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Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024. [PMID: 39120726 DOI: 10.1021/acs.chemrev.3c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Over 500 natural and synthetic amino acids have been genetically encoded in the last two decades. Incorporating these noncanonical amino acids into proteins enables many powerful applications, ranging from basic research to biotechnology, materials science, and medicine. However, major challenges remain to unleash the full potential of genetic code expansion across disciplines. Here, we provide an overview of diverse genetic code expansion methodologies and systems and their final applications in prokaryotes and eukaryotes, represented by Escherichia coli and mammalian cells as the main workhorse model systems. We highlight the power of how new technologies can be first established in simple and then transferred to more complex systems. For example, whole-genome engineering provides an excellent platform in bacteria for enabling transcript-specific genetic code expansion without off-targets in the transcriptome. In contrast, the complexity of a eukaryotic cell poses challenges that require entirely new approaches, such as striving toward establishing novel base pairs or generating orthogonally translating organelles within living cells. We connect the milestones in expanding the genetic code of living cells for encoding novel chemical functionalities to the most recent scientific discoveries, from optimizing the physicochemical properties of noncanonical amino acids to the technological advancements for their in vivo incorporation. This journey offers a glimpse into the promising developments in the years to come.
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Affiliation(s)
- Cosimo Jann
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Sabrina Giofré
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB Postdoc Programme (IPPro), 55128 Mainz, Germany
| | - Rajanya Bhattacharjee
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- IMB International PhD Programme (IPP), 55128 Mainz, Germany
| | - Edward A Lemke
- Biocenter, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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2
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Shao C, Tang B, Chu JCH, Lau KM, Wong WT, Che CM, Tai WCS, Wong WT, Wong CTT. Macrophage-engaging peptidic bispecific antibodies (pBsAbs) for immunotherapy via a facile bioconjugation strategy. Chem Sci 2024; 15:11272-11278. [PMID: 39055004 PMCID: PMC11268508 DOI: 10.1039/d4sc00851k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/29/2024] [Indexed: 07/27/2024] Open
Abstract
Bispecific antibodies are artificial molecules that fuse two different antigen-binding sites of monoclonal antibodies into one single entity. They have emerged as a promising next-generation anticancer treatment. Despite the fascinating applications of bispecific antibodies, the design and production of bispecific antibodies remain tedious and challenging, leading to a long R&D process and high production costs. We herein report an unprecedented strategy to cyclise and conjugate tumour-targeting peptides on the surface of a monoclonal antibody to form a novel type of bispecific antibody, namely the peptidic bispecific antibody (pBsAb). Such design combines the merits of highly specific monoclonal antibodies and serum-stable cyclic peptides that endows an additional tumour-targeting ability to the monoclonal antibody for binding with two different antigens. Our results show that the novel pBsAb, which comprises EGFR-binding cyclic peptides and an anti-SIRP-α monoclonal antibody, could serve as a macrophage-engaging bispecific antibody to initiate enhanced macrophage-cancer cell interaction and block the "don't eat me" signal between CD47-SIRP-α, as well as promoting antibody-dependent cellular phagocytosis and 3D cell spheroid infiltration. These findings give rise to a new type of bispecific antibody and a new platform for the rapid generation of new bispecific antibodies for research and potential therapeutic uses.
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Affiliation(s)
- Chihao Shao
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Bo Tang
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Jacky C H Chu
- Laboratory for Synthetic Chemistry and Chemical Biology Limited Units 1503-1511, 15/F, Building 17W, Hong Kong Science Park New Territories Hong Kong China
| | - Kwai Man Lau
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Wai-Ting Wong
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Chi-Ming Che
- Laboratory for Synthetic Chemistry and Chemical Biology Limited Units 1503-1511, 15/F, Building 17W, Hong Kong Science Park New Territories Hong Kong China
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - William C S Tai
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Wing-Tak Wong
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Clarence T T Wong
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
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3
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Simonson T, Mihaila V, Reveguk I. Uncovering substrate specificity determinants of class IIb aminoacyl-tRNA synthetases with machine learning. J Mol Graph Model 2024; 132:108818. [PMID: 39025021 DOI: 10.1016/j.jmgm.2024.108818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
Abstract
Specific amino acid (AA) binding by aminoacyl-tRNA synthetases (aaRSs) is necessary for correct translation of the genetic code. Sequence and structure analyses have revealed the main specificity determinants and allowed a partitioning of aaRSs into two classes and several subclasses. However, the information contributed by each determinant has not been precisely quantified, and other, minor determinants may still be unidentified. Growth of genomic data and development of machine learning classification methods allow us to revisit these questions. This work considered the subclass IIb, formed by the three enzymes aspartyl-, asparaginyl-, and lysyl-tRNA synthetase (LysRS). Over 35,000 sequences from the Pfam database were considered, and used to train a machine-learning model based on ensembles of decision trees. The model was trained to reproduce the existing classification of each sequence as AspRS, AsnRS, or LysRS, and to identify which sequence positions were most important for the classification. A few positions (5-8 depending on the AA substrate) sufficed for accurate classification. Most but not all of them were well-known specificity determinants. The machine learning models thus identified sets of mutations that distinguish the three subclass members, which might be targeted in engineering efforts to alter or swap the AA specificities for biotechnology applications.
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Affiliation(s)
- Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France.
| | - Victor Mihaila
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Ivan Reveguk
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
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4
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Xue E, Lee ACK, Chow KT, Ng DKP. Promotion and Detection of Cell-Cell Interactions through a Bioorthogonal Approach. J Am Chem Soc 2024; 146:17334-17347. [PMID: 38767615 PMCID: PMC11212048 DOI: 10.1021/jacs.4c04317] [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: 03/27/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Manipulation of cell-cell interactions via cell surface modification is crucial in tissue engineering and cell-based therapy. To be able to monitor intercellular interactions, it can also provide useful information for understanding how the cells interact and communicate. We report herein a facile bioorthogonal strategy to promote and monitor cell-cell interactions. It involves the use of a maleimide-appended tetrazine-caged boron dipyrromethene (BODIPY)-based fluorescent probe and a maleimide-substituted bicyclo[6.1.0]non-4-yne (BCN) to modify the membrane of macrophage (RAW 264.7) and cancer (HT29, HeLa, and A431) cells, respectively, via maleimide-thiol conjugation. After modification, the two kinds of cells interact strongly through inverse electron-demand Diels-Alder reaction of the surface tetrazine and BCN moieties. The coupling also disrupts the tetrazine quenching unit, restoring the fluorescence emission of the BODIPY core on the cell-cell interface, and promotes phagocytosis. Hence, this approach can promote and facilitate the detection of intercellular interactions, rendering it potentially useful for macrophage-based immunotherapy.
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Affiliation(s)
- Evelyn
Y. Xue
- Department
of Chemistry, The Chinese University of
Hong Kong, Shatin,
N.T., Hong Kong, China
| | - Alan Chun Kit Lee
- School
of Life Sciences, The Chinese University
of Hong Kong, Shatin, N.T., Hong Kong, China
- Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Kwan T. Chow
- Department
of Biomedical Sciences, City University
of Hong Kong, Kowloon, Hong Kong, China
| | - Dennis K. P. Ng
- Department
of Chemistry, The Chinese University of
Hong Kong, Shatin,
N.T., Hong Kong, China
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5
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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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6
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Butler ND, Kunjapur AM. Selective and Site-Specific Incorporation of Nonstandard Amino Acids Within Proteins for Therapeutic Applications. Methods Mol Biol 2024; 2720:35-53. [PMID: 37775656 DOI: 10.1007/978-1-0716-3469-1_3] [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: 10/01/2023]
Abstract
The incorporation of nonstandard amino acids (nsAAs) within protein sequences has broadened the chemical functionalities available for use in the study, prevention, or treatment of disease. The ability to genetically encode the introduction of nsAAs at precise sites of target recombinant proteins has enabled numerous applications such as bioorthogonal conjugation, thrombin inhibition, intrinsic biological containment of live organisms, and immunochemical termination of self-tolerance. Genetic systems that perform critical steps in enabling nsAA incorporation are known as orthogonal translation systems or orthogonal aminoacyl-tRNA synthetase/tRNA pairs. In Escherichia coli, several of these have been designed to accept novel nsAAs. Certain endogenous proteins, codon context, and standard amino acid concentrations can affect the yield of recombinant protein, the rate of nsAA incorporation within off-target proteins, and the rate of misincorporation due to near-cognate suppression or misacylation of orthogonal tRNA with standard amino acids. As a result, a significant body of work has been performed in engineering the E. coli genome to alleviate these issues. Here, we describe common methods applicable to nsAA incorporation within proteins in E. coli for sufficient purity and characterization for downstream therapeutic applications.
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Affiliation(s)
- Neil D Butler
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Aditya M Kunjapur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
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Gulyak EL, Alferova VA, Korshun VA, Sapozhnikova KA. Introduction of Carbonyl Groups into Antibodies. Molecules 2023; 28:7890. [PMID: 38067618 PMCID: PMC10707781 DOI: 10.3390/molecules28237890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Antibodies and their derivatives (scFv, Fabs, etc.) represent a unique class of biomolecules that combine selectivity with the ability to target drug delivery. Currently, one of the most promising endeavors in this field is the development of molecular diagnostic tools and antibody-based therapeutic agents, including antibody-drug conjugates (ADCs). To meet this challenge, it is imperative to advance methods for modifying antibodies. A particularly promising strategy involves the introduction of carbonyl groups into the antibody that are amenable to further modification by biorthogonal reactions, namely aliphatic, aromatic, and α-oxo aldehydes, as well as aliphatic and aryl-alkyl ketones. In this review, we summarize the preparation methods and applications of site-specific antibody conjugates that are synthesized using this approach.
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Affiliation(s)
| | | | | | - Ksenia A. Sapozhnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.L.G.); (V.A.A.); (V.A.K.)
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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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Gao R, Yu X, Kumar BVVSP, Tian L. Hierarchical Structuration in Protocellular System. SMALL METHODS 2023; 7:e2300422. [PMID: 37438327 DOI: 10.1002/smtd.202300422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/12/2023] [Indexed: 07/14/2023]
Abstract
Spatial control is one of the ubiquitous features in biological systems and the key to the functional complexity of living cells. The strategies to achieve such precise spatial control in protocellular systems are crucial to constructing complex artificial living systems with functional collective behavior. Herein, the authors review recent advances in the spatial control within a single protocell or between different protocells and discuss how such hierarchical structured protocellular system can be used to understand complex living systems or to advance the development of functional microreactors with the programmable release of various biomacromolecular payloads, or smart protocell-biological cell hybrid system.
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Affiliation(s)
- Rui Gao
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xinran Yu
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | | | - Liangfei Tian
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- Department of Ultrasound, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310027, China
- Innovation Center for Smart Medical Technologies & Devices, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China
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10
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Lightle HE, Kafley P, Lewis TR, Wang RE. Site-specific protein conjugates incorporating Para-Azido-L-Phenylalanine for cellular and in vivo imaging. Methods 2023; 219:95-101. [PMID: 37804961 PMCID: PMC10841489 DOI: 10.1016/j.ymeth.2023.10.001] [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: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023] Open
Abstract
This work features the use of amber suppression-mediated unnatural amino acid (UAA) incorporation into proteins for various imaging purposes. The site-specific incorporation of the UAA, p-azido-L-phenylalanine (pAzF), provides an azide handle that can be used to complete the strain promoted azide-alkyne click cycloaddition (SPAAC) reaction to introduce an imaging modality such as a fluorophore or a positron emission tomography (PET) tracer on the protein of interest (POI). Such methodology can be pursued directly in mammalian cell lines or on proteins expressed in vitro, thereby conferring a homogeneous pool of protein conjugates. A general procedure for UAA incorporation to use with a site-specific protein labeling method is provided allowing for in vitro and in vivo imaging applications based on the representative proteins PTEN and PD-L1. This approach would help elucidate the cellular or in vivo biological activities of the POI.
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Affiliation(s)
- Hailey E Lightle
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA
| | - Parmila Kafley
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA
| | - Todd R Lewis
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13(th) Street, Philadelphia, PA 19122, USA.
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11
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Yan X, Liu X, Zhao C, Chen GQ. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023; 8:199. [PMID: 37169742 PMCID: PMC10173249 DOI: 10.1038/s41392-023-01440-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/metabolic engineering tools and approaches. Medical and pharmaceutical demands have also pushed the development of synthetic biology, including integration of heterologous pathways into designer cells to efficiently produce medical agents, enhanced yields of natural products in cell growth media to equal or higher than that of the extracts from plants or fungi, constructions of novel genetic circuits for tumor targeting, controllable releases of therapeutic agents in response to specific biomarkers to fight diseases such as diabetes and cancers. Besides, new strategies are developed to treat complex immune diseases, infectious diseases and metabolic disorders that are hard to cure via traditional approaches. In general, synthetic biology brings new capabilities to medical and pharmaceutical researches. This review summarizes the timeline of synthetic biology developments, the past and present of synthetic biology for microbial productions of pharmaceutics, engineered cells equipped with synthetic DNA circuits for diagnosis and therapies, live and auto-assemblied biomaterials for medical treatments, cell-free synthetic biology in medical and pharmaceutical fields, and DNA engineering approaches with potentials for biomedical applications.
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Affiliation(s)
- Xu Yan
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, 101309, Beijing, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, 100084, Beijing, China.
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12
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Cheng Q, Zhang XN, Li J, Chen J, Wang Y, Zhang Y. Synthesis of Bispecific Antibody Conjugates Using Functionalized Poly-ADP-ribose Polymers. Biochemistry 2023; 62:1138-1144. [PMID: 36821831 PMCID: PMC10033384 DOI: 10.1021/acs.biochem.2c00718] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Poly-ADP-ribose (PAR) is a natural type of polymer derived from enzymatic reactions catalyzed by cellular poly(ADP-ribose) polymerases (PARPs). Given its notable solubility and biocompatibility, the PAR polymer may function as effective carriers for therapeutics in addition to modulating biomolecular interactions in cells. To explore its therapeutic potential, we herein developed a PAR polymer-based bispecific antibody targeting both human epidermal growth factor receptor 2 (HER2) and T-cell CD3 antigens. This was accomplished by conjugating anti-HER2 and anti-CD3 monoclonal antibodies to azido-functionalized PAR polymers through click chemistry. The generated PAR polymer-anti-HER2/anti-CD3 antibody conjugate could not only bind specifically to both HER2- and CD3-expressing target cells but also display potent cytotoxicity against HER2-positive breast cancer cells in the presence of non-activated human peripheral blood mononuclear cells (PBMCs). Functionalized PAR polymers provide a new strategy for synthesizing bispecific antibodies and may enable generation of PAR polymer-based conjugates with unique pharmacological activities for biomedical applications.
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Affiliation(s)
- Qinqin Cheng
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089
| | - Xiao-Nan Zhang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089
| | - Jiawei Li
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089
| | - Jingwen Chen
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089
| | - Yiling Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089
| | - Yong Zhang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089
- Department of Chemistry, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089
- Research Center for Liver Diseases, University of Southern California, Los Angeles, CA 90089
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13
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Sapozhnikova KA, Gulyak EL, Brylev VA, Misyurin VA, Oreshkov SD, Alexeeva AV, Ryazantsev DY, Simonova MA, Ryabukhina EV, Popova GP, Tikhonova NA, Lyzhko NA, Barmashov AE, Misyurin AV, Ustinov AV, Alferova VA, Korshun VA. Aminooxy Click Modification of a Periodate-Oxidized Immunoglobulin G: A General Approach to Antibody-Drug Conjugates with Dye-Mediated Expeditious Stoichiometry Control. Int J Mol Sci 2023; 24:ijms24065134. [PMID: 36982208 PMCID: PMC10049567 DOI: 10.3390/ijms24065134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
A universal approach to the construction of antibody-drug conjugates (ADCs) has been developed. It relies on periodate oxidation of naturally present glycans of immunoglobulin G, followed by oxime ligation and, optionally, copper(I)-catalyzed alkyne-azide cycloaddition for conjugation with a toxic payload. The introduction of highly absorbing cyanine dyes into the linker allows for facile determination of the drug-antibody ratio. We applied this methodology to the synthesis of cytotoxic conjugates of an antibody against the tumor-associated antigen PRAME with doxorubicin and monomethyl auristatin E (MMAE). The resultant conjugates retained their affinity to a large extent, yet their cytotoxicity in vitro varied dramatically: while the doxorubicin-based conjugate did not produce any effect on cells, the MMAE-based one demonstrated specific activity against PRAME-expressing cancer cell lines. Importantly, the latter conjugate constitutes the first reported example of a PRAME-targeting ADC.
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Affiliation(s)
- Ksenia A Sapozhnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Evgeny L Gulyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Vladimir A Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Lumiprobe RUS Ltd., Kotsyubinskogo 4, 121351 Moscow, Russia
| | - Vsevolod A Misyurin
- N.N. Blokhin National Medical Cancer Research Center, Ministry of Health of Russia, Kashirskoye sh. 24, 115478 Moscow, Russia
| | - Sergey D Oreshkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | | | - Dmitry Yu Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Maria A Simonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ekaterina V Ryabukhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Galina P Popova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | | | | | - Alexander E Barmashov
- N.N. Blokhin National Medical Cancer Research Center, Ministry of Health of Russia, Kashirskoye sh. 24, 115478 Moscow, Russia
| | | | - Alexey V Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Lumiprobe RUS Ltd., Kotsyubinskogo 4, 121351 Moscow, Russia
| | - Vera A Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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14
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Moghimianavval H, Patel C, Mohapatra S, Hwang SW, Kayikcioglu T, Bashirzadeh Y, Liu AP, Ha T. Engineering Functional Membrane-Membrane Interfaces by InterSpy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202104. [PMID: 35618485 PMCID: PMC9789529 DOI: 10.1002/smll.202202104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Engineering synthetic interfaces between membranes has potential applications in designing non-native cellular communication pathways and creating synthetic tissues. Here, InterSpy is introduced as a synthetic biology tool consisting of a heterodimeric protein engineered to form and maintain membrane-membrane interfaces between apposing synthetic as well as cell membranes through the SpyTag/SpyCatcher interaction. The inclusion of split fluorescent protein fragments in InterSpy allows tracking of the formation of a membrane-membrane interface and reconstitution of functional fluorescent protein in the space between apposing membranes. First, InterSpy is demonstrated by testing split protein designs using a mammalian cell-free expression (CFE) system. By utilizing co-translational helix insertion, cell-free synthesized InterSpy fragments are incorporated into the membrane of liposomes and supported lipid bilayers with the desired topology. Functional reconstitution of split fluorescent protein between the membranes is strictly dependent on SpyTag/SpyCatcher. Finally, InterSpy is demonstrated in mammalian cells by detecting fluorescence reconstitution of split protein at the membrane-membrane interface between two cells each expressing a component of InterSpy. InterSpy demonstrates the power of CFE systems in the functional reconstitution of synthetic membrane interfaces via proximity-inducing proteins. This technology may also prove useful where cell-cell contacts and communication are recreated in a controlled manner using minimal components.
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Affiliation(s)
- Hossein Moghimianavval
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Chintan Patel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sonisilpa Mohapatra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sung-Won Hwang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Tunc Kayikcioglu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
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15
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Aigbogun OP, Phenix CP, Krol ES, Price EW. The Chemistry of Creating Chemically Programmed Antibodies (cPAbs): Site-Specific Bioconjugation of Small Molecules. Mol Pharm 2023; 20:853-874. [PMID: 36696533 DOI: 10.1021/acs.molpharmaceut.2c00821] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Small-molecule drugs have been employed for years as therapeutics in the pharmaceutical industry. However, small-molecule drugs typically have short in vivo half-lives which is one of the largest impediments to the success of many potentially valuable pharmacologically active small molecules. The undesirable pharmacokinetics and pharmacology associated with some small molecules have led to the development of a new class of bioconjugates known as chemically programmed antibodies (cPAbs). cPAbs are bioconjugates in which antibodies are used to augment small molecules with effector functions and prolonged pharmacokinetic profiles, where the pharmacophore of the small molecule is harnessed for target binding and therefore biological targeting. Many different small molecules can be conjugated to large proteins such as full monoclonal antibodies (IgG), fragment crystallizable regions (Fc), or fragment antigen binding regions (Fab). In order to successfully and site-specifically conjugate small molecules to any class of antibodies (IgG, Fc, or Fab), the molecules must be derivatized with a functional group for ease of conjugation without altering the pharmacology of the small molecules. In this Review, we summarize the different synthetic or biological methods that have been employed to produce cPAbs. These unique chemistries have potential to be applied to other fields of antibody modification such as antibody drug conjugates, radioimmunoconjugates, and fluorophore-tagged antibodies.
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Affiliation(s)
- Omozojie P Aigbogun
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, S7N-5C9 Saskatchewan, Canada
| | - Christopher P Phenix
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, S7N-5C9 Saskatchewan, Canada
| | - Ed S Krol
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, S7N-5E5 Saskatchewan, Canada
| | - Eric W Price
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, S7N-5C9 Saskatchewan, Canada
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16
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Opuu V, Simonson T. Enzyme redesign and genetic code expansion. Protein Eng Des Sel 2023; 36:gzad017. [PMID: 37879093 DOI: 10.1093/protein/gzad017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
Enzyme design is an important application of computational protein design (CPD). It can benefit enormously from the additional chemistries provided by noncanonical amino acids (ncAAs). These can be incorporated into an 'expanded' genetic code, and introduced in vivo into target proteins. The key step for genetic code expansion is to engineer an aminoacyl-transfer RNA (tRNA) synthetase (aaRS) and an associated tRNA that handles the ncAA. Experimental directed evolution has been successfully used to engineer aaRSs and incorporate over 200 ncAAs into expanded codes. But directed evolution has severe limits, and is not yet applicable to noncanonical AA backbones. CPD can help address several of its limitations, and has begun to be applied to this problem. We review efforts to redesign aaRSs, studies that designed new proteins and functionalities with the help of ncAAs, and some of the method developments that have been used, such as adaptive landscape flattening Monte Carlo, which allows an enzyme to be redesigned with substrate or transition state binding as the design target.
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Affiliation(s)
- Vaitea Opuu
- Institut Chimie Biologie Innovation (CNRS UMR8231), Ecole Supérieure de Physique et Chimie de Paris (ESPCI), 75005 Paris, France
| | - Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
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17
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Site-Specific Antibody Conjugation with Payloads beyond Cytotoxins. Molecules 2023; 28:molecules28030917. [PMID: 36770585 PMCID: PMC9921355 DOI: 10.3390/molecules28030917] [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: 12/12/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023] Open
Abstract
As antibody-drug conjugates have become a very important modality for cancer therapy, many site-specific conjugation approaches have been developed for generating homogenous molecules. The selective antibody coupling is achieved through antibody engineering by introducing specific amino acid or unnatural amino acid residues, peptides, and glycans. In addition to the use of synthetic cytotoxins, these novel methods have been applied for the conjugation of other payloads, including non-cytotoxic compounds, proteins/peptides, glycans, lipids, and nucleic acids. The non-cytotoxic compounds include polyethylene glycol, antibiotics, protein degraders (PROTAC and LYTAC), immunomodulating agents, enzyme inhibitors and protein ligands. Different small proteins or peptides have been selectively conjugated through unnatural amino acid using click chemistry, engineered C-terminal formylglycine for oxime or click chemistry, or specific ligation or transpeptidation with or without enzymes. Although the antibody protamine peptide fusions have been extensively used for siRNA coupling during early studies, direct conjugations through engineered cysteine or lysine residues have been demonstrated later. These site-specific antibody conjugates containing these payloads other than cytotoxic compounds can be used in proof-of-concept studies and in developing new therapeutics for unmet medical needs.
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18
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Williard AC, Switzer HJ, Howard CA, Yin R, Russell BL, Sanyal R, Yu S, Myers TM, Flood BM, Kerscher O, Young DD. Protein Modification Employing Non-Canonical Amino Acids to Prepare SUMOylation Detecting Bioconjugates. Pharmaceutics 2022; 14:pharmaceutics14122826. [PMID: 36559319 PMCID: PMC9784311 DOI: 10.3390/pharmaceutics14122826] [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: 11/10/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Protein modification with non-canonical amino acids (ncAAs) represents a useful technology to afford homogenous samples of bioconjugates with site-specific modification. This technique can be directly applied to the detection of aberrant SUMOylation patterns, which are often indicative of disease states. Modified SUMO-trapping proteins, consisting of a catalytically inactive ULP1 fragment (UTAG) fused to the maltose-binding protein MBP, are useful reagents for the binding and labeling of SUMOylated proteins. Mutation of this UTAG fusion protein to facilitate amber suppression technologies for the genetic incorporation of ncAAs was assessed to provide a functional handle for modification. Ultimately, two sites in the maltose-binding protein (MBP) fusion were identified as ideal for incorporation and bioconjugation without perturbation to the SUMO-trapping ability of the UTAG protein. This functionality was then employed to label SUMOylated proteins in HeLa cells and demonstrate their enrichment in the nucleus. This modified UTAG-MBP-ncAA protein has far-reaching applications for both diagnostics and therapeutics.
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Affiliation(s)
| | - Hannah J. Switzer
- Department of Chemistry, William & Mary, Williamsburg, VA 23185, USA
| | | | - Rui Yin
- Department of Chemistry, William & Mary, Williamsburg, VA 23185, USA
| | - Brent L. Russell
- Department of Chemistry, William & Mary, Williamsburg, VA 23185, USA
| | - Ritwik Sanyal
- Department of Chemistry, William & Mary, Williamsburg, VA 23185, USA
| | - Shaun Yu
- Department of Chemistry, William & Mary, Williamsburg, VA 23185, USA
| | - Trinity M. Myers
- Department of Chemistry, William & Mary, Williamsburg, VA 23185, USA
| | - Brian M. Flood
- Department of Chemistry, William & Mary, Williamsburg, VA 23185, USA
| | - Oliver Kerscher
- Department of Biology, William & Mary, Williamsburg, VA 23185, USA
| | - Douglas D. Young
- Department of Chemistry, William & Mary, Williamsburg, VA 23185, USA
- Correspondence:
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19
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Liu D, Qi X, Wei X, Zhao L, Wang X, Li S, Wang Z, Shi L, Xu J, Hong M, Liu Z, Zhao L, Wang X, Zhang B, Zhang Y, Wang F, Cao YJ. A Novel Her2/VEGFR2/CD3 trispecific antibody with an optimal structural design showed improved T-cell-redirecting antitumor efficacy. Am J Cancer Res 2022; 12:7788-7803. [PMID: 36451856 PMCID: PMC9706591 DOI: 10.7150/thno.75037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/02/2022] [Indexed: 12/03/2022] Open
Abstract
Rationale: T-cell-redirecting bispecific antibodies (bsAbs) and trispecific antibodies (tsAbs) designed to recognize different epitopes or antigens have emerged as promising cancer therapies. Current approaches are all designed to include another antibody specific to the site of the primary antibody, and the molecular structures are generally established. However, the dimensions of target molecule and epitope location play a key role in the efficiency of the immunological synapse (IS) formation and subsequent T-cell-redirecting activities, therefore the connection flexibility of these antibodies determines the geometries of different formats of these molecules and will have a major impact on the efficacy. Methods: We describe a novel recombination strategy using various linker designs to site-specifically fuse anti-Her2 (2Rs15) or anti-VEGFR2 (3VGR19) nanobodies to different positions of the anti-CD3 antibody fragment (Fab, SP34). Based on the comparison among the various antigen-specific bsAbs, we could determine the desired fusion site of each nanobody to SP34, and further ensure the optimal structure of tsAbs with synergistic dual-antigen enhanced T-cell-redirecting activities. Results: This approach allows precise control of the formation of IS between Her2- and/or VEGFR2-expressing cancer cells and T cells, to obtain the optimal structure of the Her2/VEGFR2/CD3 tsAb without the need to map antibody-binding epitopes. Optimization of Her2/VEGFR2/CD3 tsAb results in enhanced T-cell-redirecting in vitro and in vivo antitumor efficacy compared with the corresponding bsAbs alone or in combination, and the potency to overcome tumor relapse due to antigen escape or resistance to Herceptin and Cyramza therapy. Conclusion: The novel design strategy for developing tsAbs using a site-specific recombination approach represents a promising platform for immuno-oncology and in applications other than cancer therapy.
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Affiliation(s)
- Dong Liu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Xuexiu Qi
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Xiaoyi Wei
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Lijun Zhao
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Xuechun Wang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Shuhong Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Zhidong Wang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Licai Shi
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Jiean Xu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Mei Hong
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Zhong Liu
- Lunan Pharmaceutical Group Co., Ltd, Feixian County, Shandong, 273400, China
| | - Lili Zhao
- National Engineering Laboratory of High Level Expression in Mammalian Cells, Feixian County, Shandong, 273400, China.,✉ Corresponding authors: ;
| | - Xiankun Wang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China.,Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Bo Zhang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China.,Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
| | - Yuhan Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals, Beijing Translational Center for Biopharmaceuticals Institute of Biophysics, Chinese Academy of Sciences Beijing 100101, China
| | - Feng Wang
- Key Laboratory of Protein and Peptide Pharmaceuticals, Beijing Translational Center for Biopharmaceuticals Institute of Biophysics, Chinese Academy of Sciences Beijing 100101, China
| | - Yu J. Cao
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China.,Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, China.,✉ Corresponding authors: ;
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20
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Yuan D, Zhang Y, Lim KH, Leung SKP, Yang X, Liang Y, Lau WCY, Chow KT, Xia J. Site-Selective Lysine Acetylation of Human Immunoglobulin G for Immunoliposomes and Bispecific Antibody Complexes. J Am Chem Soc 2022; 144:18494-18503. [PMID: 36167521 DOI: 10.1021/jacs.2c07594] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-selective acetylation of a single lysine residue in a protein that reaches a lysine acetyltransferase's accuracy, precision, and reliability is challenging. Here, we report a peptide-guided, proximity-driven group transfer reaction that acetylates a single lysine residue, Lys 248, of the fragment crystallizable region (Fc region) in the heavy chain of the human Immunoglobulin G (IgG). An Fc-interacting peptide bound with the Fc domain and positioned a phenolic ester close to Lys 248, which induced a nucleophilic reaction and resulted in the transfer of an acetyl group to Lys 248. The acetylation reaction proceeded to a decent yield under the physiological condition without the need for deglycosylation, unnatural amino acids, or catalysts. Along with acetylation, functional moieties such as azide, alkyne, fluorescent molecules, or biotin could also be site-selectively installed on Lys 248, allowing IgG's further derivatization. We then synthesized an antibody-lipid conjugate and constructed antibody-conjugated liposomes (immunoliposomes), targeting HER2-positive (HER2+) cancer cells. We also built a bispecific antibody complex (bsAbC) covalently linking an anti-HER2 antibody and an anti-CD3 antibody. The bsAbC showed in vitro effector-cell-mediated cytotoxicity at nanomolar concentrations. Compared with bispecific antibodies (bsAbs), bsAbCs are constructed based on native IgGs and contain two antigen-binding sites to each antigen, twice that of bsAbs. Altogether, this work reports a method of site-selective acetylation of native antibodies, highlights a facile way of site-selective IgG functionalization, and underscores the potential of bsAbCs in cancer immunotherapy.
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Affiliation(s)
- Dingdong Yuan
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Yu Zhang
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - King Hoo Lim
- Department of Biomedical Sciences, The City University of Hong Kong, Kowloon, Hong Kong SAR 999077, China
| | - Stephen King Pong Leung
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Xizi Yang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Yujie Liang
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Wilson Chun Yu Lau
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Kwan T Chow
- Department of Biomedical Sciences, The City University of Hong Kong, Kowloon, Hong Kong SAR 999077, China
| | - Jiang Xia
- Department of Chemistry and Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
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21
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Chen J, Huang C, Zhao W, Ren J, Ji F, Jia L. SnoopLigase Enables Highly Efficient Generation of C-C-Linked Bispecific Nanobodies Targeting TNF-α and IL-17A. Bioconjug Chem 2022; 33:1446-1455. [PMID: 35938675 DOI: 10.1021/acs.bioconjchem.2c00143] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bispecific antibodies (bis-Nbs) have been extensively developed since the concept was devised over the decades. Taking advantage of the superior characteristics of nanobodies, bis-Nbs exhibit an emerging tendency to become the new generation of research and diagnostic tools. Traditional strategies to connect the homo- or heterogeneous monomers are commonly applied, but there are still technical issues to generate the bispecific molecules as efficiently as designed. Here, we utilize SnoopLigase to directly tether the C terminus (C-C) of the tagged nanobodies against tumor necrosis factor-α (TNF-α) and interleukin-17A (IL-17A). Under optimal conditions, the yield of C-C-linked bis-Nbs can reach as high as 70% due to the existence of SnoopLigase. The prepared bis-Nbs possessed similar or even higher affinity as the monomers and significantly inhibited the proliferation and migration of rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS) induced by TNF-α and IL-17A. This study provides an innovative route for using SnoopLigase to realize a highly efficient generation of C-C-linked bis-Nbs. The approach can be applied to different and multicomponent systems for their potential applications in disease diagnosis and treatment.
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Affiliation(s)
- Jiewen Chen
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Chundong Huang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Wei Zhao
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, P. R. China
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22
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Taylor RJ, Geeson MB, Journeaux T, Bernardes GJL. Chemical and Enzymatic Methods for Post-Translational Protein-Protein Conjugation. J Am Chem Soc 2022; 144:14404-14419. [PMID: 35912579 PMCID: PMC9389620 DOI: 10.1021/jacs.2c00129] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fusion proteins play an essential role in the biosciences but suffer from several key limitations, including the requirement for N-to-C terminal ligation, incompatibility of constituent domains, incorrect folding, and loss of biological activity. This perspective focuses on chemical and enzymatic approaches for the post-translational generation of well-defined protein-protein conjugates, which overcome some of the limitations faced by traditional fusion techniques. Methods discussed range from chemical modification of nucleophilic canonical amino acid residues to incorporation of unnatural amino acid residues and a range of enzymatic methods, including sortase-mediated ligation. Through summarizing the progress in this rapidly growing field, the key successes and challenges associated with using chemical and enzymatic approaches are highlighted and areas requiring further development are discussed.
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Affiliation(s)
- Ross J Taylor
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Michael B Geeson
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Toby Journeaux
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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23
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Taylor RJ, Aguilar Rangel M, Geeson MB, Sormanni P, Vendruscolo M, Bernardes GJL. π-Clamp-Mediated Homo- and Heterodimerization of Single-Domain Antibodies via Site-Specific Homobifunctional Conjugation. J Am Chem Soc 2022; 144:13026-13031. [PMID: 35834748 PMCID: PMC9335888 DOI: 10.1021/jacs.2c04747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Post-translational protein–protein conjugation
produces
bioconjugates that are unavailable via genetic fusion approaches.
A method for preparing protein–protein conjugates using π-clamp-mediated
cysteine arylation with pentafluorophenyl sulfonamide functional groups
is described. Two computationally designed antibodies targeting the
SARS-CoV-2 receptor binding domain were produced (KD = 146, 581 nM) with a π-clamp sequence near the
C-terminus and dimerized using this method to provide a 10–60-fold
increase in binding (KD = 8–15
nM). When two solvent-exposed cysteine residues were present on the
second protein domain, the π-clamp cysteine residue was selectively
modified over an Asp-Cys-Glu cysteine residue, allowing for subsequent
small-molecule conjugation. With this strategy, we build molecule–protein–protein
conjugates with complete chemical control over the sites of modification.
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Affiliation(s)
- Ross J Taylor
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Mauricio Aguilar Rangel
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Michael B Geeson
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Gonçalo J L Bernardes
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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24
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Van Fossen EM, Bednar RM, Jana S, Franklin R, Beckman J, Karplus PA, Mehl RA. Nanobody assemblies with fully flexible topology enabled by genetically encoded tetrazine amino acids. SCIENCE ADVANCES 2022; 8:eabm6909. [PMID: 35522749 PMCID: PMC9075797 DOI: 10.1126/sciadv.abm6909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Assembling nanobodies (Nbs) into polyvalent multimers is a powerful strategy for improving the effectiveness of Nb-based therapeutics and biotechnological tools. However, generally effective approaches to Nb assembly are currently restricted to the amino or carboxyl termini, greatly limiting the diversity of Nb multimer topologies that can be produced. Here, we show that reactive tetrazine groups-site-specifically inserted by genetic code expansion at Nb surface sites-are compatible with Nb folding and function, enabling Nb assembly at any desired point. Using two anti-SARS-CoV-2 Nbs with viral neutralization ability, we created Nb homo- and heterodimers with improved properties compared with conventionally linked Nb homodimers, which, in the case of our tetrazine-conjugated trimer, translated into enhanced viral neutralization. Thus, this tetrazine-based approach is a generally applicable strategy that greatly increases the accessible range of Nb assembly topologies, and thereby adds the optimization of topology as an effective avenue to generate Nb assemblies with improved efficacy.
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Affiliation(s)
- Elise M Van Fossen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Riley M Bednar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Rachel Franklin
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Joseph Beckman
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
- e-MSion, Inc., 2121 NE Jack London Drive, Corvallis, OR 97330, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
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25
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Lateef OM, Akintubosun MO, Olaoba OT, Samson SO, Adamczyk M. Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications. Int J Mol Sci 2022; 23:938. [PMID: 35055121 PMCID: PMC8779196 DOI: 10.3390/ijms23020938] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.
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Affiliation(s)
- Olubodun Michael Lateef
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | | | - Olamide Tosin Olaoba
- Laboratory of Functional and Structural Biochemistry, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil;
| | - Sunday Ocholi Samson
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | - Malgorzata Adamczyk
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
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26
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Sornay C, Vaur V, Wagner A, Chaubet G. An overview of chemo- and site-selectivity aspects in the chemical conjugation of proteins. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211563. [PMID: 35116160 PMCID: PMC8790347 DOI: 10.1098/rsos.211563] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/20/2021] [Indexed: 05/03/2023]
Abstract
The bioconjugation of proteins-that is, the creation of a covalent link between a protein and any other molecule-has been studied for decades, partly because of the numerous applications of protein conjugates, but also due to the technical challenge it represents. Indeed, proteins possess inner physico-chemical properties-they are sensitive and polynucleophilic macromolecules-that make them complex substrates in conjugation reactions. This complexity arises from the mild conditions imposed by their sensitivity but also from selectivity issues, viz the precise control of the conjugation site on the protein. After decades of research, strategies and reagents have been developed to address two aspects of this selectivity: chemoselectivity-harnessing the reacting chemical functionality-and site-selectivity-controlling the reacting amino acid residue-most notably thanks to the participation of synthetic chemistry in this effort. This review offers an overview of these chemical bioconjugation strategies, insisting on those employing native proteins as substrates, and shows that the field is active and exciting, especially for synthetic chemists seeking new challenges.
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Affiliation(s)
- Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden 67400, France
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27
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Dimasi N, Kumar A, Gao C. Generation of bispecific antibodies using chemical conjugation methods. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:13-24. [PMID: 34916015 DOI: 10.1016/j.ddtec.2021.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022]
Abstract
Bispecific antibodies combine the specificity of two antibodies into one molecule. During the past two decades, advancement in protein engineering enabled the development of more than 100 bispecific formats, three of which are approved by the FDA for clinical use. In parallel to protein engineering methods, advancement in conjugation chemistries have spurred the use of chemical engineering approaches to generate bispecific antibodies. Herein, we review selected chemical strategies employed to generate bispecific antibodies that cannot be made using protein engineering methods.
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Affiliation(s)
- Nazzareno Dimasi
- Antibody Discovery and Protein Engineering, AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Amit Kumar
- Antibody Discovery and Protein Engineering, AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Changshou Gao
- Antibody Discovery and Protein Engineering, AstraZeneca, One MedImmune Way, Gaithersburg, MD 20878, USA.
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28
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Tang H, Zhang P, Luo X. Recent Technologies for Genetic Code Expansion and their Implications on Synthetic Biology Applications. J Mol Biol 2021; 434:167382. [PMID: 34863778 DOI: 10.1016/j.jmb.2021.167382] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 02/03/2023]
Abstract
Genetic code expansion (GCE) enables the site-specific incorporation of non-canonical amino acids as novel building blocks for the investigation and manipulation of proteins. The advancement of genetic code expansion has been benefited from the development of synthetic biology, while genetic code expansion also helps to create more synthetic biology tools. In this review, we summarize recent advances in genetic code expansion brought by synthetic biology progresses, including engineering of the translation machinery, genome-wide codon reassignment, and the biosynthesis of non-canonical amino acids. We highlight the emerging application of this technology in construction of new synthetic biology parts, circuits, chassis, and products.
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Affiliation(s)
- Hongting Tang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Pan Zhang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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29
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Padhi AK, Kumar A, Haruna KI, Sato H, Tamura H, Nagatoishi S, Tsumoto K, Yamaguchi A, Iraha F, Takahashi M, Sakamoto K, Zhang KYJ. An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes. Brief Bioinform 2021; 22:6355418. [PMID: 34415295 DOI: 10.1093/bib/bbab338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 01/09/2023] Open
Abstract
Protein engineering and design principles employing the 20 standard amino acids have been extensively used to achieve stable protein scaffolds and deliver their specific activities. Although this confers some advantages, it often restricts the sequence, chemical space, and ultimately the functional diversity of proteins. Moreover, although site-specific incorporation of non-natural amino acids (nnAAs) has been proven to be a valuable strategy in protein engineering and therapeutics development, its utility in the affinity-maturation of nanobodies is not fully explored. Besides, current experimental methods do not routinely employ nnAAs due to their enormous library size and infinite combinations. To address this, we have developed an integrated computational pipeline employing structure-based protein design methodologies, molecular dynamics simulations and free energy calculations, for the binding affinity prediction of an nnAA-incorporated nanobody toward its target and selection of potent binders. We show that by incorporating halogenated tyrosines, the affinity of 9G8 nanobody can be improved toward epidermal growth factor receptor (EGFR), a crucial cancer target. Surface plasmon resonance (SPR) assays showed that the binding of several 3-chloro-l-tyrosine (3MY)-incorporated nanobodies were improved up to 6-fold into a picomolar range, and the computationally estimated binding affinities shared a Pearson's r of 0.87 with SPR results. The improved affinity was found to be due to enhanced van der Waals interactions of key 3MY-proximate nanobody residues with EGFR, and an overall increase in the nanobody's structural stability. In conclusion, we show that our method can facilitate screening large libraries and predict potent site-specific nnAA-incorporated nanobody binders against crucial disease-targets.
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Affiliation(s)
- Aditya K Padhi
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Ken-Ichi Haruna
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, Kanagawa 210-8681, Japan
| | - Haruna Sato
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, Kanagawa 210-8681, 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
| | - Satoru Nagatoishi
- Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Atushi Yamaguchi
- Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Fumie Iraha
- Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mihoko Takahashi
- Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,Laboratory for Nonnatural Amino Acid Technology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kensaku Sakamoto
- Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,Laboratory for Nonnatural Amino Acid Technology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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30
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Sapozhnikova KA, Misyurin AV, Pestov NB, Meleshkina EG, Oreshkov SD, Ganzhula EP, Mikhailova AS, Korshun VA, Misyurin VA, Brylev VA. Detection of the PRAME Protein on the Surface of Melanoma Cells Using a Fluorescently Labeled Monoclonal Antibody. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021050332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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31
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Facile Generation of Potent Bispecific Fab via Sortase A and Click Chemistry for Cancer Immunotherapy. Cancers (Basel) 2021; 13:cancers13184540. [PMID: 34572769 PMCID: PMC8467688 DOI: 10.3390/cancers13184540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The formats of bispecific antibody have been investigated for many years to enhance the stability of the structure and anti-tumor efficacy. One of the formats combining two Fabs at their C termini provides unmodified variable region and comparable activity to other fragment-based bispecific antibodies that are usually combined in a head-to-tail manner. However, the current strategy to produce the BiFab molecule is limited to a semisynthetic method that introduces unnatural amino acid to antibodies’ sequences during production. To improve the application of BiFab format in investigational biodrugs, we have applied sortase A-mediated “bio-click” chemistry to generate BiFab, for facile assembly of Fab molecules that have been expressed and stored as BiFab module candidates. The BiFabs made by our method stimulate T cell proliferation and activation with favorable in vitro and in vivo anti-tumor activit. Our results indicate that BiFab made by sortase A-mediated click chemistry could be used to efficiently generate various BiFabs with high potency, which further supports personalized tumor immunotherapy in the future. Abstract Bispecific antibodies (BsAbs) for T cell engagement have shown great promise in cancer immunotherapy, and their clinical applications have been proven in treating hematological malignance. Bispecific antibody binding fragment (BiFab) represents a promising platform for generating non-Fc bispecific antibodies. However, the generation of BiFab is still challenging, especially by means of chemical conjugation. More conjugation strategies, e.g., enzymatic conjugation and modular BiFab preparation, are needed to improve the robustness and flexibility of BiFab preparation. We successfully used chemo-enzymatic conjugation approach to generate bispecific antibody (i.e., BiFab) with Fabs from full-length antibodies. Paired click handles (e.g., N3 and DBCO) was introduced to the C-terminal LPETG tag of Fabs via sortase A mediated transpeptidation, followed by site-specific conjugation between two click handle-modified Fabs for BiFab generation. Both BiFabCD20/CD3 (EC50 = 0.26 ng/mL) and BiFabHer2/CD3 exhibited superior efficacy in mediating T cells, from either PBMC or ATC, to kill target tumor cell lines while spared antigen-negative tumor cells in vitro. The BiFabCD20/CD3 also efficiently inhibited CD20-positive tumor growth in mouse xenograft model. We have established a facile sortase A-mediated click handle installation to generate homogeneous and functional BiFabs. The exemplary BiFabs against different targets showed superior efficacy in redirecting and activating T cells to specifically kill target tumor cells, demonstrating the robustness of sortase A-mediated “bio-click” chemistry in generating various potent BiFabs. This approach also holds promise for further efficient construction of a Fab derivative library for personalized tumor immunotherapy in the future.
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32
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Johnson RL, Blaber HG, Evans T, Worthy HL, Pope JR, Jones DD. Designed Artificial Protein Heterodimers With Coupled Functions Constructed Using Bio-Orthogonal Chemistry. Front Chem 2021; 9:733550. [PMID: 34422774 PMCID: PMC8371201 DOI: 10.3389/fchem.2021.733550] [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: 06/30/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
The formation of protein complexes is central to biology, with oligomeric proteins more prevalent than monomers. The coupling of functionally and even structurally distinct protein units can lead to new functional properties not accessible by monomeric proteins alone. While such complexes are driven by evolutionally needs in biology, the ability to link normally functionally and structurally disparate proteins can lead to new emergent properties for use in synthetic biology and the nanosciences. Here we demonstrate how two disparate proteins, the haem binding helical bundle protein cytochrome b 562 and the β-barrel green fluorescent protein can be combined to form a heterodimer linked together by an unnatural triazole linkage. The complex was designed using computational docking approaches to predict compatible interfaces between the two proteins. Models of the complexes where then used to engineer residue coupling sites in each protein to link them together. Genetic code expansion was used to incorporate azide chemistry in cytochrome b 562 and alkyne chemistry in GFP so that a permanent triazole covalent linkage can be made between the two proteins. Two linkage sites with respect to GFP were sampled. Spectral analysis of the new heterodimer revealed that haem binding and fluorescent protein chromophore properties were retained. Functional coupling was confirmed through changes in GFP absorbance and fluorescence, with linkage site determining the extent of communication between the two proteins. We have thus shown here that is possible to design and build heterodimeric proteins that couple structurally and functionally disparate proteins to form a new complex with new functional properties.
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Affiliation(s)
- Rachel L. Johnson
- Molecular Biosciences Division, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Hayley G. Blaber
- Molecular Biosciences Division, School of Biosciences, Cardiff University, Cardiff, United Kingdom
- The Henry Wellcome Building for Biocatalysis, Exeter University, Exeter, United Kingdom
| | - Tomas Evans
- Molecular Biosciences Division, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Harley L. Worthy
- Molecular Biosciences Division, School of Biosciences, Cardiff University, Cardiff, United Kingdom
- The Henry Wellcome Building for Biocatalysis, Exeter University, Exeter, United Kingdom
| | - Jacob R. Pope
- Molecular Biosciences Division, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - D. Dafydd Jones
- Molecular Biosciences Division, School of Biosciences, Cardiff University, Cardiff, United Kingdom
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33
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Hu Y, Schomaker JM. Recent Developments and Strategies for Mutually Orthogonal Bioorthogonal Reactions. Chembiochem 2021; 22:3254-3262. [PMID: 34261195 DOI: 10.1002/cbic.202100164] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/12/2021] [Indexed: 12/23/2022]
Abstract
Over the past decade, several different metal-free bioorthogonal reactions have been developed to enable simultaneous double-click labeling with minimal-to-no competing cross-reactivities; such transformations are termed 'mutually orthogonal'. More recently, several examples of successful triple ligation strategies have also been described. In this minireview, we discuss selected aspects of the development of orthogonal bioorthogonal reactions over the past decade, including general strategies to drive future innovations to achieve simultaneous, mutually orthogonal click reactions in one pot.
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Affiliation(s)
- Yun Hu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
| | - Jennifer M Schomaker
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA
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34
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Cao YJ, Wang X, Wang Z, Zhao L, Li S, Zhang Z, Wei X, Yun H, Choi SH, Liu Z, Zhao L, Kazane SA. Switchable CAR-T Cells Outperformed Traditional Antibody-Redirected Therapeutics Targeting Breast Cancers. ACS Synth Biol 2021; 10:1176-1183. [PMID: 33856201 DOI: 10.1021/acssynbio.1c00007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Various antibody-redirected immunotherapeutic approaches, including antibody-drug conjugates (ADCs), bispecific antibodies (bsAbs), and chimeric antigen receptor-T (CAR-T) cells, have been devised to produce specific activity against various cancer types. Using genetically encoded unnatural amino acids, we generated a homogeneous Her2-targeted ADC, a T cell-redirected bsAb, and a FITC-modified antibody capable of redirecting anti-FITC CAR-T (switchable CAR-T; sCAR-T) cells to target different Her2-expressing breast cancers. sCAR-T cells showed activity against Her2-expressing tumor cells comparable to that of conventional anti-Her2 CAR-T cells and superior to that of ADC- and bsAb-based approaches. To prevent antigen escape, we designed bispecific sCAR-T cells targeting both the Her2 receptor and IGF1R, which showed an overall improved activity against cancer cells with low Her2 expression. This study increases our understanding of various explored cancer therapeutics and underscores the efficient application of sCAR-T cells as a promising therapeutic option for breast cancer patients with low or heterogeneous antigen expression.
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Affiliation(s)
- Yu J. Cao
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Xuechun Wang
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Zhidong Wang
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Lijun Zhao
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Shuhong Li
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Zhuxia Zhang
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Xiaoyi Wei
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Hwayoung Yun
- College of Pharmacy, Pusan National University, Busan 46241, Republic of Korea
| | - Sei-hyun Choi
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Zhong Liu
- Shandong New Time Pharmaceutical Co., Ltd, No. 1 North Outer Ring Road, Feixian County, Shandong 273400, China
| | - Lili Zhao
- State Engineering Laboratory of High Expression of Mammalian Cells, No. 1 North Outer Ring Road, Feixian County, Shandong 273400, China
| | - Stephanie A. Kazane
- California Institute for Biomedical Research, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
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35
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Descalzi-Montoya D, Montel RA, Smith K, Dziopa E, Darwich A, Yang Z, Bitsaktsis C, Korngold R, Sabatino D. Synthetic Antibody Mimics Based on Cancer-Targeting Immunostimulatory Peptides. Chembiochem 2021; 22:1589-1596. [PMID: 32964656 PMCID: PMC8191480 DOI: 10.1002/cbic.202000407] [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: 06/24/2020] [Revised: 09/16/2020] [Indexed: 11/08/2022]
Abstract
De novo cancer-targeting immunostimulatory peptides have been designed and developed as synthetic antibody mimics. A series of bifunctional peptides incorporating NKp30-binding and NK-cell-activating domains were synthesized as linear dimers and then extended into branching trimeric peptides by the incorporation of GRP78-targeting and tumor-cell-binding sequences. A selected trimeric peptide from this small set of peptides displayed binding capabilities on GRP78+ HepG2 and A549 target cells. Cell binding diminished in the presence of an anti-GRP78 peptide blocker, thus suggesting GRP78-binding dependence. Similarly, the selected trimeric peptide was also found to exhibit NK cell binding in an NKp30-dependent manner, which translated into NK cell activation as indicated by cytokine secretion. In co-culture, fluorescence microscopy revealed that the target GFP-expressing A549 cells were visibly associated with the effector NK cells when pre-activated with lead trimeric peptide. Accordingly, A549 cells were found to be compromised, as evidenced by the loss of GFP signal and notable detection of early-/late-stage apoptosis. Investigation of the immunological markers related to toxicity revealed detectable secretion of pro-inflammatory cytokines and chemokines, including IFN-γ, TNF-α, and IL-8. Furthermore, administration of peptide-activated NK cells into A549-tumor-bearing mice resulted in a consistent decrease in tumor growth when compared to the untreated control group. Taken together, the identification of a lead trimeric peptide capable of targeting and activating NK cells' immunotoxicity directly towards GRP78+ /B7H6- tumors provides a novel proof-of-concept for the development of cancer-targeting immunostimulatory peptide ligands that mimic antibody-targeting and -activating functions related to cancer immunotherapy applications.
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MESH Headings
- Adjuvants, Immunologic/chemistry
- Adjuvants, Immunologic/pharmacology
- Adjuvants, Immunologic/therapeutic use
- Animals
- Antibodies/chemistry
- Antibodies/immunology
- Cell Line, Tumor
- Cytokines/metabolism
- Endoplasmic Reticulum Chaperone BiP/immunology
- Female
- Humans
- Immunotherapy/methods
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lymphocyte Activation/drug effects
- Male
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Neoplasms/drug therapy
- Neoplasms/pathology
- Peptides/chemical synthesis
- Peptides/chemistry
- Peptides/pharmacology
- Peptides/therapeutic use
- Transplantation, Heterologous
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Affiliation(s)
- Dante Descalzi-Montoya
- Center for Discovery and Innovation, Hackensack-Meridian Health, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Rachel A Montel
- Department of Biological Sciences and Chemistry and Biochemistry, Seton Hall University, 400 South Orange Avenue, South Orange, NJ 07079, USA
| | - Keith Smith
- Department of Biological Sciences and Chemistry and Biochemistry, Seton Hall University, 400 South Orange Avenue, South Orange, NJ 07079, USA
| | - Eugenia Dziopa
- Center for Discovery and Innovation, Hackensack-Meridian Health, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Andrieh Darwich
- Department of Biological Sciences and Chemistry and Biochemistry, Seton Hall University, 400 South Orange Avenue, South Orange, NJ 07079, USA
| | - Zheng Yang
- Center for Discovery and Innovation, Hackensack-Meridian Health, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - Constantine Bitsaktsis
- Department of Biological Sciences and Chemistry and Biochemistry, Seton Hall University, 400 South Orange Avenue, South Orange, NJ 07079, USA
| | - Robert Korngold
- Center for Discovery and Innovation, Hackensack-Meridian Health, 340 Kingsland Street, Nutley, NJ 07110, USA
| | - David Sabatino
- Department of Biological Sciences and Chemistry and Biochemistry, Seton Hall University, 400 South Orange Avenue, South Orange, NJ 07079, USA
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36
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Manandhar M, Chun E, Romesberg FE. Genetic Code Expansion: Inception, Development, Commercialization. J Am Chem Soc 2021; 143:4859-4878. [DOI: 10.1021/jacs.0c11938] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Miglena Manandhar
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
| | - Eugene Chun
- Synthorx, a Sanofi Company, La Jolla, California 92037, United States
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37
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An expanded genetic code facilitates antibody chemical conjugation involving the lambda light chain. Biochem Biophys Res Commun 2021; 546:35-39. [PMID: 33561746 DOI: 10.1016/j.bbrc.2021.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/20/2022]
Abstract
Most of the currently approved therapeutic antibodies are of the immunoglobulin gamma (IgG) κ isotype, leaving a vast opportunity for the use of IgGλ in medical treatments. The incorporation of designer amino acids into antibodies enables efficient and precise manufacturing of antibody chemical conjugates. Useful conjugation sites have been explored in the constant domain of the human κ-light chain (LCκ), which is no more than 38% identical to its LCλ counterpart in amino acid sequence. In the present study, we used an expanded genetic code for site-specifically incorporating Nε-(o-azidobenzyloxycarbonyl)-l-lysine (o-Az-Z-Lys) into the antigen-binding fragment (Fab) of an IgGλ, cixutumumab. Ten sites in the LCλ constant domain were found to support efficient chemical conjugation exploiting the bio-orthogonal azido chemistry. Most of the identified positions are located in regions that differ between the two light chain isotypes, thus being specific to the λ isotype. Finally, o-Az-Z-Lys was incorporated into the Fab fragments of cixutumumab and trastuzumab to chemically combine them; the resulting bispecific Fab-dimers showed a strong antagonistic activity against a cancer cell line. The present results expand the utility of the chemical conjugation method to the whole spectrum of humanized antibodies, including the λ isotype.
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38
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Abstract
Bispecific antibodies (bsAbs) target two different epitopes. These are an up-and-coming class of biologics, with two such therapeutics (emicizumab and blinatumomab) FDA approved and on the market, and many more in clinical trials. While the first reported bsAbs were constructed by chemical methods, this approach has fallen out of favour with the advent of modern genetic engineering techniques and, nowadays, the vast majority of bsAbs are produced by protein engineering. However, in recent years, relying on innovations in the fields of bioconjugation and bioorthogonal click chemistry, new chemical methods have appeared that have the potential to be competitive with protein engineering techniques and, indeed, hold some advantages. These approaches offer modularity, reproducibility and batch-to-batch consistency, as well as the integration of handles, whereby additional cargo molecules can be attached easily, e.g. to generate bispecific antibody-drug conjugates. The linker between the antibodies/antibody fragments can also be easily varied, and new formats (types, defined by structural properties or by construction methodology) can be generated rapidly. These attributes offer the potential to revolutionize the field. Here, we review chemical methods for the generation of bsAbs, showing that the newest examples of these techniques are worthy competitors to the industry-standard expression-based strategies.
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39
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Park J, Lee S, Kim Y, Yoo TH. Methods to generate site-specific conjugates of antibody and protein. Bioorg Med Chem 2021; 30:115946. [DOI: 10.1016/j.bmc.2020.115946] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023]
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40
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Honarmand Ebrahimi K. Ferritin as a Platform for Creating Antiviral Mosaic Nanocages: Prospects for Treating COVID-19. Chembiochem 2020; 22:1371-1378. [PMID: 33350032 DOI: 10.1002/cbic.202000728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/25/2020] [Indexed: 11/11/2022]
Abstract
Infectious diseases are a continues threat to human health and the economy worldwide. The latest example is the global pandemic of COVID-19 caused by SARS-CoV-2. Antibody therapy and vaccines are promising approaches to treat the disease; however, they have bottlenecks: they might have low efficacy or narrow breadth due to the continuous emergence of new strains of the virus or antibodies could cause antibody-dependent enhancement (ADE) of infection. To address these bottlenecks, I propose the use of 24-meric ferritin for the synthesis of mosaic nanocages to deliver a cocktail of antibodies or nanobodies alone or in combination with another therapeutic, like a nucleotide analogue, to mimic the viral entry process and deceive the virus, or to develop mosaic vaccines. I argue that available data showing the effectiveness of ferritin-antibody conjugates in targeting specific cells and ferritin-haemagglutinin nanocages in developing influenza vaccines strongly support my proposals.
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41
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Metcalf KJ, Kimmel BR, Sykora DJ, Modica JA, Parker KA, Berens E, Dai R, Dravid VP, Werb Z, Mrksich M. Synthetic Tuning of Domain Stoichiometry in Nanobody-Enzyme Megamolecules. Bioconjug Chem 2020; 32:143-152. [PMID: 33301672 DOI: 10.1021/acs.bioconjchem.0c00578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This paper presents a method to synthetically tune atomically precise megamolecule nanobody-enzyme conjugates for prodrug cancer therapy. Previous efforts to create heterobifunctional protein conjugates suffered from heterogeneity in domain stoichiometry, which in part led to the failure of antibody-enzyme conjugates in clinical trials. We used the megamolecule approach to synthesize anti-HER2 nanobody-cytosine deaminase conjugates with tunable numbers of nanobody and enzyme domains in a single, covalent molecule. Linking two nanobody domains to one enzyme domain improved avidity to a human cancer cell line by 4-fold but did not increase cytotoxicity significantly due to lowered enzyme activity. In contrast, a megamolecule composed of one nanobody and two enzyme domains resulted in an 8-fold improvement in the catalytic efficiency and increased the cytotoxic effect by over 5-fold in spheroid culture, indicating that the multimeric structure allowed for an increase in local drug activation. Our work demonstrates that the megamolecule strategy can be used to study structure-function relationships of protein conjugate therapeutics with synthetic control of protein domain stoichiometry.
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Affiliation(s)
- Kevin J Metcalf
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, United States.,Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Blaise R Kimmel
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Daniel J Sykora
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Justin A Modica
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Kelly A Parker
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Eric Berens
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, United States
| | - Raymond Dai
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Zena Werb
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, United States
| | - Milan Mrksich
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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42
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Lieser RM, Yur D, Sullivan MO, Chen W. Site-Specific Bioconjugation Approaches for Enhanced Delivery of Protein Therapeutics and Protein Drug Carriers. Bioconjug Chem 2020; 31:2272-2282. [DOI: 10.1021/acs.bioconjchem.0c00456] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rachel M. Lieser
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Daniel Yur
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Millicent O. Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, Delaware 19716, United States of America
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43
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Modica JA, Iderzorig T, Mrksich M. Design and Synthesis of Megamolecule Mimics of a Therapeutic Antibody. J Am Chem Soc 2020; 142:13657-13661. [PMID: 32706963 DOI: 10.1021/jacs.0c05093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This communication describes the design, synthesis, and biological activity of a megamolecule mimic of an anti-HER2 antibody. The antibody mimic was prepared by linking two Fabs from the therapeutic antibody trastuzumab, which are fused through the heavy chain variable domain to either cutinase or SnapTag, with a linker terminated in an irreversible inhibitor for each enzyme. This mimic binds HER2 with comparable avidity to trastuzumab, has similar activity in a cell-based assay, and can arrest tumor growth in a mouse xenograft BT474 tumor model. A panel of 16 bivalent anti-HER2 antibodies were prepared wherein each varied in the orientation of the fusion domain on the Fabs. The analogs displayed a range of cytotoxic activity, and surprisingly, the most active mimic binds to cells with a 10-fold lower avidity than the least active variant suggesting that structure plays a large role in their efficacy. This work suggests that the megamolecule approach can be used to prepare antibody mimics having a broad structural diversity.
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Affiliation(s)
- Justin A Modica
- Northwestern University, Departments of Chemistry and Biomedical Engineering, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Tsatsral Iderzorig
- Northwestern University, Departments of Chemistry and Biomedical Engineering, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Northwestern University, Departments of Chemistry and Biomedical Engineering, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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44
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Dhanjee HH, Saebi A, Buslov I, Loftis AR, Buchwald SL, Pentelute BL. Protein-Protein Cross-Coupling via Palladium-Protein Oxidative Addition Complexes from Cysteine Residues. J Am Chem Soc 2020; 142:9124-9129. [PMID: 32364380 DOI: 10.1021/jacs.0c03143] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Few chemical methods exist for the covalent conjugation of two proteins. We report the preparation of site-specific protein-protein conjugates that arise from the sequential cross-coupling of cysteine residues on two different proteins. The method involves the synthesis of stable palladium-protein oxidative addition complexes (Pd-protein OACs), a process that converts nucleophilic cysteine residues into an electrophilic S-aryl-Pd-X unit by taking advantage of an intramolecular oxidative addition strategy. This process is demonstrated on proteins up to 83 kDa in size and can be conveniently carried out in water and open to air. The resulting Pd-protein OACs can cross-couple with other thiol-containing proteins to arrive at homogeneous protein-protein bioconjugates.
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Affiliation(s)
- Heemal H Dhanjee
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Azin Saebi
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ivan Buslov
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alexander R Loftis
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Stephen L Buchwald
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley L Pentelute
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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45
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Better together: building protein oligomers naturally and by design. Biochem Soc Trans 2020; 47:1773-1780. [PMID: 31803901 PMCID: PMC6925524 DOI: 10.1042/bst20190283] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022]
Abstract
Protein oligomers are more common in nature than monomers, with dimers being the most prevalent final structural state observed in known structures. From a biological perspective, this makes sense as it conserves vital molecular resources that may be wasted simply by generating larger single polypeptide units, and allows new features such as cooperativity to emerge. Taking inspiration from nature, protein designers and engineers are now building artificial oligomeric complexes using a variety of approaches to generate new and useful supramolecular protein structures. Oligomerisation is thus offering a new approach to sample structure and function space not accessible through simply tinkering with monomeric proteins.
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46
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Maruani A, Szijj PA, Bahou C, Nogueira JCF, Caddick S, Baker JR, Chudasama V. A Plug-and-Play Approach for the De Novo Generation of Dually Functionalized Bispecifics. Bioconjug Chem 2020; 31:520-529. [DOI: 10.1021/acs.bioconjchem.0c00002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Antoine Maruani
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, London, United Kingdom
| | - Peter A. Szijj
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, London, United Kingdom
| | - Calise Bahou
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, London, United Kingdom
| | - João C. F. Nogueira
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, London, United Kingdom
| | - Stephen Caddick
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, London, United Kingdom
| | - James R. Baker
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, London, United Kingdom
| | - Vijay Chudasama
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, London, United Kingdom
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
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47
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One-step site-specific antibody fragment auto-conjugation using SNAP-tag technology. Nat Protoc 2019; 14:3101-3125. [DOI: 10.1038/s41596-019-0214-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/07/2019] [Indexed: 12/13/2022]
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48
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Kim E, Koo H. Biomedical applications of copper-free click chemistry: in vitro, in vivo, and ex vivo. Chem Sci 2019; 10:7835-7851. [PMID: 31762967 PMCID: PMC6855312 DOI: 10.1039/c9sc03368h] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/28/2019] [Indexed: 12/18/2022] Open
Abstract
Recently, click chemistry has provided important advances in biomedical research fields. Particularly, copper-free click chemistry including strain-promoted azide-alkyne cycloaddition (SPAAC) and inverse-electron-demand Diels-Alder (iEDDA) reactions enable fast and specific chemical conjugation under aqueous conditions without the need for toxic catalysts. Click chemistry has resulted in a change of paradigm, showing that artificial chemical reactions can occur on cell surfaces, in cell cytosol, or within the body, which is not easy with most other chemical reactions. Click chemistry in vitro allows specific labelling of cellular target proteins and studying of drug target engagement with drug surrogates in live cells. Furthermore, cellular membrane lipids and proteins could be selectively labelled with click chemistry in vitro and cells could be adhered together using click chemistry. Click chemistry in vivo enables efficient and effective molecular imaging and drug delivery for diagnosis and therapy. Click chemistry ex vivo can be used to develop molecular tools to understand tissue development, diagnosis of diseases, and therapeutic monitoring. Overall, the results from research to date suggest that click chemistry has emerged as a valuable tool in biomedical fields as well as in organic chemistry.
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Affiliation(s)
- Eunha Kim
- Department of Molecular Science and Technology , Ajou University , Suwon 16499 , Republic of Korea
| | - Heebeom Koo
- Department of Medical Life Sciences , College of Medicine , The Catholic University of Korea , 222 Banpo-daero, Seocho-gu , Seoul , 06591 , Republic of Korea .
- Department of Biomedicine & Health Sciences , College of Medicine , The Catholic University of Korea , 222 Banpo-daero, Seocho-gu , Seoul , 06591 , Republic of Korea
- Catholic Photomedicine Research Institute , College of Medicine , The Catholic University of Korea , 222 Banpo-daero, Seocho-gu , Seoul , 06591 , Republic of Korea
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49
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Worthy HL, Auhim HS, Jamieson WD, Pope JR, Wall A, Batchelor R, Johnson RL, Watkins DW, Rizkallah P, Castell OK, Jones DD. Positive functional synergy of structurally integrated artificial protein dimers assembled by Click chemistry. Commun Chem 2019. [DOI: 10.1038/s42004-019-0185-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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50
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Lee BS, Lee Y, Park J, Jeong BS, Jo M, Jung ST, Yoo TH. Construction of an immunotoxin via site-specific conjugation of anti-Her2 IgG and engineered Pseudomonas exotoxin A. J Biol Eng 2019; 13:56. [PMID: 31285754 PMCID: PMC6588878 DOI: 10.1186/s13036-019-0188-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/12/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Immunotoxins consisting of a toxin from bacteria or plants and a targeting module have been developed as potent anti-cancer therapeutics. The majority of them, especially those in preclinical or clinical testing stages, are fusion proteins of a toxin and antibody fragment. Immunotoxins based on full-length antibodies are less studied, even though the fragment crystallizable (Fc) domain plays an important role in regulating the concentration of immunoglobulin G (IgG) in the serum and in antibody-mediated immune responses against pathogens. RESULTS We devised a method to site-specifically conjugate IgG and another protein using a cysteine residue introduced into the IgG and a bio-orthogonally reactive unnatural amino acid incorporated into the other protein. The human epidermal growth factor receptor 2 (Her2)-targeting IgG, trastuzumab, was engineered to have an unpaired cysteine in the heavy chain, and an unnatural amino acid with the azido group was incorporated into an engineered Pseudomonas exotoxin A (PE24). The two protein molecules were conjugated site-specifically using a bifunctional linker having dibenzocyclooctyne and maleimide groups. Binding to Her2 and interaction with various Fc receptors of trastuzumab were not affected by the conjugation with PE24. The trastuzumab-PE24 conjugate was cytotoxic to Her2-overexpressing cell lines, which involved the inhibition of cellular protein synthesis due to the modification of elongation factor-2. CONCLUSIONS We constructed the site-specifically conjugated immunotoxin based on IgG and PE24, which induced target-specific cytotoxicity. To evaluate the molecule as a cancer therapeutic, animal studies are planned to assess tumor regression, half-life in blood, and in vivo immunogenicity. In addition, we expect that the site-specific conjugation method can be used to develop other antibody-protein conjugates for applications in therapeutics and diagnostics.
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Affiliation(s)
- Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Yumi Lee
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Jisoo Park
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Bo Seok Jeong
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
| | - Migyeong Jo
- Department of Applied Chemistry, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul, 02707 South Korea
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School of Medicine, Korea University, Seongbuk-gu, Seoul, 02841 South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499 South Korea
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