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Journeaux T, Bernardes GJL. Homogeneous multi-payload antibody-drug conjugates. Nat Chem 2024; 16:854-870. [PMID: 38760431 DOI: 10.1038/s41557-024-01507-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: 09/20/2023] [Accepted: 03/14/2024] [Indexed: 05/19/2024]
Abstract
Many systemic cancer chemotherapies comprise a combination of drugs, yet all clinically used antibody-drug conjugates (ADCs) contain a single-drug payload. These combination regimens improve treatment outcomes by producing synergistic anticancer effects and slowing the development of drug-resistant cell populations. In an attempt to replicate these regimens and improve the efficacy of targeted therapy, the field of ADCs has moved towards developing techniques that allow for multiple unique payloads to be attached to a single antibody molecule with high homogeneity. However, the methods for generating such constructs-homogeneous multi-payload ADCs-are both numerous and complex owing to the plethora of reactive functional groups that make up the surface of an antibody. Here, by summarizing and comparing the methods of both single- and multi-payload ADC generation and their key preclinical and clinical results, we provide a timely overview of this relatively new area of research. The methods discussed range from branched linker installation to the incorporation of unnatural amino acids, with a generalized comparison tool of the most promising modification strategies also provided. Finally, the successes and challenges of this rapidly growing field are critically evaluated, and from this, future areas of research and development are proposed.
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Affiliation(s)
- Toby Journeaux
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Cambridge, UK.
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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2
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Awawdeh A, Radecki AA, Vargas-Rodriguez O. Suppressor tRNAs at the interface of genetic code expansion and medicine. Front Genet 2024; 15:1420331. [PMID: 38798701 PMCID: PMC11116698 DOI: 10.3389/fgene.2024.1420331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
Suppressor transfer RNAs (sup-tRNAs) are receiving renewed attention for their promising therapeutic properties in treating genetic diseases caused by nonsense mutations. Traditionally, sup-tRNAs have been created by replacing the anticodon sequence of native tRNAs with a suppressor sequence. However, due to their complex interactome, considering other structural and functional tRNA features for design and engineering can yield more effective sup-tRNA therapies. For over 2 decades, the field of genetic code expansion (GCE) has created a wealth of knowledge, resources, and tools to engineer sup-tRNAs. In this Mini Review, we aim to shed light on how existing knowledge and strategies to develop sup-tRNAs for GCE can be adopted to accelerate the discovery of efficient and specific sup-tRNAs for medical treatment options. We highlight methods and milestones and discuss how these approaches may enlighten the research and development of tRNA medicines.
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Affiliation(s)
| | | | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, University of Connecticut School of Medicine, Farmington, CT, United States
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3
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Guo QR, Cao YJ. Applications of genetic code expansion technology in eukaryotes. Protein Cell 2024; 15:331-363. [PMID: 37847216 PMCID: PMC11074999 DOI: 10.1093/procel/pwad051] [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: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.
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Affiliation(s)
- Qiao-ru Guo
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yu J Cao
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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4
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Osgood AO, Roy SJS, Koo D, Gu R, Chatterjee A. A Genetically Encoded Photocaged Cysteine for Facile Site-Specific Introduction of Conjugation-Ready Thiol Residues in Antibodies. Bioconjug Chem 2024; 35:457-464. [PMID: 38548654 DOI: 10.1021/acs.bioconjchem.3c00513] [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] [Indexed: 04/18/2024]
Abstract
Antibody-drug conjugates (ADCs) have emerged as a powerful class of anticancer therapeutics that enable the selective delivery of toxic payloads into target cells. There is increasing appreciation for the importance of synthesizing such ADCs in a defined manner where the payload is attached at specific permissive sites on the antibody with a defined drug to antibody ratio. Additionally, the ability to systematically alter the site of attachment is important to fine-tune the therapeutic properties of the ADC. Engineered cysteine residues have been used to achieve such site-specific programmable attachment of drug molecules onto antibodies. However, engineered cysteine residues on antibodies often get "disulfide-capped" during secretion and require reductive regeneration prior to conjugation. This reductive step also reduces structurally important disulfide bonds in the antibody itself, which must be regenerated through oxidation. This multistep, cumbersome process reduces the efficiency of conjugation and presents logistical challenges. Additionally, certain engineered cysteine sites are resistant to reductive regeneration, limiting their utility and the overall scope of this conjugation strategy. In this work, we utilize a genetically encoded photocaged cysteine residue that can be site-specifically installed into the antibody. This photocaged amino acid can be efficiently decaged using light, revealing a free cysteine residue available for conjugation without disrupting the antibody structure. We show that this ncAA can be incorporated at several positions within full-length recombinant trastuzumab and decaged efficiently. We further used this method to generate a functional ADC site-specifically modified with monomethyl auristatin F (MMAF).
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Affiliation(s)
- Arianna O Osgood
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Soumya Jyoti Singha Roy
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - David Koo
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Renpeng Gu
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 201 Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, United States
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5
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Gan Q, Fan C. Orthogonal Translation for Site-Specific Installation of Post-translational Modifications. Chem Rev 2024; 124:2805-2838. [PMID: 38373737 DOI: 10.1021/acs.chemrev.3c00850] [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] [Indexed: 02/21/2024]
Abstract
Post-translational modifications (PTMs) endow proteins with new properties to respond to environmental changes or growth needs. With the development of advanced proteomics techniques, hundreds of distinct types of PTMs have been observed in a wide range of proteins from bacteria, archaea, and eukarya. To identify the roles of these PTMs, scientists have applied various approaches. However, high dynamics, low stoichiometry, and crosstalk between PTMs make it almost impossible to obtain homogeneously modified proteins for characterization of the site-specific effect of individual PTM on target proteins. To solve this problem, the genetic code expansion (GCE) strategy has been introduced into the field of PTM studies. Instead of modifying proteins after translation, GCE incorporates modified amino acids into proteins during translation, thus generating site-specifically modified proteins at target positions. In this review, we summarize the development of GCE systems for orthogonal translation for site-specific installation of PTMs.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
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6
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Loynd C, Singha Roy SJ, Ovalle VJ, Canarelli SE, Mondal A, Jewel D, Ficaretta ED, Weerapana E, Chatterjee A. Electrochemical labelling of hydroxyindoles with chemoselectivity for site-specific protein bioconjugation. Nat Chem 2024; 16:389-397. [PMID: 38082177 PMCID: PMC10932882 DOI: 10.1038/s41557-023-01375-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: 05/23/2022] [Accepted: 10/18/2023] [Indexed: 02/06/2024]
Abstract
Electrochemistry has recently emerged as a powerful approach in small-molecule synthesis owing to its numerous attractive features, including precise control over the fundamental reaction parameters, mild reaction conditions and innate scalability. Even though these advantages also make it an attractive strategy for chemoselective modification of complex biomolecules such as proteins, such applications remain poorly developed. Here we report an electrochemically promoted coupling reaction between 5-hydroxytryptophan (5HTP) and simple aromatic amines-electrochemical labelling of hydroxyindoles with chemoselectivity (eCLIC)-that enables site-specific labelling of full-length proteins under mild conditions. Using genetic code expansion technology, the 5HTP residue can be incorporated into predefined sites of a recombinant protein expressed in either prokaryotic or eukaryotic hosts for subsequent eCLIC labelling. We used the eCLIC reaction to site-specifically label various recombinant proteins, including a full-length human antibody. Furthermore, we show that eCLIC is compatible with strain-promoted alkyne-azide and alkene-tetrazine click reactions, enabling site-specific modification of proteins at two different sites with distinct labels.
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Affiliation(s)
- Conor Loynd
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | | | - Vincent J Ovalle
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Sarah E Canarelli
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Atanu Mondal
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Elise D Ficaretta
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA, USA.
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7
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Jewel D, Kelemen RE, Huang RL, Zhu Z, Sundaresh B, Malley K, Pham Q, Loynd C, Huang Z, van Opijnen T, Chatterjee A. Enhanced Directed Evolution in Mammalian Cells Yields a Hyperefficient Pyrrolysyl tRNA for Noncanonical Amino Acid Mutagenesis. Angew Chem Int Ed Engl 2024; 63:e202316428. [PMID: 38279536 PMCID: PMC10922736 DOI: 10.1002/anie.202316428] [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: 11/01/2023] [Indexed: 01/28/2024]
Abstract
Heterologous tRNAs used for noncanonical amino acid (ncAA) mutagenesis in mammalian cells typically show poor activity. We recently introduced a virus-assisted directed evolution strategy (VADER) that can enrich improved tRNA mutants from naïve libraries in mammalian cells. However, VADER was limited to processing only a few thousand mutants; the inability to screen a larger sequence space precluded the identification of highly active variants with distal synergistic mutations. Here, we report VADER2.0, which can process significantly larger mutant libraries. It also employs a novel library design, which maintains base-pairing between distant residues in the stem regions, allowing us to pack a higher density of functional mutants within a fixed sequence space. VADER2.0 enabled simultaneous engineering of the entire acceptor stem of M. mazei pyrrolysyl tRNA (tRNAPyl ), leading to a remarkably improved variant, which facilitates more efficient incorporation of a wider range of ncAAs, and enables facile development of viral vectors and stable cell-lines for ncAA mutagenesis.
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Affiliation(s)
- Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Rachel E Kelemen
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Rachel L Huang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Zeyu Zhu
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | | | - Kaitlin Malley
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Quan Pham
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Conor Loynd
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Zeyi Huang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
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8
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Burrow NK, Gourdie RK, King EA, Travis CR, Goff CM, Nimmo ZM, Berg JM, Boyt EL, Young DD. Development of Multivalent Conjugates with a Single Non-Canonical Amino Acid. Chembiochem 2023; 24:e202300565. [PMID: 37737964 DOI: 10.1002/cbic.202300565] [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: 08/10/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023]
Abstract
Proteins represent powerful biomacromolecules due to their unique functionality and broad utility both in the cell and in non-biological applications. The genetic encoding of non-canonical amino acids (ncAAs) facilitates functional diversification of these already powerful proteins. Specifically, ncAAs have been demonstrated to provide unique functional handles to bioorthogonally introduce novel functionality via conjugation reactions. Herein we examine the ability of a single ncAA to serve as a handle to generate multivalent bioconjugates to introduce two or more additional components to a protein, yielding a multivalent conjugate. To accomplish this aim, p-bromopropargyloxyphenyalanine (pBrPrF) was genetically encoded into both superfolder green fluorescent protein (sfGFP) and ubiquitin model proteins to serve as a conjugation handle. A sequential bioconjugation sequence involving a copper-assisted cycloaddition reaction coupled with a subsequent Sonogashira cross-coupling was then optimized. The linkage of two additional molecules to the model protein via these reactions yielded the desired multivalent bioconjugate. This domino approach using a single ncAA has a plethora of applications in both therapeutics and diagnostics as multiple unique moieties can be introduced into proteins in a highly controlled fashion.
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Affiliation(s)
- Naya K Burrow
- Department of Chemistry, William & Mary, Box 8795, Williamsburg, VA 23187, USA
| | - Robert K Gourdie
- Department of Chemistry, William & Mary, Box 8795, Williamsburg, VA 23187, USA
| | - Elizabeth A King
- Department of Chemistry, William & Mary, Box 8795, Williamsburg, VA 23187, USA
| | | | - Cameron M Goff
- Department of Chemistry, William & Mary, Box 8795, Williamsburg, VA 23187, USA
| | - Zachary M Nimmo
- Department of Chemistry, William & Mary, Box 8795, Williamsburg, VA 23187, USA
| | - Justin M Berg
- Department of Chemistry, William & Mary, Box 8795, Williamsburg, VA 23187, USA
| | - Emily L Boyt
- Department of Chemistry, William & Mary, Box 8795, Williamsburg, VA 23187, USA
| | - Douglas D Young
- Department of Chemistry, William & Mary, Box 8795, Williamsburg, VA 23187, USA
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9
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Meineke B, Heimgärtner J, Caridha R, Block MF, Kimler KJ, Pires MF, Landreh M, Elsässer SJ. Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery. CELL REPORTS METHODS 2023; 3:100626. [PMID: 37935196 PMCID: PMC10694491 DOI: 10.1016/j.crmeth.2023.100626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/22/2023] [Accepted: 10/12/2023] [Indexed: 11/09/2023]
Abstract
Stop codon suppression using dedicated tRNA/aminoacyl-tRNA synthetase (aaRS) pairs allows for genetically encoded, site-specific incorporation of non-canonical amino acids (ncAAs) as chemical handles for protein labeling and modification. Here, we demonstrate that piggyBac-mediated genomic integration of archaeal pyrrolysine tRNA (tRNAPyl)/pyrrolysyl-tRNA synthetase (PylRS) or bacterial tRNA/aaRS pairs, using a modular plasmid design with multi-copy tRNA arrays, allows for homogeneous and efficient genetically encoded ncAA incorporation in diverse mammalian cell lines. We assess opportunities and limitations of using ncAAs for fluorescent labeling applications in stable cell lines. We explore suppression of ochre and opal stop codons and finally incorporate two distinct ncAAs with mutually orthogonal click chemistries for site-specific, dual-fluorophore labeling of a cell surface receptor on live mammalian cells.
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Affiliation(s)
- Birthe Meineke
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 17165 Stockholm, Sweden.
| | - Johannes Heimgärtner
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Rozina Caridha
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Matthias F Block
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden
| | - Kyle J Kimler
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden
| | - Maria F Pires
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, 17165 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, 17165 Stockholm, Sweden.
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