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Yamazaki S, Takahashi K, Matsuda Y. Tag-free protein modification by lipoate ligase A: exploring substrate tolerance. ANAL SCI 2024; 40:1111-1119. [PMID: 38504072 DOI: 10.1007/s44211-024-00534-6] [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: 01/13/2024] [Accepted: 02/10/2024] [Indexed: 03/21/2024]
Abstract
This study delves into the functional intricacies of lipoate ligase A (LplA), an enzyme showing great promise in bioconjugation due to its unique capacity for introducing azido groups into proteins without requiring a genetic tag. We aimed to enhance the understanding of LplA's functionality, particularly its substrate tolerance and the reliability of various analytical techniques. A pivotal aspect of our approach was incorporating azido groups into a range of proteins, followed by the addition of the fluorescent molecule Cy3 via click chemistry. Analysis of fluorescent intensity in the altered proteins indicated varying degrees of conjugation. Additionally, phenyl resin-based RP-HPLC facilitated effective separation of modified proteins, unmodified proteins, and remaining fluorescent tags post-separation. SASA analysis provided insights into conjugation trends, guiding the identification of proteins amenable to LplA's tag-free modification. Our findings demonstrate LplA's broad substrate tolerability for protein modification.
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Affiliation(s)
- Shunsuke Yamazaki
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki, Kanagawa, 210-8681, Japan.
| | | | - Yutaka Matsuda
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki, Kanagawa, 210-8681, Japan.
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Zou Z, Ji Y, Schwaneberg U. Empowering Site-Specific Bioconjugations In Vitro and In Vivo: Advances in Sortase Engineering and Sortase-Mediated Ligation. Angew Chem Int Ed Engl 2024; 63:e202310910. [PMID: 38081121 DOI: 10.1002/anie.202310910] [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: 07/31/2023] [Indexed: 12/23/2023]
Abstract
Sortase-mediated ligation (SML) has emerged as a powerful and versatile methodology for site-specific protein conjugation, functionalization/labeling, immobilization, and design of biohybrid molecules and systems. However, the broader application of SML faces several challenges, such as limited activity and stability, dependence on calcium ions, and reversible reactions caused by nucleophilic side-products. Over the past decade, protein engineering campaigns and particularly directed evolution, have been extensively employed to overcome sortase limitations, thereby expanding the potential application of SML in multiple directions, including therapeutics, biorthogonal chemistry, biomaterials, and biosensors. This review provides an overview of achieved advancements in sortase engineering and highlights recent progress in utilizing SML in combination with other state-of-the-art chemical and biological methodologies. The aim is to encourage scientists to employ sortases in their conjugation experiments.
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Affiliation(s)
- Zhi Zou
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074, Aachen, Germany
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
| | - Yu Ji
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
| | - Ulrich Schwaneberg
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074, Aachen, Germany
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
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Yamazaki S, Ito K, Aoki T, Arashida N, Watanabe T, Fujii T, Matsuda Y. Biological Evaluation of Antibody-Drug Conjugates Produced by Tag-Free Lipoate Ligase A Modification. Biochemistry 2024; 63:644-650. [PMID: 38350078 DOI: 10.1021/acs.biochem.3c00513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
The concept of tag-free protein modification has attracted considerable interest in chemical biology because of its flexible and straightforward reaction process. In 2021, a groundbreaking approach using lipoate ligase A (LplA) for tag-free enzymatic modification of antibodies was unveiled, demonstrating its potential for the generation of precise antibody conjugates. In this study, to further explore LplA-mediated antibody-drug conjugate (ADC) synthesis, we performed initial biological evaluations of ADCs synthesized using LplA. Using the anti-HER2 antibody trastuzumab, we introduced octanoic acid azide using LplA and subsequently obtained an ADC using click chemistry with the drug DBCO-VC-PAB-MMAE. The bioactivity of the synthesized anti-HER2-ADC was evaluated using HER2-positive SKBR-3 and HER2-negative MCF7 cells. Its toxicity and selectivity were found to be comparable to those of the FDA-approved Kadcyla. In addition, a stability study involving rat and human plasma demonstrated the stability of the LplA-mediated ADC. Additionally, the affinity for the neonatal Fc receptor (FcRn) was retained after conjugation. These preliminary in vitro evaluations suggested that LplA-derived ADCs can have considerable pharmaceutical potential. Our results can set the stage for further in vivo evaluations and safety assessments. We suggest that the integration of tag-free LplA methods into the production of ADCs can offer a novel and promising approach for biopharmaceutical manufacturing.
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Affiliation(s)
- Shunsuke Yamazaki
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Kanagawa, Japan
| | - Kenichiro Ito
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Kanagawa, Japan
| | - Tsubasa Aoki
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Kanagawa, Japan
| | - Naoko Arashida
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Kanagawa, Japan
| | - Tomohiro Watanabe
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Kanagawa, Japan
| | - Tomohiro Fujii
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Kanagawa, Japan
| | - Yutaka Matsuda
- Ajinomoto Co., Inc., 1-1 Suzuki-cho, Kawasaki 210-8681, Kanagawa, Japan
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Wang Z, Zhang D, Hu S, Bi X, Lescar J, Tam JP, Liu CF. PAL-Mediated Ligation for Protein and Cell-Surface Modification. Methods Mol Biol 2022; 2530:177-193. [PMID: 35761050 DOI: 10.1007/978-1-0716-2489-0_13] [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: 06/15/2023]
Abstract
Peptidyl Asx-specific ligases (PALs) effect peptide ligation by catalyzing transpeptidation reactions at Asn/Asp-peptide bonds. Owing to their high efficiency and mild aqueous reaction conditions, these ligases have emerged as powerful biotechnological tools for protein manipulation in recent years. PALs are enzymes of the asparaginyl endopeptidase (AEP) superfamily but have predominant transpeptidase activity as opposed to typical AEPs which are predominantly hydrolases. Butelase-1 and VyPAL2, two PALs discovered by our teams, have been used successfully in a wide range of applications, including macrocyclization of synthetic peptides and recombinant proteins, protein N- or C-terminal modification, and cell-surface labeling. As shown in numerous reports, PAL-mediated ligation is highly efficient at Asn junctions. Although considerably less efficient, Asp-specific ligation has also been shown to be practically useful under suitable conditions. Herein, we describe the methods of using VyPAL2 for protein macrocyclization and labeling at an Asp residue as well as for protein dual labeling through orthogonal Asp- and Asn-directed ligations. We also describe a method for cell-surface protein modification using butelase-1, demonstrating its advantageous features over previous methods.
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Affiliation(s)
- Zhen Wang
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
| | - Dingpeng Zhang
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
| | - Side Hu
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
| | - Xiaobao Bi
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Zhejiang, China
| | - Julien Lescar
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
| | - James P Tam
- School of Biological Science, Nanyang Technological University, Singapore, Singapore
| | - Chuan-Fa Liu
- School of Biological Science, Nanyang Technological University, Singapore, Singapore.
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Schirer A, Rouch A, Marcheteau E, Stojko J, Sophie Landron, Jeantet E, Fould B, Ferry G, Boutin JA. Further assessments of ligase LplA-mediated modifications of proteins in vitro and in cellulo. Mol Biol Rep 2021; 49:149-161. [PMID: 34718939 DOI: 10.1007/s11033-021-06853-5] [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: 06/23/2021] [Accepted: 09/23/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Posttranslational modifications of proteins are catalyzed by a large family of enzymes catalyzing many chemical modifications. One can hijack the natural use of those enzymes to modify targeted proteins with synthetic chemical moieties. The lipoic acid ligase LplA mutants can be used to introduce onto the lysine sidechain lipoic acid moiety synthetic analogues. Substrate protein candidates of the ligase must obey a few a priori rules. METHODS AND RESULTS In the present report, we technically detailed the use of a cell line stably expressing both the ligase and a model protein (thioredoxin). Although the goal can be reach, and the protein visualized in situ, many experimental difficulties must be fixed. The sequence of events comprises (i) in cellulo labeling of the target protein with a N3-lipoic acid derivative catalyzed by the mutant ligase, (ii) the further introduction by click chemistry onto this lysine sidechain of a fluorophore and (iii) the following of the labeled protein in living cells. One of the main difficulties was to assess the click chemistry step onto the living cells, because images from both control and experimental cells were similar. Alternatively, we describe at that stage, the preferred use of another technique: the Halo-Tag one that led to the obtention of clear images of the targeted protein in its cellular context. Although the ligase-mediated labeling of protein in situ is a rich domain for which many cellular tools must be developed, many difficulties must be considered before entering a systematic use of this approach. CONCLUSIONS In the present contribution, we added several steps of analytical characterization, both in vitro and in cellulo that were previously lacking. Furthermore, we show that the use of the click chemistry should be manipulated with care, as the claimed specificity might be not complete whenever living cells are used. Finally, we added another approach-the Halo Tag-to complete the previously suggested approaches for labelling proteins in cells, as we found difficult to strictly apply the previously reported methodology.
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Affiliation(s)
- Alicia Schirer
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France.,, Techno Parc de Thudinie 2, 6536, Thuin, Belgium
| | - Anne Rouch
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Estelle Marcheteau
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Johann Stojko
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Sophie Landron
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Elodie Jeantet
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Benjamin Fould
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Gilles Ferry
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France
| | - Jean A Boutin
- PEX Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, 78290, Croissy-sur-Seine, France. .,Institut de Recherches Internationales Servier, 50 rue Carnot, 92284, Suresnes, France. .,Faculté de Pharmacie, PHARMADEV (Pharmacochimie et Biologie Pour le Développement), Université Toulouse 3 Paul Sabatier, 35 chemin des maraîchers, 31062, Toulouse Cedex 9, France.
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Plaks JG, Brewer JA, Jacobsen NK, McKenna M, Uzarski JR, Lawton TJ, Filocamo SF, Kaar JL. Rosetta-Enabled Structural Prediction of Permissive Loop Insertion Sites in Proteins. Biochemistry 2020; 59:3993-4002. [PMID: 32970423 DOI: 10.1021/acs.biochem.0c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While loop motifs frequently play a major role in protein function, our understanding of how to rationally engineer proteins with novel loop domains remains limited. In the absence of rational approaches, the incorporation of loop domains often destabilizes proteins, thereby requiring massive screening and selection to identify sites that can accommodate loop insertion. We developed a computational strategy for rapidly scanning the entire structure of a scaffold protein to determine the impact of loop insertion at all possible amino acid positions. This approach is based on the Rosetta kinematic loop modeling protocol and was demonstrated by identifying sites in lipase that were permissive to insertion of the LAP peptide. Interestingly, the identification of permissive sites was dependent on the contribution of the residues in the near-loop environment on the Rosetta score and did not correlate with conventional structural features (e.g., B-factors). As evidence of this, several insertion sites (e.g., following residues 17, 47-49, and 108), which were predicted and confirmed to be permissive, interrupted helices, while others (e.g., following residues 43, 67, 116, 119, and 121), which are situated in loop regions, were nonpermissive. This approach was further shown to be predictive for β-glucosidase and human phosphatase and tensin homologue (PTEN), and to facilitate the engineering of insertion sites through in silico mutagenesis. By enabling the design of loop-containing protein libraries with high probabilities of soluble expression, this approach has broad implications in many areas of protein engineering, including antibody design, improving enzyme activity, and protein modification.
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Affiliation(s)
- Joseph G Plaks
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Jeff A Brewer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Nicole K Jacobsen
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Michael McKenna
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Joshua R Uzarski
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Timothy J Lawton
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Shaun F Filocamo
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
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