1
|
Yap SY, Butcher T, Spears RJ, McMahon C, Thanasi IA, Baker JR, Chudasama V. Chemo- and regio-selective differential modification of native cysteines on an antibody via the use of dehydroalanine forming reagents. Chem Sci 2024; 15:8557-8568. [PMID: 38846383 PMCID: PMC11151841 DOI: 10.1039/d4sc00392f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Protein modification has garnered increasing interest over the past few decades and has become an important tool in many aspects of chemical biology. In recent years, much effort has focused on site-selective modification strategies that generate more homogenous bioconjugates, and this is particularly so in the antibody modification space. Modifying native antibodies by targeting solvent-accessible cysteines liberated by interchain disulfide reduction is, perhaps, the predominant strategy for achieving more site-selectivity on an antibody scaffold. This is evidenced by numerous approved antibody therapeutics that have utilised cysteine-directed conjugation reagents and the plethora of methods/strategies focused on antibody cysteine modification. However, all of these methods have a common feature in that after the reduction of native solvent-accessible cystines, the liberated cysteines are all reacted in the same manner. Herein, we report the discovery and application of dehydroalanine forming reagents (including novel reagents) capable of regio- and chemo-selectively modifying these cysteines (differentially) on a clinically relevant antibody fragment and a full antibody. We discovered that these reagents could enable differential reactivity between light chain C-terminal cysteines, heavy chain hinge region cysteines (cysteines with an adjacent proline residue, Cys-Pro), and other heavy chain internal cysteines. This differential reactivity was also showcased on small molecules and on the peptide somatostatin. The application of these dehydroalanine forming reagents was exemplified in the preparation of a dually modified antibody fragment and full antibody. Additionally, we discovered that readily available amide coupling agents can be repurposed as dehydroalanine forming reagents, which could be of interest to the broader field of chemical biology.
Collapse
Affiliation(s)
- Steven Y Yap
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Tobias Butcher
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Richard J Spears
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Clíona McMahon
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Ioanna A Thanasi
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - James R Baker
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Vijay Chudasama
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| |
Collapse
|
2
|
Hanaee-Ahvaz H, Cserjan-Puschmann M, Mayer F, Tauer C, Albrecht B, Furtmüller PG, Wiltschi B, Hahn R, Striedner G. Antibody fragments functionalized with non-canonical amino acids preserving structure and functionality - A door opener for new biological and therapeutic applications. Heliyon 2023; 9:e22463. [PMID: 38046162 PMCID: PMC10686840 DOI: 10.1016/j.heliyon.2023.e22463] [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: 07/28/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/05/2023] Open
Abstract
Functionalization of proteins by incorporating reactive non-canonical amino acids (ncAAs) has been widely applied for numerous biological and therapeutic applications. The requirement not to lose the intrinsic properties of these proteins is often underestimated and not considered. Main purpose of this study was to answer the question whether functionalization via residue-specific incorporation of the ncAA N6-[(2-Azidoethoxy) carbonyl]-l-lysine (Azk) influences the properties of the anti-tumor-necrosis-factor-α-Fab (FTN2). Therefore, FTN2Azk variants with different Azk incorporation sites were designed and amber codon suppression was used for production. The functionalized FTN2Azk variants were efficiently produced in fed-batch like μ-bioreactor cultivations in the periplasm of E. coli displaying correct structure and antigen binding affinities comparable to those of wild-type FTN2. Our FTN2Azk variants with reactive handles for diverse conjugates enable tracking of recombinant protein in the production cell, pharmacological studies and translation into new pharmaceutical applications.
Collapse
Affiliation(s)
- Hana Hanaee-Ahvaz
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Florian Mayer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Christopher Tauer
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Bernd Albrecht
- Biopharma Austria, Process Science, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, A-1121, Vienna, Austria
| | - Paul G. Furtmüller
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, 1190, Vienna, Austria
| | - Birgit Wiltschi
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Rainer Hahn
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Bioprocess Science and Engineering, Muthgasse 18, 1190, Vienna, Austria
| |
Collapse
|
3
|
Oeller M, Kang RJD, Bolt HL, Gomes Dos Santos AL, Weinmann AL, Nikitidis A, Zlatoidsky P, Su W, Czechtizky W, De Maria L, Sormanni P, Vendruscolo M. Sequence-based prediction of the intrinsic solubility of peptides containing non-natural amino acids. Nat Commun 2023; 14:7475. [PMID: 37978172 PMCID: PMC10656490 DOI: 10.1038/s41467-023-42940-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
Non-natural amino acids are increasingly used as building blocks in the development of peptide-based drugs as they expand the available chemical space to tailor function, half-life and other key properties. However, while the chemical space of modified amino acids (mAAs) such as residues containing post-translational modifications (PTMs) is potentially vast, experimental methods for measuring the developability properties of mAA-containing peptides are expensive and time consuming. To facilitate developability programs through computational methods, we present CamSol-PTM, a method that enables the fast and reliable sequence-based prediction of the intrinsic solubility of mAA-containing peptides in aqueous solution at room temperature. From a computational screening of 50,000 mAA-containing variants of three peptides, we selected five different small-size mAAs for a total number of 37 peptide variants for experimental validation. We demonstrate the accuracy of the predictions by comparing the calculated and experimental solubility values. Our results indicate that the computational screening of mAA-containing peptides can extend by over four orders of magnitude the ability to explore the solubility chemical space of peptides and confirm that our method can accurately assess the solubility of peptides containing mAAs. This method is available as a web server at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolptm .
Collapse
Affiliation(s)
- Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ryan J D Kang
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Bolt
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ana L Gomes Dos Santos
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Annika Langborg Weinmann
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Antonios Nikitidis
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pavol Zlatoidsky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wu Su
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| |
Collapse
|
4
|
Liu C, Lin H, Cao L, Wang K, Sui J. Research progress on unique paratope structure, antigen binding modes, and systematic mutagenesis strategies of single-domain antibodies. Front Immunol 2022; 13:1059771. [PMID: 36479130 PMCID: PMC9720397 DOI: 10.3389/fimmu.2022.1059771] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/07/2022] [Indexed: 11/22/2022] Open
Abstract
Single-domain antibodies (sdAbs) showed the incredible advantages of small molecular weight, excellent affinity, specificity, and stability compared with traditional IgG antibodies, so their potential in binding hidden antigen epitopes and hazard detection in food, agricultural and veterinary fields were gradually explored. Moreover, its low immunogenicity, easy-to-carry target drugs, and penetration of the blood-brain barrier have made sdAbs remarkable achievements in medical treatment, toxin neutralization, and medical imaging. With the continuous development and maturity of modern molecular biology, protein analysis software and database with different algorithms, and next-generation sequencing technology, the unique paratope structure and different antigen binding modes of sdAbs compared with traditional IgG antibodies have aroused the broad interests of researchers with the increased related studies. However, the corresponding related summaries are lacking and needed. Different antigens, especially hapten antigens, show distinct binding modes with sdAbs. So, in this paper, the unique paratope structure of sdAbs, different antigen binding cases, and the current maturation strategy of sdAbs were classified and summarized. We hope this review lays a theoretical foundation to elucidate the antigen-binding mechanism of sdAbs and broaden the further application of sdAbs.
Collapse
|
5
|
He F, Wang J, Yuan D, Liu Y, Liu R, Zong W. Ferric ions release from iron-binding protein: Interaction between acrylamide and human serum transferrin and the underlying mechanisms of their binding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157583. [PMID: 35882343 DOI: 10.1016/j.scitotenv.2022.157583] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Acrylamide (ACR) is a surprisingly common chemical due to its widespread use in industry and various other applications. However, its toxicity is a matter of grave concern for public health. Even worse, ACR is frequently detected in numerous fried or baked carbohydrate-rich foods due to the Maillard browning reaction. Herein, this study intends to delineate the underlying molecular mechanisms of Fe ions released from iron-binding protein transferrin (TF) after acrylamide binding by combining multiple methods, including multiple complementary spectroscopic techniques (UV-Vis, fluorescence, and circular dichroism spectroscopy), isothermal titration calorimetry, ICP-MS measurements, and modeling simulations. Results indicated that free Fe was released from TF only under high-dose ACR exposure (>100 μM). Acrylamide binding induced the loosening and unfolding of the backbone and polypeptide chain and destroyed the secondary structure of TF, thereby leading to protein misfolding and denaturation of TF and forming a larger size of TF agglomerates. Of which, H-binding and van der Waals force are the primary driving force during the binding interaction between ACR and TF. Further modeling simulations illustrated that ACR prefers to bind to the hinge region connecting the C-lobe and N-lobe, after that it attaches to the Fe binding sites of this protein, which is the cause of free Fe release from TF. Moreover, ACR interacted with the critical fluorophore residues (Tyr, Trp, and Phe) in the binding pocket, which might explain such a phenomenon of fluorescence sensitization. The two binding sites (Site 2 and Site 3) located around the Fe (III) ions with low-energy conformations are more suitable for ACR binding. Collectively, our study demonstrated that the loss of iron in TF caused by acrylamide-induced structural and conformational changes of transferrin.
Collapse
Affiliation(s)
- Falin He
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Jinhu Wang
- College of Chemistry, Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong 277160, PR China
| | - Dong Yuan
- Department of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250013, PR China.
| | - Yang Liu
- Department of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250013, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China.
| | - Wansong Zong
- College of Geography and Environment, Shandong Normal University, 88# East Wenhua Road, Jinan, Shandong 250014, PR China
| |
Collapse
|
6
|
Stadler KA, Becker W, Darnhofer B, Birner-Gruenberger R, Zangger K. Overexpression of recombinant proteins containing non-canonical amino acids in Vibrio natriegens: p-azido-L-phenylalanine as coupling site for 19F-tags. Amino Acids 2022; 54:1041-1053. [PMID: 35419750 PMCID: PMC9217835 DOI: 10.1007/s00726-022-03148-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/27/2022] [Indexed: 11/26/2022]
Abstract
Vibrio natriegens is the fastest growing organism identified so far. The minimum doubling time of only 9.4 min, the ability to utilize over 60 different carbon sources and its non-pathogenic properties make it an interesting alternative to E. coli as a new production host for recombinant proteins. We investigated the ability of the engineered V. natriegens strain, Vmax™ Express, to incorporate the non-canonical amino acid (ncAA) p-azido-L-phenylalanine (AzF) into recombinant proteins for NMR applications. AzF was incorporated into enhanced yellow fluorescent protein (EYFP) and MlaC, an intermembrane transport protein, by stop codon suppression. AzF incorporation into EYFP resulted in an improved suppression efficiency (SE) of up to 35.5 ± 0.8% and a protein titer of 26.7 ± 0.7 mg/L. The expression levels of MlaC-AzF even exceeded those of E. coli BL21 cells. For the recording of 1H-15N and 19F NMR spectra, EYFP-AzF was expressed and isotopically labeled in minimal medium and the newly introduced azido-group was used as coupling site for NMR sensitive 19F-tags. Our findings show that Vmax is a flexible expression host, suitable for the incorporation of ncAAs in recombinant proteins with the potential to surpass protein yields of E. coli. The presented method suggests the implementation of V. natriegens for expression of isotopically labeled proteins containing ncAAs, which can be chemically modified for the application in protein-observed 19F-NMR.
Collapse
Affiliation(s)
- Karina A Stadler
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Walter Becker
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 17177, Stockholm, Sweden
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
| | - Ruth Birner-Gruenberger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Technische Universität Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - Klaus Zangger
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria.
| |
Collapse
|
7
|
Ge Y, Masoura A, Yang J, Aprile FA. A Chemical Mutagenesis Approach to Insert Post-translational Modifications in Aggregation-Prone Proteins. ACS Chem Neurosci 2022; 13:1714-1718. [PMID: 35609278 PMCID: PMC9204764 DOI: 10.1021/acschemneuro.2c00077] [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] [Indexed: 11/30/2022] Open
Abstract
Neurodegenerative diseases are a class of disorders linked to the formation in the nervous system of fibrillar protein aggregates called amyloids. This aggregation process is affected by a variety of post-translational modifications, whose specific mechanisms are not fully understood yet. Emerging chemical mutagenesis technology is currently striving to address the challenge of introducing protein post-translational modifications, while maintaining the stability and solubility of the proteins during the modification reaction. Several amyloidogenic proteins are highly aggregation-prone, and current modification procedures can lead to unexpected precipitation of these proteins, affecting their yield and downstream characterization. Here, we present a method for maintaining amyloidogenic protein solubility during chemical mutagenesis. As proof-of-principle, we applied our method to mimic the phosphorylation of serine-26 and the acetylation of lysine-28 of the 40-residue long variant of amyloid-β peptide, whose aggregation is linked to Alzheimer's disease.
Collapse
Affiliation(s)
- Ying Ge
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
| | - Athina Masoura
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
| | - Jingzhou Yang
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
| | - Francesco A. Aprile
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom,Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom,
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Lin J, Figazzolo C, Metrick MA, Sormanni P, Vendruscolo M. Computational maturation of a single-domain antibody against Aβ42 aggregation. Chem Sci 2021; 12:13940-13948. [PMID: 35475123 PMCID: PMC8901120 DOI: 10.1039/d1sc03898b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/23/2021] [Indexed: 02/02/2023] Open
Abstract
The expansion of structural databases and the increase in computing power are enabling approaches for antibody discovery based on computational design. It has already been shown that it is possible to use this approach to generate antibodies for specific epitopes on challenging targets. Here we describe an application of this procedure for antibody maturation through the computational design of mutational variants of increased potency. We illustrate this procedure in the case of a single-domain antibody targeting an epitope in the N-terminal region of Aβ42, a peptide whose aggregation is closely associated with Alzheimer's disease. We show that this approach enables the generation of an antibody variant with over 200-fold increased potency against the primary nucleation process in Aβ42 aggregation. Our results thus demonstrate that potentiated antibody variants can be obtained by computational maturation. A computational maturation method enables the generation of an antibody variant with over 200-fold increased potency against the primary nucleation process in Aβ42 aggregation.![]()
Collapse
Affiliation(s)
- Jiacheng Lin
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Chiara Figazzolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Michael A Metrick
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| |
Collapse
|
10
|
Laserna V, Abegg D, Afonso CF, Martin EM, Adibekian A, Ravn P, Corzana F, Bernardes GJL. Dichloro Butenediamides as Irreversible Site‐Selective Protein Conjugation Reagent. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Victor Laserna
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Daniel Abegg
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter Fl 33458 USA
| | - Cláudia F. Afonso
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Esther M. Martin
- AstraZeneca R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE), Milstein Building Granta Park Cambridge CB21 6GH UK
| | - Alexander Adibekian
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter Fl 33458 USA
| | - Peter Ravn
- AstraZeneca R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE), Milstein Building Granta Park Cambridge CB21 6GH UK
- Department of Biotherapeutic Discovery H. Lundbeck A/S Ottiliavej 9 2500 Valby Denmark
| | - Francisco Corzana
- Departamento de Química Centro de Investigación en Síntesis Química Universidad de La Rioja 26006 Logroño Spain
| | - Gonçalo J. L. Bernardes
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road CB2 1EW Cambridge UK
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| |
Collapse
|
11
|
Laserna V, Abegg D, Afonso CF, Martin EM, Adibekian A, Ravn P, Corzana F, Bernardes GJL. Dichloro Butenediamides as Irreversible Site-Selective Protein Conjugation Reagent. Angew Chem Int Ed Engl 2021; 60:23750-23755. [PMID: 34472678 PMCID: PMC8596790 DOI: 10.1002/anie.202108791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/04/2021] [Indexed: 01/21/2023]
Abstract
We describe maleic-acid derivatives as robust cysteine-selective reagents for protein labelling with comparable kinetics and superior stability relative to maleimides. Diamide and amido-ester derivatives proved to be efficient protein-labelling species with a common mechanism in which a spontaneous cyclization occurs upon addition to cysteine. Introduction of chlorine atoms in their structures triggers ring hydrolysis or further conjugation with adjacent residues, which results in conjugates that are completely resistant to retro-Michael reactions in the presence of biological thiols and human plasma. By controlling the microenvironment of the reactive site, we can control selectivity towards the hydrolytic pathway, forming homogeneous conjugates. The method is applicable to several scaffolds and enables conjugation of different payloads. The synthetic accessibility of these reagents and the mild conditions required for fast and complete conjugation together with the superior stability of the conjugates make this strategy an important alternative to maleimides in bioconjugation.
Collapse
Affiliation(s)
- Victor Laserna
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Daniel Abegg
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Fl, 33458, USA
| | - Cláudia F Afonso
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Esther M Martin
- AstraZeneca, R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE), Milstein Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Fl, 33458, USA
| | - Peter Ravn
- AstraZeneca, R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE), Milstein Building, Granta Park, Cambridge, CB21 6GH, UK.,Department of Biotherapeutic Discovery, H. Lundbeck A/S, Ottiliavej 9, 2500, Valby, Denmark
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006, Logroño, Spain
| | - Gonçalo J L Bernardes
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| |
Collapse
|
12
|
Islam M, Kehoe HP, Lissoos JB, Huang M, Ghadban CE, Sánchez GB, Lane HZ, Van Deventer JA. Chemical Diversification of Simple Synthetic Antibodies. ACS Chem Biol 2021; 16:344-359. [PMID: 33482061 PMCID: PMC8096149 DOI: 10.1021/acschembio.0c00865] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibodies possess properties that make them valuable as therapeutics, diagnostics, and basic research tools. However, antibody chemical reactivity and covalent antigen binding are constrained, or even prevented, by the narrow range of chemistries encoded in canonical amino acids. In this work, we investigate strategies for leveraging an expanded range of chemical functionality using yeast displayed antibodies containing noncanonical amino acids (ncAAs) in or near antibody complementarity determining regions (CDRs). To enable systematic characterization of the effects of ncAA incorporation on antibody function, we first investigated whether diversification of a single antibody loop would support the isolation of binding clones against immunoglobulins from three species. We constructed and screened a billion-member library containing canonical amino acid diversity and loop length diversity only within the third complementarity determining region of the heavy chain (CDR-H3). Isolated clones exhibited moderate affinities (double- to triple-digit nanomolar affinities) and, in several cases, single-species specificity, confirming that antibody specificity can be mediated by a single CDR. This constrained diversity enabled the utilization of additional CDRs for the installation of chemically reactive and photo-cross-linkable ncAAs. Binding studies of ncAA-substituted antibodies revealed that ncAA incorporation is reasonably well tolerated, with observed changes in affinity occurring as a function of ncAA side chain identity, substitution site, and the ncAA incorporation machinery used. Multiple azide-containing ncAAs supported copper-catalyzed azide-alkyne cycloaddition (CuAAC) and strain-promoted azide-alkyne cycloaddition (SPAAC) without the abrogation of binding function. Similarly, several alkyne substitutions facilitated CuAAC without the apparent disruption of binding. Finally, antibodies substituted with a photo-cross-linkable ncAA were evaluated for ultraviolet-mediated cross-linking on the yeast surface. Competition-based assays revealed position-dependent covalent linkages, strongly suggesting successful cross-linking. Key findings regarding CuAAC reactions and photo-cross-linking on the yeast surface were confirmed using soluble forms of ncAA-substituted clones. The consistency of findings on the yeast surface and in solution suggest that chemical diversification can be incorporated into yeast display screening approaches. Taken together, our results highlight the power of integrating the use of yeast display and ncAAs in search of proteins with "chemically augmented" binding functions. This includes strategies for systematically introducing small molecule functionality within binding protein structures and evaluating protein-based covalent target binding. The efficient preparation and chemical diversification of antibodies on the yeast surface open up new possibilities for discovering "drug-like" protein leads in high throughput.
Collapse
Affiliation(s)
- Mariha Islam
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Haixing P. Kehoe
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Jacob B. Lissoos
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Manjie Huang
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Christopher E. Ghadban
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Greg B. Sánchez
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Hanan Z. Lane
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| |
Collapse
|