobodies for Disease Treatment. Front Immunol 2022; 12:838082. [PMID: 35116045 PMCID: PMC8804282 DOI: 10.3389/fimmu.2021.838082] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/30/2021] [Indexed: 12/22/2022] Open
Abstract
Recombinant antibodies such as nanobodies are progressively demonstrating to be a valid alternative to conventional monoclonal antibodies also for clinical applications. Furthermore, they do not solely represent a substitute for monoclonal antibodies but their unique features allow expanding the applications of biotherapeutics and changes the pattern of disease treatment. Nanobodies possess the double advantage of being small and simple to engineer. This combination has promoted extremely diversified approaches to design nanobody-based constructs suitable for particular applications. Both the format geometry possibilities and the functionalization strategies have been widely explored to provide macromolecules with better efficacy with respect to single nanobodies or their combination. Nanobody multimers and nanobody-derived reagents were developed to image and contrast several cancer diseases and have shown their effectiveness in animal models. Their capacity to block more independent signaling pathways simultaneously is considered a critical advantage to avoid tumor resistance, whereas the mass of these multimeric compounds still remains significantly smaller than that of an IgG, enabling deeper penetration in solid tumors. When applied to CAR-T cell therapy, nanobodies can effectively improve the specificity by targeting multiple epitopes and consequently reduce the side effects. This represents a great potential in treating malignant lymphomas, acute myeloid leukemia, acute lymphoblastic leukemia, multiple myeloma and solid tumors. Apart from cancer treatment, multispecific drugs and imaging reagents built with nanobody blocks have demonstrated their value also for detecting and tackling neurodegenerative, autoimmune, metabolic, and infectious diseases and as antidotes for toxins. In particular, multi-paratopic nanobody-based constructs have been developed recently as drugs for passive immunization against SARS-CoV-2 with the goal of impairing variant survival due to resistance to antibodies targeting single epitopes. Given the enormous research activity in the field, it can be expected that more and more multimeric nanobody molecules will undergo late clinical trials in the next future. Systematic Review Registration.
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Affiliation(s)
- Jiewen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Guangbo Kang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Haibin Yuan
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia
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16
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Kielczewska A, D'Angelo I, Amador MS, Wang T, Sudom A, Min X, Rathanaswami P, Pigott C, Foltz IN. Development of a potent high-affinity human therapeutic antibody via novel application of recombination signal sequence-based affinity maturation. J Biol Chem 2021; 298:101533. [PMID: 34973336 PMCID: PMC8808179 DOI: 10.1016/j.jbc.2021.101533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 12/01/2022] Open
Abstract
Therapeutic antibody development requires discovery of an antibody molecule with desired specificities and drug-like properties. For toxicological studies, a therapeutic antibody must bind the ortholog antigen with a similar affinity to the human target to enable relevant dosing regimens, and antibodies falling short of this affinity design goal may not progress as therapeutic leads. Herein, we report the novel use of mammalian recombination signal sequence (RSS)–directed recombination for complementarity-determining region–targeted protein engineering combined with mammalian display to close the species affinity gap of human interleukin (IL)-13 antibody 731. This fully human antibody has not progressed as a therapeutic in part because of a 400-fold species affinity gap. Using this nonhypothesis-driven affinity maturation method, we generated multiple antibody variants with improved IL-13 affinity, including the highest affinity antibody reported to date (34 fM). Resolution of a cocrystal structure of the optimized antibody with the cynomolgus monkey (or nonhuman primate) IL-13 protein revealed that the RSS-derived mutations introduced multiple successive amino-acid substitutions resulting in a de novo formation of a π–π stacking–based protein–protein interaction between the affinity-matured antibody heavy chain and helix C on IL-13, as well as an introduction of an interface-distant residue, which enhanced the light chain–binding affinity to target. These mutations synergized binding of heavy and light chains to the target protein, resulting in a remarkably tight interaction, and providing a proof of concept for a new method of protein engineering, based on synergizing a mammalian display platform with novel RSS-mediated library generation.
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Affiliation(s)
| | - Igor D'Angelo
- Amgen Inc, Therapeutic Discovery, Thousand Oaks, California, USA
| | - Maria Sheena Amador
- Amgen British Columbia, Therapeutic Discovery, Burnaby, British Columbia, Canada
| | - Tina Wang
- Amgen British Columbia, Therapeutic Discovery, Burnaby, British Columbia, Canada
| | - Athena Sudom
- Amgen San Francisco, Therapeutic Discovery, San Francisco, California, USA
| | - Xiaoshan Min
- Amgen San Francisco, Therapeutic Discovery, San Francisco, California, USA
| | | | - Craig Pigott
- Innovative Targeting Solutions, Burnaby, British Columbia, Canada
| | - Ian N Foltz
- Amgen British Columbia, Therapeutic Discovery, Burnaby, British Columbia, Canada
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17
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Kang SH, Lee CH. Development of Therapeutic Antibodies and Modulating the Characteristics of Therapeutic Antibodies to Maximize the Therapeutic Efficacy. BIOTECHNOL BIOPROC E 2021; 26:295-311. [PMID: 34220207 PMCID: PMC8236339 DOI: 10.1007/s12257-020-0181-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023]
Abstract
Monoclonal antibodies (mAb) have been used as therapeutic agents for various diseases, and immunoglobulin G (IgG) is mainly used among antibody isotypes due to its structural and functional properties. So far, regardless of the purpose of the therapeutic antibody, wildtype IgG has been mainly used, but recently, the engineered antibodies with various strategies according to the role of the therapeutic antibody have been used to maximize the therapeutic efficacy. In this review paper, first, the overall structural features and functional characteristics of antibody IgG, second, the old and new techniques for antibody discovery, and finally, several antibody engineering strategies for maximizing therapeutic efficacy according to the role of a therapeutic antibody will be introduced.
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Affiliation(s)
- Seung Hyun Kang
- grid.31501.360000 0004 0470 5905Department of Pharmacology, Seoul National University College of Medicine, Seoul, 03080 Korea
| | - Chang-Han Lee
- grid.31501.360000 0004 0470 5905Department of Pharmacology, Seoul National University College of Medicine, Seoul, 03080 Korea ,grid.31501.360000 0004 0470 5905Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080 Korea ,Hongcheon, 25159 Korea ,grid.31501.360000 0004 0470 5905SNU Dementia Research Center, Seoul National University College of Medicine, Seoul, 03080 Korea
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18
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Brewis N. Improvement of Key Characteristics of Antibodies. LEARNING MATERIALS IN BIOSCIENCES 2021. [DOI: 10.1007/978-3-030-54630-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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19
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Wagner TR, Rothbauer U. Nanobodies Right in the Middle: Intrabodies as Toolbox to Visualize and Modulate Antigens in the Living Cell. Biomolecules 2020; 10:biom10121701. [PMID: 33371447 PMCID: PMC7767433 DOI: 10.3390/biom10121701] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 01/01/2023] Open
Abstract
In biomedical research, there is an ongoing demand for new technologies to elucidate disease mechanisms and develop novel therapeutics. This requires comprehensive understanding of cellular processes and their pathophysiology based on reliable information on abundance, localization, post-translational modifications and dynamic interactions of cellular components. Traceable intracellular binding molecules provide new opportunities for real-time cellular diagnostics. Most prominently, intrabodies derived from antibody fragments of heavy-chain only antibodies of camelids (nanobodies) have emerged as highly versatile and attractive probes to study and manipulate antigens within the context of living cells. In this review, we provide an overview on the selection, delivery and usage of intrabodies to visualize and monitor cellular antigens in living cells and organisms. Additionally, we summarize recent advances in the development of intrabodies as cellular biosensors and their application to manipulate disease-related cellular processes. Finally, we highlight switchable intrabodies, which open entirely new possibilities for real-time cell-based diagnostics including live-cell imaging, target validation and generation of precisely controllable binding reagents for future therapeutic applications.
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Affiliation(s)
- Teresa R. Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
- Correspondence: ; Tel.: +49-7121-5153-0415; Fax: +49-7121-5153-0816
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20
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Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis. Sci Rep 2020; 10:17590. [PMID: 33067496 PMCID: PMC7567794 DOI: 10.1038/s41598-020-74545-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/05/2020] [Indexed: 01/21/2023] Open
Abstract
The generation of a wide range of candidate antibodies is important for the successful development of drugs that simultaneously satisfy multiple requirements. To find cooperative mutations and increase the diversity of mutants, an in silico double-point mutation approach, in which 3D models of all possible double-point mutant/antigen complexes are constructed and evaluated using interaction analysis, was developed. Starting from an antibody with very high affinity, four double-point mutants were designed in silico. Two of the double-point mutants exhibited improved affinity or affinity comparable to that of the starting antibody. The successful identification of two active double-point mutants showed that a cooperative mutation could be found by utilizing information regarding the interactions. The individual single-point mutants of the two active double-point mutants showed decreased affinity or no expression. These results suggested that the two active double-point mutants cannot be obtained through the usual approach i.e. a combination of improved single-point mutants. In addition, a triple-point mutant, which combines the distantly located active double-point mutation and an active single-point mutation collaterally obtained in the process of the double-point mutation strategy, was designed. The triple-point mutant showed improved affinity. This finding suggested that the effects of distantly located mutations are independent and additive. The double-point mutation approach using the interaction analysis of 3D structures expands the design repertoire for mutants, and hopefully paves a way for the identification of cooperative multiple-point mutations.
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21
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Vascon F, Gasparotto M, Giacomello M, Cendron L, Bergantino E, Filippini F, Righetto I. Protein electrostatics: From computational and structural analysis to discovery of functional fingerprints and biotechnological design. Comput Struct Biotechnol J 2020; 18:1774-1789. [PMID: 32695270 PMCID: PMC7355722 DOI: 10.1016/j.csbj.2020.06.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/31/2022] Open
Abstract
Computationally driven engineering of proteins aims to allow them to withstand an extended range of conditions and to mediate modified or novel functions. Therefore, it is crucial to the biotechnological industry, to biomedicine and to afford new challenges in environmental sciences, such as biocatalysis for green chemistry and bioremediation. In order to achieve these goals, it is important to clarify molecular mechanisms underlying proteins stability and modulating their interactions. So far, much attention has been given to hydrophobic and polar packing interactions and stability of the protein core. In contrast, the role of electrostatics and, in particular, of surface interactions has received less attention. However, electrostatics plays a pivotal role along the whole life cycle of a protein, since early folding steps to maturation, and it is involved in the regulation of protein localization and interactions with other cellular or artificial molecules. Short- and long-range electrostatic interactions, together with other forces, provide essential guidance cues in molecular and macromolecular assembly. We report here on methods for computing protein electrostatics and for individual or comparative analysis able to sort proteins by electrostatic similarity. Then, we provide examples of electrostatic analysis and fingerprints in natural protein evolution and in biotechnological design, in fields as diverse as biocatalysis, antibody and nanobody engineering, drug design and delivery, molecular virology, nanotechnology and regenerative medicine.
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Affiliation(s)
- Filippo Vascon
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Italy
| | - Matteo Gasparotto
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Italy
| | - Marta Giacomello
- Bioenergetic Organelles Unit, Department of Biology, University of Padua, Italy
- Department of Biomedical Sciences, University of Padua, Italy
| | - Laura Cendron
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Italy
| | - Elisabetta Bergantino
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Italy
| | - Francesco Filippini
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Italy
| | - Irene Righetto
- Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padua, Italy
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22
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Hacisuleyman A, Erman B. ModiBodies: A computational method for modifying nanobodies in nanobody-antigen complexes to improve binding affinity and specificity. J Biol Phys 2020; 46:189-208. [PMID: 32418062 DOI: 10.1007/s10867-020-09548-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/28/2020] [Indexed: 11/26/2022] Open
Abstract
Nanobodies are special derivatives of antibodies, which consist of single domain fragments. They have become of considerable interest as next-generation biotechnological tools for antigen recognition. They can be easily engineered due to their high stability and compact size. Nanobodies have three complementarity-determining regions, CDRs, which are enlarged to provide a similar binding surface to that of human immunoglobulins. Here, we propose a benchmark testing algorithm that uses 3D structures of already existing protein-nanobody complexes as initial structures followed by successive mutations on the CDR domains. The aim is to find optimum binding amino acids for hypervariable residues of CDRs. We use molecular dynamics simulations to compare the binding energies of the resulting complexes with that of the known complex and accept those that are improved by mutations. We use the MDM4-VH9 complex, (PDB id 2VYR), fructose-bisphosphate aldolase from Trypanosoma congolense (PDB id 5O0W) and human lysozyme (PDB id 4I0C) as benchmark complexes. By using this algorithm, better binding nanobodies can be generated in a short amount of time. We suggest that this method can complement existing immune and synthetic library-based methods, without a need for extensive experimentation or large libraries.
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Affiliation(s)
- Aysima Hacisuleyman
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey.
| | - Burak Erman
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
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de Marco A. Recombinant expression of nanobodies and nanobody-derived immunoreagents. Protein Expr Purif 2020; 172:105645. [PMID: 32289357 PMCID: PMC7151424 DOI: 10.1016/j.pep.2020.105645] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022]
Abstract
Antibody fragments for which the sequence is available are suitable for straightforward engineering and expression in both eukaryotic and prokaryotic systems. When produced as fusions with convenient tags, they become reagents which pair their selective binding capacity to an orthogonal function. Several kinds of immunoreagents composed by nanobodies and either large proteins or short sequences have been designed for providing inexpensive ready-to-use biological tools. The possibility to choose among alternative expression strategies is critical because the fusion moieties might require specific conditions for correct folding or post-translational modifications. In the case of nanobody production, the trend is towards simpler but reliable (bacterial) methods that can substitute for more cumbersome processes requiring the use of eukaryotic systems. The use of these will not disappear, but will be restricted to those cases in which the final immunoconstructs must have features that cannot be obtained in prokaryotic cells. At the same time, bacterial expression has evolved from the conventional procedure which considered exclusively the nanobody and nanobody-fusion accumulation in the periplasm. Several reports show the advantage of cytoplasmic expression, surface-display and secretion for at least some applications. Finally, there is an increasing interest to use as a model the short nanobody sequence for the development of in silico methodologies aimed at optimizing the yields, stability and affinity of recombinant antibodies. There is an increasing request for immunoreagents based on nanobodies. The multiplicity of their applications requires constructs with different structural complexity. Alternative expression methods are necessary to achieve such structural requirements. In silico optimization of nanobody biophysical characteristics becomes more and more reliable.
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Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, S-5000, Nova Gorica, Slovenia.
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24
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Teil M, Arotcarena ML, Faggiani E, Laferriere F, Bezard E, Dehay B. Targeting α-synuclein for PD Therapeutics: A Pursuit on All Fronts. Biomolecules 2020; 10:biom10030391. [PMID: 32138193 PMCID: PMC7175302 DOI: 10.3390/biom10030391] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 12/15/2022] Open
Abstract
Parkinson's Disease (PD) is characterized both by the loss of dopaminergic neurons in the substantia nigra and the presence of cytoplasmic inclusions called Lewy Bodies. These Lewy Bodies contain the aggregated α-synuclein (α-syn) protein, which has been shown to be able to propagate from cell to cell and throughout different regions in the brain. Due to its central role in the pathology and the lack of a curative treatment for PD, an increasing number of studies have aimed at targeting this protein for therapeutics. Here, we reviewed and discussed the many different approaches that have been studied to inhibit α-syn accumulation via direct and indirect targeting. These analyses have led to the generation of multiple clinical trials that are either completed or currently active. These clinical trials and the current preclinical studies must still face obstacles ahead, but give hope of finding a therapy for PD with time.
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Affiliation(s)
- Margaux Teil
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France; (M.T.); (M.-L.A.); (E.F.); (F.L.); (E.B.)
- CNRS, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France
| | - Marie-Laure Arotcarena
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France; (M.T.); (M.-L.A.); (E.F.); (F.L.); (E.B.)
- CNRS, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France
| | - Emilie Faggiani
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France; (M.T.); (M.-L.A.); (E.F.); (F.L.); (E.B.)
- CNRS, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France
| | - Florent Laferriere
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France; (M.T.); (M.-L.A.); (E.F.); (F.L.); (E.B.)
- CNRS, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France
| | - Erwan Bezard
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France; (M.T.); (M.-L.A.); (E.F.); (F.L.); (E.B.)
- CNRS, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France
| | - Benjamin Dehay
- Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France; (M.T.); (M.-L.A.); (E.F.); (F.L.); (E.B.)
- CNRS, Institut des Maladies Neurodégénératives, UMR 5293, F-33000 Bordeaux, France
- Correspondence:
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25
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Optimizing intracellular antibodies (intrabodies/nanobodies) to treat neurodegenerative disorders. Neurobiol Dis 2020; 134:104619. [DOI: 10.1016/j.nbd.2019.104619] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/05/2019] [Accepted: 09/19/2019] [Indexed: 01/27/2023] Open
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26
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Akiba H, Tamura H, Caaveiro JMM, Tsumoto K. Computer-guided library generation applied to the optimization of single-domain antibodies. Protein Eng Des Sel 2019; 32:423-431. [PMID: 32167147 DOI: 10.1093/protein/gzaa006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/30/2020] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
Computer-guided library generation is a plausible strategy to optimize antibodies. Herein, we report the improvement of the affinity of a single-domain camelid antibody for its antigen using such approach. We first conducted experimental and computational alanine scanning to describe the precise energetic profile of the antibody-antigen interaction surface. Based on this characterization, we hypothesized that in-silico mutagenesis could be employed to guide the development of a small library for phage display with the goal of improving the affinity of an antibody for its antigen. Optimized antibody mutants were identified after three rounds of selection, in which an alanine residue at the core of the antibody-antigen interface was substituted by residues with large side-chains, generating diverse kinetic responses, and resulting in greater affinity (>10-fold) for the antigen.
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Affiliation(s)
- Hiroki Akiba
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki 567-0085, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroko Tamura
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kouhei Tsumoto
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki 567-0085, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Medical Proteomics Laboratory, Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8629, Japan
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Soler MA, Medagli B, Semrau MS, Storici P, Bajc G, de Marco A, Laio A, Fortuna S. A consensus protocol for the in silico optimisation of antibody fragments. Chem Commun (Camb) 2019; 55:14043-14046. [PMID: 31690899 DOI: 10.1039/c9cc06182g] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We present an in silico mutagenetic protocol for improving the binding affinity of single domain antibodies (or nanobodies, VHHs). The method iteratively attempts random mutations in the interacting region of the protein and evaluates the resulting binding affinity towards the target by scoring, with a collection of scoring functions, short explicit solvent molecular dynamics trajectories of the binder-target complexes. The acceptance/rejection of each attempted mutation is carried out by a consensus decision-making algorithm, which considers all individual assessments derived from each scoring function. The method was benchmarked by evolving a single complementary determining region (CDR) of an anti-HER2 VHH hit obtained by direct panning of a phage display library. The optimised VHH mutant showed significantly enhanced experimental affinity with respect to the original VHH it matured from. The protocol can be employed as it is for the optimization of peptides, antibody fragments, and (given enough computational power) larger antibodies.
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Affiliation(s)
- Miguel A Soler
- International School for Advanced Studies (SISSA), Via Bonomea 265, 34136, Trieste, Italy.
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Longhena F, Faustini G, Brembati V, Pizzi M, Bellucci A. The good and bad of therapeutic strategies that directly target α-synuclein. IUBMB Life 2019; 72:590-600. [PMID: 31693290 DOI: 10.1002/iub.2194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/12/2019] [Indexed: 12/16/2022]
Abstract
Synucleinopathies are neurodegenerative diseases characterized by the accumulation of either neuronal/axonal or glial insoluble proteinaceous aggregates mainly composed of α-synuclein (α-syn). Among them, the most common disorders are Parkinson's disease, dementia with Lewy bodies, multiple system atrophy, and some forms of familial parkinsonism. Both α-syn fibrils and oligomers have been found to exert toxic effects on neurons or oligodendroglial cells, can activate neuroinflammatory responses, and mediate the spreading of α-syn pathology. This poses the question of which is the most toxic α-syn species. What is worst, α-syn appears as a very peculiar protein, exerting multiple physiological functions in neurons, especially at synapses, but without acquiring a stable tertiary structure. Its conformation is particularly plastic, and the protein can exist in a natively unfolded state (mainly in solution), partially α-helical folded state (when it interacts with biological membranes), or oligomeric state (tetramers or dimers with debated functional profile). The extent of α-syn expression impinges on the resilience of neuronal cells, as multiplications of its gene locus, or overexpression, can cause neurodegeneration and onset of motor phenotype. For these reasons, one of the main challenges in the field of synucleinopathies, which still nowadays can only be managed by symptomatic therapies, has been the development of strategies aimed at reducing α-syn levels, oligomer formation, fibrillation, or cell-to-cell transmission. This review resumes the therapeutic approaches that have been proposed or are under development to counteract α-syn pathology by direct targeting of this protein and discuss their pros and cons in relation to the current state-of-the-art α-syn biology.
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Affiliation(s)
- Francesca Longhena
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Gaia Faustini
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Viviana Brembati
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Marina Pizzi
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Arianna Bellucci
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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29
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Tabasinezhad M, Talebkhan Y, Wenzel W, Rahimi H, Omidinia E, Mahboudi F. Trends in therapeutic antibody affinity maturation: From in-vitro towards next-generation sequencing approaches. Immunol Lett 2019; 212:106-113. [PMID: 31247224 DOI: 10.1016/j.imlet.2019.06.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/08/2019] [Accepted: 06/24/2019] [Indexed: 12/12/2022]
Abstract
Current advances in antibody engineering driving the strongest growth area in biotherapeutic agents development. Affinity improvement that is mainly important for biological activity and clinical efficacy of therapeutic antibodies, has still remained a challenging task. In the human body, during a course of immune response affinity maturation increase antibody activity by several rounds of somatic hypermutation and clonal selection in the germinal center. The final outputs are antibodies representing higher affinity and specificity against a particular antigen. In the realm of biotechnology, exploring of mutations which improve antibody affinity while preserving its specificity and stability is an extremely time-consuming and laborious process. Recent advances in computational algorithms and DNA sequencing technologies help researchers to redesign antibody structure to achieve desired properties such as improved binding affinity. In this review, we briefly described the principle of affinity maturation and different corresponding in vitro techniques. Also, we recapitulated the most recent advancements in the field of antibody affinity maturation including computational approaches and next-generation sequencing (NGS).
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Affiliation(s)
- Maryam Tabasinezhad
- Biotechnology Research Centre, Pasteur Institute of Iran, Tehran, Iran; Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Yeganeh Talebkhan
- Biotechnology Research Centre, Pasteur Institute of Iran, Tehran, Iran
| | - Wolfgang Wenzel
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Hamzeh Rahimi
- Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
| | - Eskandar Omidinia
- Genetics & Metabolism Research Centre, Pasteur Institute of Iran, Tehran, Iran.
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30
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Cannon DA, Shan L, Du Q, Shirinian L, Rickert KW, Rosenthal KL, Korade M, van Vlerken-Ysla LE, Buchanan A, Vaughan TJ, Damschroder MM, Popovic B. Experimentally guided computational antibody affinity maturation with de novo docking, modelling and rational design. PLoS Comput Biol 2019; 15:e1006980. [PMID: 31042706 PMCID: PMC6513101 DOI: 10.1371/journal.pcbi.1006980] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/13/2019] [Accepted: 03/27/2019] [Indexed: 01/05/2023] Open
Abstract
Antibodies are an important class of therapeutics that have significant clinical impact for the treatment of severe diseases. Computational tools to support antibody drug discovery have been developing at an increasing rate over the last decade and typically rely upon a predetermined co-crystal structure of the antibody bound to the antigen for structural predictions. Here, we show an example of successful in silico affinity maturation of a hybridoma derived antibody, AB1, using just a homology model of the antibody fragment variable region and a protein-protein docking model of the AB1 antibody bound to the antigen, murine CCL20 (muCCL20). In silico affinity maturation, together with alanine scanning, has allowed us to fine-tune the protein-protein docking model to subsequently enable the identification of two single-point mutations that increase the affinity of AB1 for muCCL20. To our knowledge, this is one of the first examples of the use of homology modelling and protein docking for affinity maturation and represents an approach that can be widely deployed.
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Affiliation(s)
- Daniel A. Cannon
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Cambridge, United Kingdom
| | - Lu Shan
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, United States of America
| | - Qun Du
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, United States of America
| | - Lena Shirinian
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, United States of America
| | - Keith W. Rickert
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, United States of America
| | - Kim L. Rosenthal
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, United States of America
| | - Martin Korade
- Department of Oncology Research, AstraZeneca, Gaithersburg, Maryland, United States of America
| | | | - Andrew Buchanan
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Cambridge, United Kingdom
| | - Tristan J. Vaughan
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Cambridge, United Kingdom
| | - Melissa M. Damschroder
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Gaithersburg, Maryland, United States of America
| | - Bojana Popovic
- Department of Antibody Discovery and Protein Engineering, AstraZeneca, Cambridge, United Kingdom
- * E-mail:
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