1
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Kofoed C, Tay NES, Ye X, Erkalo G, Muir TW. Cell surface sculpting using logic-gated protein actuators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572113. [PMID: 38187604 PMCID: PMC10769198 DOI: 10.1101/2023.12.18.572113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Cell differentiation and tissue specialization lead to unique cellular surface landscapes and exacerbated or loss of expression patterns can result in further heterogenicity distinctive of pathological phenotypes1-3. Immunotherapies and emerging protein therapeutics seek to exploit such differences by engaging cell populations selectively based on their surface markers. Since a single surface antigen rarely defines a specific cell type4,5, the development of programmable molecular systems that integrate multiple cell surface features to convert on-target inputs to user-defined outputs is highly desirable. Here, we describe an autonomous decision-making protein device driven by proximity-gated protein trans-splicing that allows local generation of an active protein from two otherwise inactive fragments. We show that this protein actuator platform can perform various Boolean logic operations on cell surfaces, allowing highly selective recruitment of enzymatic and cytotoxic activities to specific cells within mixed populations. Due to its intrinsic modularity and tunability, this technology is expected to be compatible with different types of inputs, targeting modalities and functional outputs, and as such will have broad application in the synthetic biology and biotechnology areas.
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Affiliation(s)
- Christian Kofoed
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | | | - Xuanjia Ye
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Girum Erkalo
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA
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2
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Joest EF, Tampé R. Design principles for engineering light-controlled antibodies. Trends Biotechnol 2023; 41:1501-1517. [PMID: 37507295 DOI: 10.1016/j.tibtech.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023]
Abstract
Engineered antibodies are essential tools for research and advanced pharmacy. In the development of therapeutics, antibodies are excellent candidates as they offer both target recognition and modulation. Thanks to the latest advances in biotechnology, light-activated antibody fragments can be constructed to control spontaneous antigen interaction with high spatiotemporal precision. To implement conditional antigen binding, several optogenetic and optochemical engineering concepts have recently been developed. Here, we highlight the various strategies and discuss the features of opto-conditional antibodies. Each concept offers intrinsic advantages beneficial to different applications. In summary, the novel design approaches constitute a complementary toolset to promote current and upcoming antibody technologies with ultimate precision.
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Affiliation(s)
- Eike F Joest
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany.
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany.
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3
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Bridge T, Sachdeva A. Engineering Homogeneous Photoactive Antibody Fragments. Methods Mol Biol 2023; 2676:21-40. [PMID: 37277622 DOI: 10.1007/978-1-0716-3251-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Genetically encoded site-specifically incorporated noncanonical amino acids (ncAAs) have been used to modulate properties of several proteins. Here, we describe a procedure for engineering photoactive antibody fragments that bind to their target antigen only after irradiation with 365 nm light. The procedure starts with identification of tyrosine residues in antibody fragments that are important for antibody-antigen binding and thus targets for replacement with photocaged tyrosine (pcY). This is followed by cloning of plasmids and expression of pcY-containing antibody fragments in E. coli. Finally, we describe a cost-effective and biologically-relevant method for measuring the binding affinity of photoactive antibody fragments to antigens expressed on the surface of live cancer cells.
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Affiliation(s)
- Thomas Bridge
- School of Chemistry, University of East Anglia, Norwich, UK
| | - Amit Sachdeva
- School of Chemistry, University of East Anglia, Norwich, UK.
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4
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Allen GM, Lim WA. Rethinking cancer targeting strategies in the era of smart cell therapeutics. Nat Rev Cancer 2022; 22:693-702. [PMID: 36175644 DOI: 10.1038/s41568-022-00505-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/09/2022] [Indexed: 02/08/2023]
Abstract
In the past several decades, the development of cancer therapeutics has largely focused on precision targeting of single cancer-associated molecules. Despite great advances, such targeted therapies still show incomplete precision and the eventual development of resistance due to target heterogeneity or mutation. However, the recent development of cell-based therapies such as chimeric antigen receptor (CAR) T cells presents a revolutionary opportunity to reframe strategies for targeting cancers. Immune cells equipped with synthetic circuits are essentially living computers that can be programmed to recognize tumours based on multiple signals, including both tumour cell-intrinsic and microenvironmental. Moreover, cells can be programmed to launch broad but highly localized therapeutic responses that can limit the potential for escape while still maintaining high precision. Although these emerging smart cell engineering capabilities have yet to be fully implemented in the clinic, we argue here that they will become much more powerful when combined with machine learning analysis of genomic data, which can guide the design of therapeutic recognition programs that are the most discriminatory and actionable. The merging of cancer analytics and synthetic biology could lead to nuanced paradigms of tumour recognition, more akin to facial recognition, that have the ability to more effectively address the complex challenges of treating cancer.
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Affiliation(s)
- Greg M Allen
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Cell Design Institute, University of California San Francisco, San Francisco, CA, USA
| | - Wendell A Lim
- Cell Design Institute, University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
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5
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Oostindie SC, Rinaldi DA, Zom GG, Wester MJ, Paulet D, Al-Tamimi K, van der Meijden E, Scheick JR, Wilpshaar T, de Jong B, Hoff-van den Broek M, Grattan RM, Oosterhoff JJ, Vignau J, Verploegen S, Boross P, Beurskens FJ, Lidke DS, Schuurman J, de Jong RN. Logic-gated antibody pairs that selectively act on cells co-expressing two antigens. Nat Biotechnol 2022; 40:1509-1519. [PMID: 35879362 PMCID: PMC9546771 DOI: 10.1038/s41587-022-01384-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/02/2022] [Indexed: 01/11/2023]
Abstract
The use of therapeutic monoclonal antibodies is constrained because single antigen targets often do not provide sufficient selectivity to distinguish diseased from healthy tissues. We present HexElect®, an approach to enhance the functional selectivity of therapeutic antibodies by making their activity dependent on clustering after binding to two different antigens expressed on the same target cell. lmmunoglobulin G (lgG)-mediated clustering of membrane receptors naturally occurs on cell surfaces to trigger complement- or cell-mediated effector functions or to initiate intracellular signaling. We engineer the Fc domains of two different lgG antibodies to suppress their individual homo-oligomerization while promoting their pairwise hetero-oligomerization after binding co-expressed antigens. We show that recruitment of complement component C1q to these hetero-oligomers leads to clustering-dependent activation of effector functions such as complement mediated killing of target cells or activation of cell surface receptors. HexElect allows selective antibody activity on target cells expressing unique, potentially unexplored combinations of surface antigens.
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Affiliation(s)
- Simone C Oostindie
- Genmab, Utrecht, the Netherlands
- Department of Immunology, Leiden University Medical Center, Leiden, the Netherlands
| | - Derek A Rinaldi
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | | | - Michael J Wester
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | | | | | | | | | | | | | | | - Rachel M Grattan
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | | | | | | | | | | | - Diane S Lidke
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, USA
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
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6
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Jedlitzke B, Mootz HD. A light-activatable photocaged variant of the ultra-high affinity ALFA-tag nanobody. Chembiochem 2022; 23:e202200079. [PMID: 35411584 PMCID: PMC9324849 DOI: 10.1002/cbic.202200079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/18/2022] [Indexed: 11/25/2022]
Abstract
Nanobodies against short linear peptide‐epitopes are widely used to detect and bind proteins of interest (POI) in fusion constructs. Engineered nanobodies that can be controlled by light have found very recent attention for various extra‐ and intracellular applications. We here report the design of a photocaged variant of the ultra‐high affinity ALFA‐tag nanobody, also termed ALFA‐tag photobody. ortho‐Nitrobenzyl tyrosine was incorporated into the paratope region of the nanobody by genetic code expansion technology and resulted in a ≥9,200 to 100,000‐fold impairment of the binding affinity. Irradiation with light (365 nm) leads to decaging and reconstitutes the native nanobody. We show the light‐dependent binding of the ALFA‐tag photobody to HeLa cells presenting the ALFA‐tag. The generation of the first photobody directed against a short peptide epitope underlines the generality of our photobody design concept. We envision that this photobody will be useful for the spatiotemporal control of proteins in many applications using cultured cells.
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Affiliation(s)
- Benedikt Jedlitzke
- Institute of BiochemistryDepartment of Chemistry and PharmacyUniversity of MuensterCorrensstr. 3648149MünsterGermany
| | - Henning D. Mootz
- Institute of BiochemistryDepartment of Chemistry and PharmacyUniversity of MuensterCorrensstr. 3648149MünsterGermany
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7
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Orozco CT, Bersellini M, Irving LM, Howard WW, Hargreaves D, Devine PWA, Siouve E, Browne GJ, Bond NJ, Phillips JJ, Ravn P, Jackson SE. Mechanistic insights into the rational design of masked antibodies. MAbs 2022; 14:2095701. [PMID: 35799328 PMCID: PMC9272835 DOI: 10.1080/19420862.2022.2095701] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Although monoclonal antibodies have greatly improved cancer therapy, they can trigger side effects due to on-target, off-tumor toxicity. Over the past decade, strategies have emerged to successfully mask the antigen-binding site of antibodies, such that they are only activated at the relevant site, for example, after proteolytic cleavage. However, the methods for designing an ideal affinity-based mask and what parameters are important are not yet well understood. Here, we undertook mechanistic studies using three masks with different properties and identified four critical factors: binding site and affinity, as well as association and dissociation rate constants, which also played an important role. HDX-MS was used to identify the location of binding sites on the antibody, which were subsequently validated by obtaining a high-resolution crystal structure for one of the mask-antibody complexes. These findings will inform future designs of optimal affinity-based masks for antibodies and other therapeutic proteins.
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Affiliation(s)
- Carolina T Orozco
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.,Biologics Engineering, R&D, AstraZeneca, Cambridge, UK.,Analytical Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | | | | | - Wesley W Howard
- Analytical Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Gaithersburg, MD, USA
| | | | - Paul W A Devine
- Analytical Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | - Elise Siouve
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK.,Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | | | - Nicholas J Bond
- Analytical Sciences, Biopharmaceutical Development, R&D, AstraZeneca, Cambridge, UK
| | | | - Peter Ravn
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK.,Department of Biotherapeutic Discovery, H. Lundbeck A/S, Copenhagen, Denmark
| | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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8
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Maruyama K, Ishiyama T, Seki Y, Sakai K, Togo T, Oisaki K, Kanai M. Protein Modification at Tyrosine with Iminoxyl Radicals. J Am Chem Soc 2021; 143:19844-19855. [PMID: 34787412 DOI: 10.1021/jacs.1c09066] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Post-translational modifications (PTMs) of proteins are a biological mechanism for reversibly controlling protein function. Synthetic protein modifications (SPMs) at specific canonical amino acids can mimic PTMs. However, reversible SPMs at hydrophobic amino acid residues in proteins are especially limited. Here, we report a tyrosine (Tyr)-selective SPM utilizing persistent iminoxyl radicals, which are readily generated from sterically hindered oximes via single-electron oxidation. The reactivity of iminoxyl radicals with Tyr was dependent on the steric and electronic demands of oximes; isopropyl methyl piperidinium oxime 1f formed stable adducts, whereas the reaction of tert-butyl methyl piperidinium oxime 1o was reversible. The difference in reversibility between 1f and 1o, differentiated only by one methyl group, is due to the stability of iminoxyl radicals, which is partly dictated by the bond dissociation energy of oxime O-H groups. The Tyr-selective modifications with 1f and 1o proceeded under physiologically relevant, mild conditions. Specifically, the stable Tyr-modification with 1f introduced functional small molecules, including an azobenzene photoswitch, to proteins. Moreover, masking critical Tyr residues by SPM with 1o, and subsequent deconjugation triggered by the treatment with a thiol, enabled on-demand control of protein functions. We applied this reversible Tyr modification with 1o to alter an enzymatic activity and the binding affinity of a monoclonal antibody with an antigen upon modification/deconjugation. The on-demand ON/OFF switch of protein functions through Tyr-selective and reversible covalent-bond formation will provide unique opportunities in biological research and therapeutics.
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Affiliation(s)
- Katsuya Maruyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Ishiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yohei Seki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kentaro Sakai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takaya Togo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kounosuke Oisaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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9
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Massana Roquero D, McCorduck B, Bollella P, Smutok O, Melman A, Katz E. Biomolecule Release from Alginate Composite Hydrogels Triggered by Logically Processed Signals. Chemphyschem 2021; 22:1967-1975. [PMID: 34309163 DOI: 10.1002/cphc.202100458] [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: 06/14/2021] [Revised: 07/16/2021] [Indexed: 12/31/2022]
Abstract
Alginate composite hydrogels that exhibit highly sensitive stimuli-responsive behavior were used for signal-stimulated release of pre-loaded insulin. The alginate pores, particularly located at the periphery, were blocked by interpenetration of polyvinyl alcohol (PVA) cross-linked with 1,3-benzenediboronic acid (IPN), thus, significantly reducing uncontrolled leakage of the entrapped biomolecules. The beads were loaded with insulin and various enzymes mimicking different Boolean logic gates (AND, OR, NOR, IMP, INHIB). The enzymes were activated with biologically relevant input signals applied in four logic combinations: 0,0; 1,0; 0,1; 1,1, having the production of H2 O2 as the result of the biocatalytic reactions. The "successful" combination of the input signals leading to the H2 O2 production was different for different logic gates, following the corresponding truth tables of the logic gates. When H2 O2 was produced, boronate ester bonds were oxidized and the IPN was irreversibly degraded, thus re-opening the original pores of the hydrogel. This process allowed release of insulin from the alginate beads. The smart soft material that we have developed tackled well-known limitations of these systems and it may prove valuable in future medical diagnostics or treatments.
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Affiliation(s)
- Daniel Massana Roquero
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Brandon McCorduck
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Paolo Bollella
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.,Department of Chemistry, University of Bari A. Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Oleh Smutok
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Artem Melman
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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10
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Lucchi R, Bentanachs J, Oller-Salvia B. The Masking Game: Design of Activatable Antibodies and Mimetics for Selective Therapeutics and Cell Control. ACS CENTRAL SCIENCE 2021; 7:724-738. [PMID: 34079893 PMCID: PMC8161478 DOI: 10.1021/acscentsci.0c01448] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Indexed: 05/04/2023]
Abstract
The high selectivity and affinity of antibody binding have made antibodies all-pervasive tools in therapy, diagnosis, and basic science. A plethora of chemogenetic approaches has been devised to make antibodies responsive to stimuli ranging from light to enzymatic activity, temperature, pH, ions, and effector molecules. Within a single decade, the field of activatable antibodies has yielded marketed therapeutics capable of engaging antigens that could not be targeted with traditional antibodies, as well as new tools to control intracellular protein location and investigate biological processes. Many opportunities remain untapped, waiting for more efficient and generally applicable masking strategies to be developed at the interface between chemistry and biotechnology.
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Affiliation(s)
- Roberta Lucchi
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Jordi Bentanachs
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
| | - Benjamí Oller-Salvia
- Grup d’Enginyeria
de Materials, Institut Químic de
Sarrià (IQS), Universitat Ramon Llull, 08017 Barcelona, Spain
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11
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Ekanayake AI, Sobze L, Kelich P, Youk J, Bennett NJ, Mukherjee R, Bhardwaj A, Wuest F, Vukovic L, Derda R. Genetically Encoded Fragment-Based Discovery from Phage-Displayed Macrocyclic Libraries with Genetically Encoded Unnatural Pharmacophores. J Am Chem Soc 2021; 143:5497-5507. [PMID: 33784084 DOI: 10.1021/jacs.1c01186] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetically encoded macrocyclic peptide libraries with unnatural pharmacophores are valuable sources for the discovery of ligands for many targets of interest. Traditionally, generation of such libraries employs "early stage" incorporation of unnatural building blocks into the chemically or translationally produced macrocycles. Here, we describe a divergent late-stage approach to such libraries starting from readily available starting material: genetically encoded libraries of peptides. A diketone linchpin 1,5-dichloropentane-2,4-dione converts peptide libraries displayed on phage to 1,3-diketone bearing macrocyclic peptides (DKMP): shelf-stable precursors for Knorr pyrazole synthesis. Ligation of diverse hydrazine derivatives onto DKMP libraries displayed on phage that carries silent DNA-barcodes yields macrocyclic libraries in which the amino acid sequence and the pharmacophore are encoded by DNA. Selection of this library against carbonic anhydrase enriched macrocycles with benzenesulfonamide pharmacophore and nanomolar Kd. The methodology described in this manuscript can graft diverse pharmacophores into many existing genetically encoded phage libraries and significantly increase the value of such libraries in molecular discoveries.
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Affiliation(s)
- Arunika I Ekanayake
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Lena Sobze
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Payam Kelich
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Jihea Youk
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Nicholas J Bennett
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Raja Mukherjee
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Atul Bhardwaj
- Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Frank Wuest
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Cross Cancer Institute, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Lela Vukovic
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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12
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Lindstedt PR, Aprile FA, Sormanni P, Rakoto R, Dobson CM, Bernardes GJL, Vendruscolo M. Systematic Activity Maturation of a Single-Domain Antibody with Non-canonical Amino Acids through Chemical Mutagenesis. Cell Chem Biol 2021; 28:70-77.e5. [PMID: 33217338 PMCID: PMC7837213 DOI: 10.1016/j.chembiol.2020.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/03/2020] [Accepted: 11/02/2020] [Indexed: 12/16/2022]
Abstract
Great advances have been made over the last four decades in therapeutic and diagnostic applications of antibodies. The activity maturation of antibody candidates, however, remains a significant challenge. To address this problem, we present a method that enables the systematic enhancement of the activity of a single-domain antibody through the post-translational installation of non-canonical side chains by chemical mutagenesis. We illustrate this approach by performing a structure-activity relationship study beyond the 20 naturally occurring amino acids on a single-domain antibody designed in silico to inhibit the aggregation of the amyloid-β peptide, a process closely linked to Alzheimer's disease. We found that this approach can improve, by five orders of magnitude, the anti-aggregation activity of the starting single-domain antibody, without affecting its stability. These results show that the expansion of the chemical space available to antibodies through chemical mutagenesis can be exploited for the systematic enhancement of the activity of these molecules.
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Affiliation(s)
- Philip R Lindstedt
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Francesco A Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK; Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Robertinah Rakoto
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Gonçalo J L Bernardes
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Protugal.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK.
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13
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14
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Khowsathit J, Bazzoli A, Cheng H, Karanicolas J. Computational Design of an Allosteric Antibody Switch by Deletion and Rescue of a Complex Structural Constellation. ACS CENTRAL SCIENCE 2020; 6:390-403. [PMID: 32232139 PMCID: PMC7099597 DOI: 10.1021/acscentsci.9b01065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 05/08/2023]
Abstract
Therapeutic monoclonal antibodies have transformed medicine, especially with regards to treating cancers and disorders of the immune system. More than 50 antibody-derived drugs have already reached the clinic, the majority of which target cytokines or cell-surface receptors. Unfortunately, many of these targets have pleiotropic functions: they serve multiple different roles, and often not all of these roles are disease-related. This can be problematic because antibodies act throughout the body, and systemic neutralization of such targets can lead to safety concerns. To address this, we have developed a strategy whereby an antibody's ability to recognize its antigen is modulated by a second layer of control, relying on addition of an exogenous small molecule. In previous studies, we began to explore this idea by introducing a deactivating tryptophan-to-glycine mutation in the domain-domain interface of a single-chain variable fragment (scFv), and then restoring activity by adding back indole to fit the designed cavity. Here, we now describe a novel computational strategy for enumerating larger cavities that can be formed by simultaneously introducing multiple adjacent large-to-small mutations; we then carry out a complementary virtual screen to identify druglike compounds to match each candidate cavity. We first demonstrate the utility of this strategy in a fluorescein-binding single-chain variable fragment (scFv) and experimentally characterize a triple mutant with reduced antigen-binding (Rip-3) that can be rescued using a complementary ligand (Stitch-3). Because our design is built upon conserved residues in the antibody framework, we then show that the same mutation/ligand pair can also be used to modulate antigen-binding in an scFv build from a completely unrelated framework. This set of residues is present in many therapeutic antibodies as well, suggesting that this mutation/ligand pair may serve as a general starting point for introducing ligand-dependence into many clinically relevant antibodies.
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Affiliation(s)
- Jittasak Khowsathit
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
| | - Andrea Bazzoli
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
| | - Hong Cheng
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
| | - John Karanicolas
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
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15
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Bridge T, Shaikh SA, Thomas P, Botta J, McCormick PJ, Sachdeva A. Site-Specific Encoding of Photoactivity in Antibodies Enables Light-Mediated Antibody-Antigen Binding on Live Cells. Angew Chem Int Ed Engl 2019; 58:17986-17993. [PMID: 31609054 PMCID: PMC6973043 DOI: 10.1002/anie.201908655] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/11/2019] [Indexed: 12/20/2022]
Abstract
Antibodies have found applications in several fields, including, medicine, diagnostics, and nanotechnology, yet methods to modulate antibody-antigen binding using an external agent remain limited. Here, we have developed photoactive antibody fragments by genetic site-specific replacement of single tyrosine residues with photocaged tyrosine, in an antibody fragment, 7D12. A simple and robust assay is adopted to evaluate the light-mediated binding of 7D12 mutants to its target, epidermal growth factor receptor (EGFR), on the surface of cancer cells. Presence of photocaged tyrosine reduces 7D12-EGFR binding affinity by over 20-fold in two out of three 7D12 mutants studied, and binding is restored upon exposure to 365 nm light. Molecular dynamics simulations explain the difference in effect of photocaging on 7D12-EGFR interaction among the mutants. Finally, we demonstrate the application of photoactive antibodies in delivering fluorophores to EGFR-positive live cancer cells in a light-dependent manner.
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Affiliation(s)
- Thomas Bridge
- School of ChemistryUniversity of East AngliaNorwichNR4 7TJUK
| | - Saher A. Shaikh
- School of ChemistryUniversity of East AngliaNorwichNR4 7TJUK
| | - Paul Thomas
- The Henry Wellcome Laboratory of Cell ImagingUniversity of East AngliaNorwichNR4 7TJUK
| | - Joaquin Botta
- Centre of EndocrinologyWilliam Harvey Research InstituteQueen Mary University LondonCharterhouse SquareLondonEC1M 6BQUK
| | - Peter J. McCormick
- Centre of EndocrinologyWilliam Harvey Research InstituteQueen Mary University LondonCharterhouse SquareLondonEC1M 6BQUK
| | - Amit Sachdeva
- School of ChemistryUniversity of East AngliaNorwichNR4 7TJUK
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16
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Bridge T, Shaikh SA, Thomas P, Botta J, McCormick PJ, Sachdeva A. Site‐Specific Encoding of Photoactivity in Antibodies Enables Light‐Mediated Antibody–Antigen Binding on Live Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908655] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Thomas Bridge
- School of ChemistryUniversity of East Anglia Norwich NR4 7TJ UK
| | - Saher A. Shaikh
- School of ChemistryUniversity of East Anglia Norwich NR4 7TJ UK
| | - Paul Thomas
- The Henry Wellcome Laboratory of Cell ImagingUniversity of East Anglia Norwich NR4 7TJ UK
| | - Joaquin Botta
- Centre of EndocrinologyWilliam Harvey Research InstituteQueen Mary University London Charterhouse Square London EC1M 6BQ UK
| | - Peter J. McCormick
- Centre of EndocrinologyWilliam Harvey Research InstituteQueen Mary University London Charterhouse Square London EC1M 6BQ UK
| | - Amit Sachdeva
- School of ChemistryUniversity of East Anglia Norwich NR4 7TJ UK
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17
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Tregubov AA, Nikitin PI, Nikitin MP. Advanced Smart Nanomaterials with Integrated Logic-Gating and Biocomputing: Dawn of Theranostic Nanorobots. Chem Rev 2018; 118:10294-10348. [DOI: 10.1021/acs.chemrev.8b00198] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Andrey A. Tregubov
- Moscow Institute of Physics and Technology (State University), 1A Kerchenskaya St, Moscow 117303, Russia
| | - Petr I. Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov Street, Moscow 119991, Russia
| | - Maxim P. Nikitin
- Moscow Institute of Physics and Technology (State University), 1A Kerchenskaya St, Moscow 117303, Russia
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18
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Dadová J, Galan SR, Davis BG. Synthesis of modified proteins via functionalization of dehydroalanine. Curr Opin Chem Biol 2018; 46:71-81. [PMID: 29913421 DOI: 10.1016/j.cbpa.2018.05.022] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/02/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
Abstract
Dehydroalanine has emerged in recent years as a non-proteinogenic residue with strong chemical utility in proteins for the study of biology. In this review we cover the several methods now available for its flexible and site-selective incorporation via a variety of complementary chemical and biological techniques and examine its reactivity, allowing both creation of modified protein side-chains through a variety of bond-forming methods (C-S, C-N, C-Se, C-C) and as an activity-based probe in its own right. We illustrate its utility with selected examples of biological and technological discovery and application.
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Affiliation(s)
- Jitka Dadová
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sébastien Rg Galan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom.
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19
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Freedy A, Matos MJ, Boutureira O, Corzana F, Guerreiro A, Akkapeddi P, Somovilla VJ, Rodrigues T, Nicholls K, Xie B, Jiménez-Osés G, Brindle KM, Neves AA, Bernardes GJL. Chemoselective Installation of Amine Bonds on Proteins through Aza-Michael Ligation. J Am Chem Soc 2017; 139:18365-18375. [PMID: 29206031 PMCID: PMC5799870 DOI: 10.1021/jacs.7b10702] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 12/30/2022]
Abstract
Chemical modification of proteins is essential for a variety of important diagnostic and therapeutic applications. Many strategies developed to date lack chemo- and regioselectivity as well as result in non-native linkages that may suffer from instability in vivo and adversely affect the protein's structure and function. We describe here the reaction of N-nucleophiles with the amino acid dehydroalanine (Dha) in a protein context. When Dha is chemically installed in proteins, the addition of a wide-range N-nucleophiles enables the rapid formation of amine linkages (secondary and tertiary) in a chemoselective manner under mild, biocompatible conditions. These new linkages are stable at a wide range of pH values (pH 2.8 to 12.8), under reducing conditions (biological thiols such as glutathione) and in human plasma. This method is demonstrated for three proteins and is shown to be fully compatible with disulfide bridges, as evidenced by the selective modification of recombinant albumin that displays 17 structurally relevant disulfides. The practicability and utility of our approach is further demonstrated by the construction of a chemically modified C2A domain of Synaptotagmin-I protein that retains its ability to preferentially bind to apoptotic cells at a level comparable to the native protein. Importantly, the method was useful for building a homogeneous antibody-drug conjugate with a precise drug-to-antibody ratio of 2. The kinase inhibitor crizotinib was directly conjugated to Dha through its piperidine motif, and its antibody-mediated intracellular delivery results in 10-fold improvement of its cancer cell-killing efficacy. The simplicity and exquisite site-selectivity of the aza-Michael ligation described herein allows the construction of stable secondary and tertiary amine-linked protein conjugates without affecting the structure and function of biologically relevant proteins.
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Affiliation(s)
- Allyson
M. Freedy
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Maria J. Matos
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Omar Boutureira
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Francisco Corzana
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Ana Guerreiro
- Instituto
de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Padma Akkapeddi
- Instituto
de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Víctor J. Somovilla
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Tiago Rodrigues
- Instituto
de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Karl Nicholls
- Albumedix
Ltd., Castle Court, 59
Castle Boulevard, NG7 1FD Nottingham, U.K.
| | - Bangwen Xie
- Li
Ka Shing Centre, Cancer Research UK Cambridge
Institute, Robinson Way, CB2 0RE Cambridge, U.K.
| | - Gonzalo Jiménez-Osés
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Kevin M. Brindle
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
- Li
Ka Shing Centre, Cancer Research UK Cambridge
Institute, Robinson Way, CB2 0RE Cambridge, U.K.
| | - André A. Neves
- Li
Ka Shing Centre, Cancer Research UK Cambridge
Institute, Robinson Way, CB2 0RE Cambridge, U.K.
| | - Gonçalo J. L. Bernardes
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
- Instituto
de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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20
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Wright TH, Davis BG. Post-translational mutagenesis for installation of natural and unnatural amino acid side chains into recombinant proteins. Nat Protoc 2017. [DOI: 10.1038/nprot.2017.087] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Jongkees SAK, Umemoto S, Suga H. Linker-free incorporation of carbohydrates into in vitro displayed macrocyclic peptides. Chem Sci 2016; 8:1474-1481. [PMID: 28572907 PMCID: PMC5452274 DOI: 10.1039/c6sc04381j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 10/18/2016] [Indexed: 12/13/2022] Open
Abstract
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates.
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates. These reactions are selective for cysteine, and do not interfere with amplification of the nucleic acid component of an mRNA-displayed peptide. Furthermore, these reactions are shown to be compatible with two different macrocyclisation chemistries, and when applied to a peptide containing an N-terminal cysteine give a ketone that can be functionalised in an orthogonal manner. This new strategy can overcome a limitation of ribosomal translation, providing a means to incorporate untranslatable groups such as carbohydrates in amino acid side chains, and will allow for the ribosomal generation of glycopeptides, requiring only the introduction of a free thiol in the molecule to be incorporated. In combination with in vitro selection techniques, this strategy is envisaged to allow the discovery of biologically-active glycopeptides with a near-natural, but hydrolytically stable, thioglycosidic bond.
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Affiliation(s)
- S A K Jongkees
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - S Umemoto
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - H Suga
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan . .,JST CREST , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan
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22
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Gunnoo SB, Madder A. Chemical Protein Modification through Cysteine. Chembiochem 2016; 17:529-53. [DOI: 10.1002/cbic.201500667] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Smita B. Gunnoo
- Organic & Biomimetic Chemistry Research Group; Department of Organic and Macromolecular Chemistry; Ghent University; Krijgslaan 281 9000 Gent Belgium
| | - Annemieke Madder
- Organic & Biomimetic Chemistry Research Group; Department of Organic and Macromolecular Chemistry; Ghent University; Krijgslaan 281 9000 Gent Belgium
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