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Zhang S, De Leon Rodriguez LM, Li FF, Brimble MA. Recent developments in the cleavage, functionalization, and conjugation of proteins and peptides at tyrosine residues. Chem Sci 2023; 14:7782-7817. [PMID: 37502317 PMCID: PMC10370606 DOI: 10.1039/d3sc02543h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Peptide and protein selective modification at tyrosine residues has become an exploding field of research as tyrosine constitutes a robust alternative to lysine and cysteine-targeted traditional peptide/protein modification protocols. This review offers a comprehensive summary of the latest advances in tyrosine-selective cleavage, functionalization, and conjugation of peptides and proteins from the past three years. This updated overview complements the extensive body of work on site-selective modification of peptides and proteins, which holds significant relevance across various disciplines, including chemical, biological, medical, and material sciences.
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Affiliation(s)
- Shengping Zhang
- Center for Translational Medicine, Shenzhen Bay Laboratory New Zealand
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
| | | | - Freda F Li
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
- School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
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2
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Thoreau F, Rochet LNC, Baker JR, Chudasama V. Enabling the formation of native mAb, Fab' and Fc-conjugates using a bis-disulfide bridging reagent to achieve tunable payload-to-antibody ratios (PARs). Chem Sci 2023; 14:3752-3762. [PMID: 37035695 PMCID: PMC10074397 DOI: 10.1039/d2sc06318b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Either as full IgGs or as fragments (Fabs, Fc, etc.), antibodies have received tremendous attention in the development of new therapeutics such as antibody-drug conjugates (ADCs). The production of ADCs involves the grafting of active payloads onto an antibody, which is generally enabled by the site-selective modification of native or engineered antibodies via chemical or enzymatic methods. Whatever method is employed, controlling the payload-antibody ratio (PAR) is a challenge in terms of multiple aspects including: (i) obtaining homogeneous protein conjugates; (ii) obtaining unusual PARs (PAR is rarely other than 2, 4 or 8); (iii) using a single method to access a range of different PARs; (iv) applicability to various antibody formats; and (v) flexibility for the production of heterofunctional antibody-conjugates (e.g. attachment of multiple types of payloads). In this article, we report a single pyridazinedione-based trifunctional dual bridging linker that enables, in a two-step procedure (re-bridging/click), the generation of either mAb-, Fab'-, or Fc-conjugates from native mAb, (Fab')2 or Fc formats, respectively. Fc and (Fab')2 formats were generated via enzymatic digestion of native mAbs. Whilst the same reduction and re-bridging protocols were applied to all three of the protein formats, the subsequent click reaction(s) employed to graft payload(s) drove the generation of a range of PARs, including heterofunctional PARs. As such, exploiting click reactivity and/or orthogonality afforded mAb-conjugates with PARs of 6, 4, 2 or 4 + 2, and Fab'- and Fc-conjugates with a PAR of 3, 2, 1 or 2 + 1 on-demand. We believe that the homogeneity, novelty and variety in accessible PARs, as well as the applicability to various antibody-conjugate formats enabled by our non-recombinant method could be a suitable tool for antibody-drug conjugates optimisation (optimal PAR value, optimal payloads combination) and boost the development of new antibody therapeutics (Fab'- and Fc-conjugates).
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Affiliation(s)
- Fabien Thoreau
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Léa N C Rochet
- 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
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3
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Oslund RC, Reyes-Robles T, White CH, Tomlinson JH, Crotty KA, Bowman EP, Chang D, Peterson VM, Li L, Frutos S, Vila-Perelló M, Vlerick D, Cromie K, Perlman DH, Ingale S, Hara SDO, Roberts LR, Piizzi G, Hett EC, Hazuda DJ, Fadeyi OO. Detection of cell-cell interactions via photocatalytic cell tagging. Nat Chem Biol 2022; 18:850-858. [PMID: 35654846 DOI: 10.1038/s41589-022-01044-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/22/2022] [Indexed: 02/07/2023]
Abstract
The growing appreciation of immune cell-cell interactions within disease environments has led to extensive efforts to develop immunotherapies. However, characterizing complex cell-cell interfaces in high resolution remains challenging. Thus, technologies leveraging therapeutic-based modalities to profile intercellular environments offer opportunities to study cell-cell interactions with molecular-level insight. We introduce photocatalytic cell tagging (PhoTag) for interrogating cell-cell interactions using single-domain antibodies (VHHs) conjugated to photoactivatable flavin-based cofactors. Following irradiation with visible light, the flavin photocatalyst generates phenoxy radical tags for targeted labeling. Using this technology, we demonstrate selective synaptic labeling across the PD-1/PD-L1 axis in antigen-presenting cell-T cell systems. In combination with multiomics single-cell sequencing, we monitored interactions between peripheral blood mononuclear cells and Raji PD-L1 B cells, revealing differences in transient interactions with specific T cell subtypes. The utility of PhoTag in capturing cell-cell interactions will enable detailed profiling of intercellular communication across different biological systems.
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Affiliation(s)
- Rob C Oslund
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA. .,InduPro, Cambridge, MA, USA.
| | | | - Cory H White
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Jake H Tomlinson
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Kelly A Crotty
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Edward P Bowman
- Discovery Research, Merck & Co., Inc., San Francisco, CA, USA
| | - Dan Chang
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | | | - Lixia Li
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | | | | | | | | | - David H Perlman
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Sampat Ingale
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | | | - Lee R Roberts
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Grazia Piizzi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Erik C Hett
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Daria J Hazuda
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA.,Infectious Diseases and Vaccine Research, Merck & Co., Inc., West Point, PA, USA
| | - Olugbeminiyi O Fadeyi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA. .,InduPro, Cambridge, MA, USA.
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4
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Cavaco M, Frutos S, Oliete P, Valle J, Andreu D, Castanho MARB, Vila-Perelló M, Neves V. Conjugation of a Blood Brain Barrier Peptide Shuttle to an Fc Domain for Brain Delivery of Therapeutic Biomolecules. ACS Med Chem Lett 2021; 12:1663-1668. [PMID: 36060671 PMCID: PMC9437899 DOI: 10.1021/acsmedchemlett.1c00225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The frequency of brain disease has increased significantly in the past years. After diagnosis, therapeutic options are usually limited, which demands the development of innovative therapeutic strategies. The use of antibody-drug conjugates (ADCs) is promising but highly limited by the existence of the blood-brain barrier (BBB). To overcome the impermeability of this barrier, antibody fragments can be engineered and conjugated to BBB peptide shuttles (BBBpS), which are capable of brain penetration. Herein, we linked the highly efficient BBBpS, PepH3, to the IgG fragment crystallizable (Fc) domain using the streamlined expressed protein ligation (SEPL) method. With this strategy, we obtained an Fc-PepH3 scaffold that can carry different payloads. Fc-PepH3 was shown to be nontoxic, capable of crossing an in vitro cellular BBB model, and able to bind to the neonatal Fc receptor (FcRn), which is responsible for antibody long half-life (t 1/2). Overall, we demonstrated the potential of Fc-PepH3 as a versatile platform readily adaptable to diverse drugs of therapeutic value to treat different brain conditions.
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Affiliation(s)
- Marco Cavaco
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof Egas Moniz, 1649-028 Lisboa, Portugal
- Proteomics
and Protein Chemistry Unit, Department of Experimental and Health
Sciences, Pompeu Fabra University, Dr. Aiguader 88, Barcelona Biomedical
Research Park, 08003 Barcelona, Spain
| | - Silvia Frutos
- SpliceBio
S.L., Baldiri Reixac
10-12, 08028 Barcelona, Spain
| | - Paula Oliete
- SpliceBio
S.L., Baldiri Reixac
10-12, 08028 Barcelona, Spain
| | - Javier Valle
- Proteomics
and Protein Chemistry Unit, Department of Experimental and Health
Sciences, Pompeu Fabra University, Dr. Aiguader 88, Barcelona Biomedical
Research Park, 08003 Barcelona, Spain
| | - David Andreu
- Proteomics
and Protein Chemistry Unit, Department of Experimental and Health
Sciences, Pompeu Fabra University, Dr. Aiguader 88, Barcelona Biomedical
Research Park, 08003 Barcelona, Spain
| | - Miguel A. R. B. Castanho
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof Egas Moniz, 1649-028 Lisboa, Portugal
| | | | - Vera Neves
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof Egas Moniz, 1649-028 Lisboa, Portugal
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5
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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6
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Abstract
Protein semisynthesis is a powerful tool for studying proteins and has contributed to a better understanding of protein structure and function and also driven innovations in protein science. Expressed protein ligation (EPL) is a widely used method to generate chemically modified proteins. However, EPL has some limitations, particularly relevant to modify challenging proteins such as antibodies. The method termed streamlined expressed protein ligation (SEPL) overcomes some of the problems of EPL, and other methods of protein semisynthesis, to generate challenging modified proteins such as antibody-drug conjugates (ADCs). ADCs targeting highly cytotoxic molecules to cancer cells, offer an attractive strategy to selectively eliminate tumor cells with improved therapeutic index than the antibodies or cytotoxic molecules themselves. Despite the potential of ADCs, the development of such complex molecules is challenging. We provide here protocols to prepare site-specifically modified ADCs by streamlined expressed protein ligation (SEPL), which does not require the incorporation of unnatural modifications into the antibody. Therefore, fully native antibodies, with only the desired cytotoxic molecules attached, can be generated.
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7
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Frutos S, Hernández JL, Otero A, Calvis C, Adan J, Mitjans F, Vila-Perelló M. Site-Specific Antibody Drug Conjugates Using Streamlined Expressed Protein Ligation. Bioconjug Chem 2018; 29:3503-3508. [PMID: 30346741 DOI: 10.1021/acs.bioconjchem.8b00630] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Antibody-Drug Conjugates (ADCs) have been shown to produce clinical benefit in cancer patient thanks to their ability to target highly cytotoxic small molecules to tumor cells. However, the development of these complex molecules faces significant challenges due to the need to combine a large biologic drug with a small molecule drug to generate the desired bioconjugate. We describe here the use of a protein ligation methodology, based on the native chemical ligation reaction to generate site-specific Antibody-Drug Conjugates, which does not require the incorporation of unnatural modifications into the antibody. Fully native antibodies, with only the desired cytotoxic molecules attached, can be generated, thus minimizing the risk that additional modifications required for the site-specific conjugation pose a risk to the antibody activity. We demonstrate that our approach can be used to generate site-specifically modified ADCs, with potent in vitro and in vivo antitumor activity in a breast cancer tumor model.
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Affiliation(s)
- Silvia Frutos
- ProteoDesign , C/Baldiri Reixach 10 , Barcelona 08028 , Spain
| | - Jose Luis Hernández
- LEITAT Technological Center , Biomed Division , C/Baldiri Reixach 15-21 , Barcelona 08028 , Spain
| | - Anabel Otero
- ProteoDesign , C/Baldiri Reixach 10 , Barcelona 08028 , Spain
| | - Carme Calvis
- LEITAT Technological Center , Biomed Division , C/Baldiri Reixach 15-21 , Barcelona 08028 , Spain
| | - Jaume Adan
- LEITAT Technological Center , Biomed Division , C/Baldiri Reixach 15-21 , Barcelona 08028 , Spain
| | - Francesc Mitjans
- LEITAT Technological Center , Biomed Division , C/Baldiri Reixach 15-21 , Barcelona 08028 , Spain
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8
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Kilic S, Boichenko I, Lechner CC, Fierz B. A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage. Chem Sci 2018; 9:3704-3709. [PMID: 29780501 PMCID: PMC5935033 DOI: 10.1039/c8sc00681d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/15/2018] [Indexed: 12/18/2022] Open
Abstract
The cellular response to DNA damage results in a signaling cascade that primes chromatin for repair. Combinatorial post-translational modifications (PTMs) play an important role in this process by altering the physical properties of chromatin and recruiting downstream factors. One key signal integrator is the histone variant H2A.X, which is phosphorylated at a C-terminal serine (S139ph), and ubiquitylated within its N-terminal tail at lysines 13 and 15 (K13/15ub). How these PTMs directly impact chromatin structure and thereby facilitate DNA repair is not well understood. Detailed studies require synthetic access to such N- and C-terminally modified proteins. This is complicated by the requirement for protecting groups allowing multi-fragment assembly. Here, we report a semi-synthetic route to generate simultaneously N- and C-terminally modified proteins using genetically encoded orthogonal masking groups. Applied to H2A.X, expression of a central protein fragment, containing a protected N-terminal cysteine and a C-terminal thioester masked as a split intein, enables sequential C- and N-terminal protein modification and results in the convergent production of H2A.X carrying K15ub and S139ph. Using single-molecule FRET between defined nucleosomes in synthetic chromatin fibers, we then show that K15 ubiquitylation (but not S139ph) impairs nucleosome stacking in tetranucleosome units, opening chromatin during DNA repair.
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Affiliation(s)
- Sinan Kilic
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
| | - Iuliia Boichenko
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
| | - Carolin C Lechner
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules , Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland .
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Cavaco M, Castanho MARB, Neves V. Peptibodies: An elegant solution for a long-standing problem. Biopolymers 2017; 110. [PMID: 29266205 DOI: 10.1002/bip.23095] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 01/09/2023]
Abstract
Chimeric proteins composed of a biologically active peptide and a fragment crystallizable (Fc) domain of immunoglobulin G (IgG) are known as peptibodies. They present an extended half-life due to neonatal Fc receptor (FcRn) salvage pathway, a decreased renal clearance rate owing to its increased size (≈70 kDa) and, depending on the peptide used in the design of the peptibody, an active-targeting moiety. Also, the peptides therapeutic activity is boosted by the number of peptides in the fusion protein (at least two peptides) and to some peptides' alterations. Peptibodies are mainly obtained through recombinant DNA technology. However, to improve peptide properties, "unnatural" changes have been introduced to the original peptides' sequence, for instance, the incorporation of D- or non-natural amino acid residues or even cyclization thus, limiting the application of genetic engineering in the production of peptibodies, since these peptides must be obtained via chemical synthesis. This constrains prompted the development of new methods for conjugation of peptides to Fc domains. Another challenge, subject of intense research, relates to the large-scale production of such peptibodies using these new techniques, which can be minimized by their proved value. To date, two peptibodies, romiplostim and dulaglutide, have been approved and stay as the standard of care in their areas of action. Furthermore, a considerable number of peptibodies are currently in preclinical and clinical development.
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Affiliation(s)
- Marco Cavaco
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, 1649-028, Portugal
| | - Miguel A R B Castanho
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, 1649-028, Portugal
| | - Vera Neves
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, 1649-028, Portugal
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