1
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Tang TMS, Luk LYP. Towards controlling activity of a peptide asparaginyl ligase (PAL) by lumazine synthetase compartmentalization. Faraday Discuss 2024. [PMID: 38832470 DOI: 10.1039/d4fd00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Peptide asparaginyl ligases (PALs) hold significant potential in protein bioconjugation due to their excellent kinetic properties and broad substrate compatibility. However, realizing their full potential in biocatalytic applications requires precise control of their activity. Inspired by nature, we aimed to compartmentalize a representative PAL, OaAEP1-C247A, within protein containers to create artificial organelles with substrate sorting capability. Two encapsulation approaches were explored using engineered lumazine synthases (AaLS). The initial strategy involved tagging the PAL with a super-positively charged GFP(+36) for encapsulation into the super-negatively charged AaLS-13 variant, but it resulted in undesired truncation of the enzyme. The second approach involved genetic fusion of the OaAEP1-C247A with a circularly permutated AaLS variant (cpAaLS) and its co-production with AaLS-13, which successfully enabled compartmentalization of the PAL within a patch-work protein cage. Although the caged PAL retained its activity, it was significantly reduced compared to the free enzyme (∼30-40-fold), likely caused by issues related to OaAEP1-C247A stability and folding. Nevertheless, these findings demonstrated the feasibility of the AaLS encapsulation approach and encourage further optimization in the design of peptide-ligating artificial organelles in E. coli, aiming for a more effective and stable system for protein modifications.
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Affiliation(s)
- T M Simon Tang
- School of Chemistry & Cardiff Catalysis Institute, Cardiff University, Main Building, Room 1.54, Park Place, Cardiff, CF10 3AT, UK.
| | - Louis Y P Luk
- School of Chemistry & Cardiff Catalysis Institute, Cardiff University, Main Building, Room 1.54, Park Place, Cardiff, CF10 3AT, UK.
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2
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Zhang Y, Yang Z, Saimi D, Shen X, Ye J, Yu B, Pefaur N, Scheer JM, Nixon AE, Chen Z. Geometric Antibody Engineering Reveals the Spatial Factor on the Efficacy of Bispecific T Cell Engagers. ACS Chem Biol 2024; 19:916-925. [PMID: 38491942 DOI: 10.1021/acschembio.3c00728] [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: 03/18/2024]
Abstract
Bispecific antibodies (BsAbs) represent an emerging class of biologics that can recognize two different antigens or epitopes. T-cell engagers (TcEs) bind two targets in trans on the cell surface of the effector and target cell to induce proximal immune effects, opening exciting windows for immunotherapies. To date, the engineering of BsAbs has been mainly focused on tuning the molecular weight and valency. However, the effects of spatial factors on the biological functions of BsAbs have been less explored due to the lack of biochemical methods to precisely manipulate protein geometry. Here, we studied the geometric effects of the TcEs. First, by genetically inserting rigidly designed ankyrin repeat proteins into TcEs, we revealed that the efficacy progressively decreased as the spacer distance of the two binding domains increased. Then, we constructed 26 pairs of TcEs with the same size but varying orientations using click chemistry-mediated conjugation at different mutation sites. We found that linear ligation sites play a minor role in modulating cell-killing efficacy. Next, we rendered the TcEs' advanced topology by cyclization chemistry using the SpyTag/SpyCatcher pair or sortase ligation approaches. Cyclized TcEs were generally more potent than their linear counterparts. Particularly, sortase A cyclized TcEs, bearing a minimal tagging motif, exhibited better cell-killing efficacy in vitro and improved stability both in vitro and in vivo compared to the linear TcE. This work combines modern bioconjugation chemistry and protein engineering tools for antibody engineering, shedding light on the elusive spatial factors of BsAbs functionality.
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Affiliation(s)
- Yu Zhang
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhe Yang
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Dilizhatai Saimi
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Xiaowen Shen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Junqing Ye
- Department of Research Beyond Borders, Boehringer Ingelheim, Investment Co., Ltd., Beijing 100027, China
| | - Bingke Yu
- Department of Research Beyond Borders, Boehringer Ingelheim, Investment Co., Ltd., Shanghai 200040, China
| | - Noah Pefaur
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Justin M Scheer
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Andrew E Nixon
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Zhixing Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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3
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Tang J, Hao M, Liu J, Chen Y, Wufuer G, Zhu J, Zhang X, Zheng T, Fang M, Zhang S, Li T, Ge S, Zhang J, Xia N. Design of a recombinant asparaginyl ligase for site-specific modification using efficient recognition and nucleophile motifs. Commun Chem 2024; 7:87. [PMID: 38637620 PMCID: PMC11026461 DOI: 10.1038/s42004-024-01173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Asparaginyl ligases have been extensively utilized as valuable tools for site-specific bioconjugation or surface-modification. However, the application is hindered by the laborious and poorly reproducible preparation processes, unstable activity and ambiguous substrate requirements. To address these limitations, this study employed a structure-based rational approach to obtain a high-yield and high-activity protein ligase called OaAEP1-C247A-aa55-351. It was observed that OaAEP1-C247A-aa55-351 exhibits appreciable catalytic activities across a wide pH range, and the addition of the Fe3+ metal ion effectively enhances the catalytic power. Importantly, this study provides insight into the recognition and nucleophile peptide profiles of OaAEP1-C247A-aa55-351. The ligase demonstrates a higher recognition ability for the "Asn-Ala-Leu" motif and an N-terminus "Arg-Leu" as nucleophiles, which significantly increases the reaction yield. Consequently, the catalytic activity of OaAEP1-C247A-aa55-351 with highly efficient recognition and nucleophile motif, "Asn-Ala-Leu" and "Arg-Leu" under the buffer containing Fe3+ is 70-fold and 2-fold higher than previously reported OaAEP1-C247A and the most efficient butelase-1, respectively. Thus, the designed OaAEP1-C247A-aa55-351, with its highly efficient recognition and alternative nucleophile options, holds promising potential for applications in protein engineering, chemo-enzymatic modification, and the development of drugs.
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Affiliation(s)
- Jiabao Tang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Mengling Hao
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Junxian Liu
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Yaling Chen
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Gulimire Wufuer
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Jie Zhu
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Petrochemical Engineering, Changzhou University, 213164, Changzhou, China
| | - Xuejie Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Tingquan Zheng
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Mujin Fang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Shiyin Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Tingdong Li
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China.
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China.
| | - Shengxiang Ge
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China.
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China.
| | - Jun Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
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4
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Zhu T, Zhang X, Li R, Wu B. Efficient production of peptidylglycine α-hydroxylating monooxygenase in yeast for protein C-terminal functionalization. Int J Biol Macromol 2024; 263:130443. [PMID: 38417749 DOI: 10.1016/j.ijbiomac.2024.130443] [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: 02/01/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Peptidylglycine α-hydroxylating monooxygenase (PHM) is pivotal for C-terminal amidation of bioactive peptides in animals, offering substantial potential for customized protein synthesis. However, efficient PHM production has been hindered by the complexity of animal cell culture and the absence of glycosylation in bacterial hosts. Here, we demonstrate the recombinant expression of Caenorhabditis elegans PHM in the yeast Pichia pastoris, achieving a remarkable space-time yield of 28.8 U/L/day. This breakthrough surpasses prior PHM production rates and eliminates the need for specialized cultivation equipment or complex transfection steps. Mass spectrometry revealed N-glycosylation at residue N182 of recombinant CePHM, which impacts the enzyme's activity as indicated by biochemical experiments. To showcase the utility of CePHM, we performed C-terminal amidation on ubiquitin at a substrate loading of 30 g/L, a concentration meeting the requirements for pharmaceutical peptide production. Overall, this work establishes an efficient PHM production method, promising advancements in scalable manufacturing of C-terminally modified bioactive peptides and probe proteins.
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Affiliation(s)
- Tong Zhu
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuanshuo Zhang
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruifeng Li
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Bian Wu
- AIM center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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5
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Budimir ZL, Patel RS, Eggly A, Evans CN, Rondon-Cordero HM, Adams JJ, Das C, Parkinson EI. Biocatalytic cyclization of small macrolactams by a penicillin-binding protein-type thioesterase. Nat Chem Biol 2024; 20:120-128. [PMID: 38062262 PMCID: PMC10999230 DOI: 10.1038/s41589-023-01495-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Macrocyclic peptides represent promising scaffolds for chemical tools and potential therapeutics. Synthetic methods for peptide macrocyclization are often hampered by C-terminal epimerization and oligomerization, leading to difficult scalability. While chemical strategies to circumvent this issue exist, they often require specific amino acids to be present in the peptide sequence. Herein, we report the characterization of Ulm16, a peptide cyclase belonging to the penicillin-binding protein-type class of thioesterases that catalyze head-to-tail macrolactamization of nonribosmal peptides. Ulm16 efficiently cyclizes various nonnative peptides ranging from 4 to 6 amino acids with catalytic efficiencies of up to 3 × 106 M-1 s-1. Unlike many previously described homologs, Ulm16 tolerates a variety of C- and N-terminal amino acids. The crystal structure of Ulm16, along with modeling of its substrates and site-directed mutagenesis, allows for rationalization of this wide substrate scope. Overall, Ulm16 represents a promising tool for the biocatalytic production of macrocyclic peptides.
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Affiliation(s)
| | - Rishi S Patel
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Alyssa Eggly
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Claudia N Evans
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Jessica J Adams
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Elizabeth I Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
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6
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Tang TM, Mason JM. Intracellular Application of an Asparaginyl Endopeptidase for Producing Recombinant Head-to-Tail Cyclic Proteins. JACS AU 2023; 3:3290-3296. [PMID: 38155637 PMCID: PMC10751764 DOI: 10.1021/jacsau.3c00591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 12/30/2023]
Abstract
Peptide backbone cyclization is commonly observed in nature and is increasingly applied to proteins and peptides to improve thermal and chemical stability and resistance to proteolytic enzymes and enhance biological activity. However, chemical synthesis of head-to-tail cyclic peptides and proteins is challenging, is often low yielding, and employs toxic and unsustainable reagents. Plant derived asparaginyl endopeptidases such as OaAEP1 have been employed to catalyze the head-to-tail cyclization of peptides in vitro, offering a safer and more sustainable alternative to chemical methods. However, while asparaginyl endopeptidases have been used in vitro and in native and transgenic plant species, they have never been used to generate recombinant cyclic proteins in live recombinant organisms outside of plants. Using dihydrofolate reductase as a proof of concept, we show that a truncated OaAEP1 variant C247A is functional in the Escherichia coli physiological environment and can therefore be coexpressed with a substrate protein to enable concomitant in situ cyclization. The bacterial system is ideal for cyclic protein production owing to the fast growth rate, durability, ease of use, and low cost. This streamlines cyclic protein production via a biocatalytic process with fast kinetics and minimal ligation scarring, while negating the need to purify the enzyme, substrate, and reaction mixtures individually. The resulting cyclic protein was characterized in vitro, demonstrating enhanced thermal stability compared to the corresponding linear protein without impacting enzyme activity. We anticipate this convenient method for generating cyclic peptides will have broad utility in a range of biochemical and chemical applications.
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Affiliation(s)
- T. M.
Simon Tang
- Department
of Life Sciences, University of Bath, Claverton Down, Bath, North Somerset BA2
7AY, U.K.
| | - Jody M. Mason
- Department
of Life Sciences, University of Bath, Claverton Down, Bath, North Somerset BA2
7AY, U.K.
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7
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Fang J, Li T, Lee J, Im D, Xu L, Liu Y, Seo J, Zhang WB. A single-domain protein catenane of dihydrofolate reductase. Natl Sci Rev 2023; 10:nwad304. [PMID: 38188024 PMCID: PMC10769465 DOI: 10.1093/nsr/nwad304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 01/09/2024] Open
Abstract
A single-domain protein catenane refers to two mechanically interlocked polypeptide rings that fold synergistically into a compact and integrated structure, which is extremely rare in nature. Here, we report a single-domain protein catenane of dihydrofolate reductase (cat-DHFR). This design was achieved by rewiring the connectivity between secondary motifs to introduce artificial entanglement and synthesis was readily accomplished through a series of programmed and streamlined post-translational processing events in cells without any additional in vitro reactions. The target molecule contained few exogenous motifs and was thoroughly characterized using a combination of ultra-performance liquid chromatography-mass spectrometry, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, protease cleavage experiments and ion mobility spectrometry-mass spectrometry. Compared with the linear control, cat-DHFR retained its catalytic capability and exhibited enhanced stability against thermal or chemical denaturation due to conformational restriction. These results suggest that linear proteins may be converted into their concatenated single-domain counterparts with almost identical chemical compositions, well-preserved functions and elevated stabilities, representing an entirely new horizon in protein science.
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Affiliation(s)
- Jing Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tianzuo Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiyeon Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Dahye Im
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Lianjie Xu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jongcheol Seo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Beijing Academy of Artificial Intelligence, Beijing 100084, China
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8
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Yasuzawa Y, Shibuya R, Senga Y, Miyafusa T, Honda S. Determination of the optimal connector length to enhance stability of backbone-circularized granulocyte colony-stimulating factor. FEBS Open Bio 2023; 13:1910-1921. [PMID: 37574212 PMCID: PMC10549227 DOI: 10.1002/2211-5463.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 07/19/2023] [Accepted: 08/11/2023] [Indexed: 08/15/2023] Open
Abstract
Improving protein stability is important for industrial applications, and one promising method for achieving this is backbone circularization. As connector length affects stability, predicting and elucidating a more stable connector length is necessary for development of the backbone circularization method. However, the relationship between connector length and protein stability has not been completely elucidated. Here, we determined the most stable connector length for granulocyte colony-stimulating factor by changing one residue at a time to produce connector length variants and then measuring their thermal stability. Analysis of the local structures obtained from the predicted structures of the circularized variants revealed that an approach using helix length, dihedral backbone angle, and number of unbonded hydrogen bond donors and acceptors is suitable for identifying connector lengths with higher stability.
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Affiliation(s)
- Yosuke Yasuzawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoJapan
| | - Risa Shibuya
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoJapan
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Yukako Senga
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Takamitsu Miyafusa
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
- Bioproduction Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
| | - Shinya Honda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoJapan
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)TsukubaJapan
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9
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Keeble AH, Wood DP, Howarth M. Design and Evolution of Enhanced Peptide-Peptide Ligation for Modular Transglutaminase Assembly. Bioconjug Chem 2023. [PMID: 37289810 DOI: 10.1021/acs.bioconjchem.3c00122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Robust and precise tools are needed to enhance the functionality and resilience of synthetic nanoarchitectures. Here, we have employed directed evolution and rational design to build a fast-acting molecular superglue from a bacterial adhesion protein. We have generated the SnoopLigase2 coupling system, a genetically encoded route for efficient transamidation between SnoopTag2 and DogTag2 peptides. Each peptide was selected for rapid reaction by phage display screening. The optimized set allows more than 99% completion and is compatible with diverse buffers, pH values, and temperatures, accelerating the reaction over 1000-fold. SnoopLigase2 directs a specific reaction in the mammalian secretory pathway, allowing covalent display on the plasma membrane. Transglutaminase 2 (TG2) has a network of interactions and substrates amidst the mammalian cell surface and extracellular matrix. We expressed a modified TG2 with resistance to oxidative inactivation and minimal self-reactivity. SnoopLigase2 enables TG2 functionalization with transforming growth factor alpha (TGFα) in routes that would be impossible through genetic fusion. The TG2:TGFα conjugate retained transamidase activity, stably anchored TGFα for signal activation in the extracellular environment, and reprogrammed cell behavior. This modular toolbox should create new opportunities for molecular assembly, both for novel biomaterials and complex cellular environments.
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Affiliation(s)
- Anthony H Keeble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Dominic P Wood
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
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10
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Hemu X, Chan NY, Liew HT, Hu S, Zhang X, Serra A, Lescar J, Liu CF, Tam JP. Substrate-binding glycine residues are major determinants for hydrolase and ligase activity of plant legumains. THE NEW PHYTOLOGIST 2023; 238:1534-1545. [PMID: 36843268 DOI: 10.1111/nph.18841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Peptide asparaginyl ligases (PALs) are useful tools for precision modifications of proteins and live-cell surfaces by ligating peptides after Asn/Asp (Asx). They share high sequence and structural similarity to plant legumains that are generally known as asparaginyl endopeptidases (AEPs), thus making it challenging to identify PALs from AEPs. In this study, we investigate 875 plant species from algae to seed plants with available sequence data in public databases to identify new PALs. We conducted evolutionary trace analysis on 1500 plant legumains, including eight known PALs, to identify key residues that could differentiate ligases and proteases, followed by recombinant expression and functional validation of 16 novel legumains. Previously, we showed that the substrate-binding sequences flanking the catalytic site can strongly influence the enzymatic direction of a legumain and which we named as ligase-activity determinants (LADs). Here, we show that two conserved substrate-binding Gly residues of LADs are critical, but negative determinants for ligase activity. Our results suggest that specific glycine residues are molecular determinants to identify PALs and AEPs as two different legumain subfamilies, accounting for c. 1% and 88%, respectively.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Ning-Yu Chan
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Heng Tai Liew
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Side Hu
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Aida Serra
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- Neuroscience Area, +Pec Proteomics Research Group (+PPRG), Faculty of Medicine, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRB Lleida), University of Lleida, Av. Rovira Roure, 80, Lleida, 25198, Spain
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
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11
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Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
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Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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12
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Xia Y, Li F, Zhang X, Balamkundu S, Tang F, Hu S, Lescar J, Tam JP, Liu CF. A Cascade Enzymatic Reaction Scheme for Irreversible Transpeptidative Protein Ligation. J Am Chem Soc 2023; 145:6838-6844. [PMID: 36924109 DOI: 10.1021/jacs.2c13628] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Enzymatic peptide ligation holds great promise in the study of protein functions and development of protein therapeutics. Owing to their high catalytic efficiency and a minimal tripeptide recognition motif, peptidyl asparaginyl ligases (PALs) are particularly useful tools for bioconjugation. However, as an inherent limitation of transpeptidases, PAL-mediated ligation is reversible, requiring a large excess of one of the ligation partners to shift the reaction equilibrium in the forward direction. Herein, we report a method to make PAL-mediated intermolecular ligation irreversible by coupling it to glutaminyl cyclase (QC)-catalyzed pyroglutamyl formation. In this method, the acyl donor substrate of PALs is designed to have glutamine at the P1' position of the Asn-P1'-P2' tripeptide PAL recognition motif. Upon ligation with an acyl acceptor substrate, the acyl donor substrate releases a leaving group in which the exposed N-terminal glutamine is cyclized by QC, quenching the Gln Nα-amine in a lactam. Using this method, PAL-mediated ligation can achieve near-quantitative yields even at an equal molar ratio between the two ligation partners. We have demonstrated this method for a wide range of applications, including protein-to-protein ligations. We anticipate that this cascade enzymatic reaction scheme will make PAL enzymes well suited for numerous new uses in biotechnology.
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Affiliation(s)
- Yiyin Xia
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Fupeng Li
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | | | - Fan Tang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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13
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Antonenko A, Singh AK, Mosna K, Krężel A. OaAEP1 Ligase-Assisted Chemoenzymatic Synthesis of Full Cysteine-Rich Metal-Binding Cyanobacterial Metallothionein SmtA. Bioconjug Chem 2023. [PMID: 36921066 PMCID: PMC10119931 DOI: 10.1021/acs.bioconjchem.3c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Among all approaches used for the semisynthesis of natural or chemically modified products, enzyme-assisted ligation is among the most promising and dynamically developing approaches. Applying an efficient C247A mutant of Oldenlandia affinis plant ligase OaAEP1 and solid-phase peptide synthesis chemistry, we present the chemoenzymatic synthesis of a complete sequence of the cysteine-rich and metal-binding cyanobacterial metallothionein Synechococcus metallothionein A (SmtA). Zn(II) and Cd(II) binding to the newly synthesized SmtA showed identical properties to the protein expressed in Escherichia coli. The presented approach is the first example of the use of OaAEP1 mutant for total protein synthesis of metallothionein, which occurs in mild conditions preventing cysteine thiol oxidation. The recognition motif of the applied enzyme could naturally occur in the protein structure or be synthetically or genetically incorporated in some loops or secondary structure elements. Therefore, we envision that this strategy can be used for efficiently obtaining SmtA and for a wide range of proteins and their derivatives.
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Affiliation(s)
- Anastasiia Antonenko
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Avinash Kumar Singh
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Karolina Mosna
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
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14
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Hemu X, Zhang X, Chang HY, Poh JE, Tam JP. Consensus design and engineering of an efficient and high-yield peptide asparaginyl ligase for protein cyclization and ligation. J Biol Chem 2023; 299:102997. [PMID: 36764523 PMCID: PMC10017362 DOI: 10.1016/j.jbc.2023.102997] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Plant legumains are Asn/Asp-specific endopeptidases that have diverse functions in plants. Peptide asparaginyl ligases (PALs) are a special legumain subtype that primarily catalyze peptide bond formation rather than hydrolysis. PALs are versatile protein engineering tools but are rarely found in nature. To overcome this limitation, here we describe a two-step method to design and engineer a high-yield and efficient recombinant PAL based on commonly found asparaginyl endopeptidases. We first constructed a consensus sequence derived from 1500 plant legumains to design the evolutionarily stable legumain conLEG that could be produced in E. coli with 20-fold higher yield relative to that for natural legumains. We then applied the ligase-activity determinant hypothesis to exploit conserved residues in PAL substrate-binding pockets and convert conLEG into conPAL1-3. Functional studies showed that conLEG is primarily a hydrolase, whereas conPALs are ligases. Importantly, conPAL3 is a superefficient and broadly active PAL for protein cyclization and ligation.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hong Yi Chang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Jin En Poh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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15
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Cebrián R, Martínez-García M, Fernández M, García F, Martínez-Bueno M, Valdivia E, Kuipers OP, Montalbán-López M, Maqueda M. Advances in the preclinical characterization of the antimicrobial peptide AS-48. Front Microbiol 2023; 14:1110360. [PMID: 36819031 PMCID: PMC9936517 DOI: 10.3389/fmicb.2023.1110360] [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: 11/28/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Antimicrobial resistance is a natural and inevitable phenomenon that constitutes a severe threat to global public health and economy. Innovative products, active against new targets and with no cross- or co-resistance with existing antibiotic classes, novel mechanisms of action, or multiple therapeutic targets are urgently required. For these reasons, antimicrobial peptides such as bacteriocins constitute a promising class of new antimicrobial drugs under investigation for clinical development. Here, we review the potential therapeutic use of AS-48, a head-to-tail cyclized cationic bacteriocin produced by Enterococcus faecalis. In the last few years, its potential against a wide range of human pathogens, including relevant bacterial pathogens and trypanosomatids, has been reported using in vitro tests and the mechanism of action has been investigated. AS-48 can create pores in the membrane of bacterial cells without the mediation of any specific receptor. However, this mechanism of action is different when susceptible parasites are studied and involves intracellular targets. Due to these novel mechanisms of action, AS-48 remains active against the antibiotic resistant strains tested. Remarkably, the effect of AS-48 against eukaryotic cell lines and in several animal models show little effect at the doses needed to inhibit susceptible species. The characteristics of this molecule such as low toxicity, microbicide activity, blood stability and activity, high stability at a wide range of temperatures or pH, resistance to proteases, and the receptor-independent effect make AS-48 unique to fight a broad range of microbial infections, including bacteria and some important parasites.
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Affiliation(s)
- Rubén Cebrián
- Department of Clinical Microbiology, Instituto de Investigación Biosanitaria Ibs.GRANADA, University Hospital San Cecilio, Granada, Spain,*Correspondence: Rubén Cebrián, ✉
| | | | | | - Federico García
- Department of Clinical Microbiology, Instituto de Investigación Biosanitaria Ibs.GRANADA, University Hospital San Cecilio, Granada, Spain,Biomedicinal Research Network Center, Infectious Diseases (CIBERINFEC), Madrid, Spain
| | | | - Eva Valdivia
- Department of Microbiology, University of Granada, Granada, Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands
| | - Manuel Montalbán-López
- Department of Microbiology, University of Granada, Granada, Spain,Manuel Montalbán-López, ✉
| | - Mercedes Maqueda
- Department of Microbiology, University of Granada, Granada, Spain
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16
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Fischer NH, Oliveira MT, Diness F. Chemical modification of proteins - challenges and trends at the start of the 2020s. Biomater Sci 2023; 11:719-748. [PMID: 36519403 DOI: 10.1039/d2bm01237e] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomally expressed proteins perform multiple, versatile, and specialized tasks throughout Nature. In modern times, chemically modified proteins, including improved hormones, enzymes, and antibody-drug-conjugates have become available and have found advanced industrial and pharmaceutical applications. Chemical modification of proteins is used to introduce new functionalities, improve stability or drugability. Undertaking chemical reactions with proteins without compromising their native function is still a core challenge as proteins are large conformation dependent multifunctional molecules. Methods for functionalization ideally should be chemo-selective, site-selective, and undertaken under biocompatible conditions in aqueous buffer to prevent denaturation of the protein. Here the present challenges in the field are discussed and methods for modification of the 20 encoded amino acids as well as the N-/C-termini and protein backbone are presented. For each amino acid, common and traditional modification methods are presented first, followed by more recent ones.
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Affiliation(s)
- Niklas Henrik Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Maria Teresa Oliveira
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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17
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Wang Z, Rabb JD, Lin Q. Orthogonal Crosslinking: A Strategy to Generate Novel Protein Topology and Function. Chemistry 2023; 29:e202202828. [PMID: 36251567 PMCID: PMC9839582 DOI: 10.1002/chem.202202828] [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: 09/10/2022] [Indexed: 11/27/2022]
Abstract
Compared to the disulfide bond, other naturally occurring intramolecular crosslinks have received little attention, presumably due to their rarity in the vast protein space. Here we presented examples of natural non-disulfide crosslinks, which we refer to as orthogonal crosslinks, emphasizing their effect on protein topology and function. We summarize recent efforts on expanding orthogonal crosslinks by using either the enzymes that catalyze protein circularization or the genetic code expansion strategy to add electrophilic amino acids site-specifically in proteins. The advantages and disadvantages of each method are discussed, along with their applications to generate novel protein topology and function. In particular, we highlight our recent work on spontaneous orthogonal crosslinking, in which a carbamate-based crosslink was generated in situ, and its applications in designing orthogonally crosslinked domain antibodies with their topology-mimicking bacterial adhesins.
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Affiliation(s)
- Zheng Wang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Johnathan D Rabb
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
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18
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Hu S, El Sahili A, Kishore S, Wong YH, Hemu X, Goh BC, Zhipei S, Wang Z, Tam JP, Liu CF, Lescar J. Structural basis for proenzyme maturation, substrate recognition, and ligation by a hyperactive peptide asparaginyl ligase. THE PLANT CELL 2022; 34:4936-4949. [PMID: 36099055 PMCID: PMC9709980 DOI: 10.1093/plcell/koac281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Peptide ligases are versatile enzymes that can be utilized for precise protein conjugation for bioengineering applications. Hyperactive peptide asparaginyl ligases (PALs), such as butelase-1, belong to a small class of enzymes from cyclotide-producing plants that can perform site-specific, rapid ligation reactions after a target peptide asparagine/aspartic acid (Asx) residue binds to the active site of the ligase. How PALs specifically recognize their polypeptide substrates has remained elusive, especially at the prime binding side of the enzyme. Here we report crystal structures that capture VyPAL2, a catalytically efficient PAL from Viola yedoensis, in an activated state, with and without a bound substrate. The bound structure shows one ligase with the N-terminal polypeptide tail from another ligase molecule trapped at its active site, revealing how Asx inserts in the enzyme's S1 pocket and why a hydrophobic residue is required at the P2' position. Besides illustrating the anchoring role played by P1 and P2' residues, these results uncover a role for the Gatekeeper residue at the surface of the S2 pocket in shifting the nonprime portion of the substrate and, as a result, the activity toward ligation or hydrolysis. These results suggest a picture for proenzyme maturation in the vacuole and will inform the rational design of peptide ligases with tailored specificities.
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Affiliation(s)
- Side Hu
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
| | - Abbas El Sahili
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
| | - Srujana Kishore
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
| | - Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
| | - Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
| | - Boon Chong Goh
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore City, 138602, Singapore
| | - Sang Zhipei
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
| | - Zhen Wang
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, 636921, Singapore
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19
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Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:life12091438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying “magic bullets” amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand–target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural–energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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20
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Wu WH, Guo J, Zhang L, Zhang WB, Gao W. Peptide/protein-based macrocycles: from biological synthesis to biomedical applications. RSC Chem Biol 2022; 3:815-829. [PMID: 35866174 PMCID: PMC9257627 DOI: 10.1039/d1cb00246e] [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: 12/17/2021] [Accepted: 06/08/2022] [Indexed: 11/21/2022] Open
Abstract
Living organisms have evolved cyclic or multicyclic peptides and proteins with enhanced stability and high bioactivity superior to their linear counterparts for diverse purposes. Herein, we review recent progress in applying this concept to artificial peptides and proteins to exploit the functional benefits of these macrocycles. Not only have simple cyclic forms been prepared, numerous macrocycle variants, such as knots and links, have also been developed. The chemical tools and synthetic strategies are summarized for the biological synthesis of these macrocycles, demonstrating it as a powerful alternative to chemical synthesis. Its further application to therapeutic peptides/proteins has led to biomedicines with profoundly improved pharmaceutical performances. Finally, we present our perspectives on the field and its future developments.
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Affiliation(s)
- Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Jianwen Guo
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
| | - Longshuai Zhang
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 P. R. China
| | - Weiping Gao
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Biomedical Engineering Department, Peking University Beijing 100191 P. R. China
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21
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Loo S, Tay SV, Kam A, Lee W, Tam JP. Hololectin Interdomain Linker Determines Asparaginyl Endopeptidase-Mediated Maturation of Antifungal Hevein-Like Peptides in Oats. FRONTIERS IN PLANT SCIENCE 2022; 13:899740. [PMID: 35620686 PMCID: PMC9127739 DOI: 10.3389/fpls.2022.899740] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/20/2022] [Indexed: 05/28/2023]
Abstract
Heveins and hevein-containing (hev-) lectins play important roles in stress and pathogenic responses in plants but cause health concerns in humans. Hev-hololectins contain multiple modular hev-peptide domains and are abundantly present in cereals and pseudocereals. However, it is unclear why some cereal hev-hololectins are presented as different forms of proteolytically processed proteoforms. Here we show the precursor architectures of hev-hololectins lead to different processing mechanisms to give either hololectins or hevein-like peptides. We used mass spectrometry and datamining to screen hev-peptides from common cereals, and identified from the oat plant Avena sativa nine novel hevein-like peptides, avenatide aV1-aV9. Bioinformatic analysis revealed that asparaginyl endopeptidase (AEP) can be responsible for the maturation of the highly homologous avenatides from five oat hev-hololectin precursors, each containing four tandemly repeating, hev-like avenatide domains connected by AEP-susceptible linkers with 13-16 residues in length. Further analysis of cereal hev-hololectins showed that the linker lengths provide a distinguishing feature between their cleavable and non-cleavable precursors, with the cleavables having considerably longer linkers (>13 amino acids) than the non-cleavables (<6 amino acids). A detailed study of avenatide aV1 revealed that it contains eight cysteine residues which form a structurally compact, metabolic-resistant cystine-knotted framework with a well-defined chitin-binding site. Antimicrobial assays showed that avenatide aV1 is anti-fungal and inhibits the growth of phyto-pathogenic fungi. Together, our findings of cleavable and non-cleavable hololectins found in cereals expand our knowledge to their biosynthesis and provide insights for hololectin-related health concerns in human.
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22
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Study on activation mechanism and cleavage sites of recombinant butelase-1 zymogen derived from Clitoria ternatea. Biochimie 2022; 199:12-22. [DOI: 10.1016/j.biochi.2022.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 11/15/2022]
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23
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Rehm FBH, Tyler TJ, de Veer SJ, Craik DJ, Durek T. Enzymatic C-to-C Protein Ligation. Angew Chem Int Ed Engl 2022; 61:e202116672. [PMID: 35018698 PMCID: PMC9303898 DOI: 10.1002/anie.202116672] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Indexed: 01/11/2023]
Abstract
Transpeptidase‐catalyzed protein and peptide modifications have been widely utilized for generating conjugates of interest for biological investigation or therapeutic applications. However, all known transpeptidases are constrained to ligating in the N‐to‐C orientation, limiting the scope of attainable products. Here, we report that an engineered asparaginyl ligase accepts diverse incoming nucleophile substrate mimetics, particularly when a means of selectively quenching the reactivity of byproducts released from the recognition sequence is employed. In addition to directly catalyzing formation of l‐/d‐ or α‐/β‐amino acid junctions, we find C‐terminal Leu‐ethylenediamine (Leu‐Eda) motifs to be bona fide mimetics of native N‐terminal Gly‐Leu sequences. Appending a C‐terminal Leu‐Eda to synthetic peptides or, via an intein‐splicing approach, to recombinant proteins enables direct transpeptidase‐catalyzed C‐to‐C ligations. This work significantly expands the synthetic scope of enzyme‐catalyzed protein transpeptidation reactions.
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Affiliation(s)
- Fabian B H Rehm
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tristan J Tyler
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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24
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Rodríguez V. Insights into post-translational modification enzymes from RiPPs: A toolkit for applications in peptide synthesis. Biotechnol Adv 2022; 56:107908. [PMID: 35032597 DOI: 10.1016/j.biotechadv.2022.107908] [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: 03/05/2021] [Revised: 12/30/2021] [Accepted: 01/09/2022] [Indexed: 11/02/2022]
Abstract
The increasing length and complexity of peptide drug candidates foster the development of novel strategies for their manufacture, which should include sustainable and efficient technologies. In this context, including enzymatic catalysis in the production of peptide molecules has gained interest. Here, several enzymes from ribosomally synthesized and post-translationally modified peptides biosynthesis pathways are reviewed, with attention to their capacity to introduce stability-promoting structural features on peptides, providing an initial framework towards their use in therapeutic peptide production processes.
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Affiliation(s)
- Vida Rodríguez
- Faculty of Engineering, Science and Technology, Bernardo O'Higgins University, Viel 1497, Santiago, Chile.
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25
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Rehm FBH, Tyler TJ, de Veer SJ, Craik DJ, Durek T. Enzymatic C‐to‐C Protein Ligation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fabian B. H. Rehm
- The University of Queensland Institute for Molecular Bioscience Chemistry and Structural Biology AUSTRALIA
| | - Tristan J. Tyler
- The University of Queensland Institute for Molecular Bioscience Chemistry and Structural Biology AUSTRALIA
| | - Simon J. de Veer
- The University of Queensland Institute for Molecular Bioscience Chemistry and Structural Biology AUSTRALIA
| | - David J. Craik
- The University of Queensland Institute for Molecular Bioscience Chemistry and Structural Biology AUSTRALIA
| | - Thomas Durek
- The University of Queensland Institute for Molecular Bioscience 306 Carmody RdLvl 7 North 4072 Brisbane AUSTRALIA
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26
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Narayanan KB, Han SS. Peptide ligases: A Novel and potential enzyme toolbox for catalytic cross-linking of protein/peptide-based biomaterial scaffolds for tissue engineering. Enzyme Microb Technol 2022; 155:109990. [PMID: 35030384 DOI: 10.1016/j.enzmictec.2022.109990] [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: 09/15/2021] [Revised: 12/17/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022]
Abstract
The fabrication of novel biomaterial scaffolds with improved biological interactions and mechanical properties is an important aspect of tissue engineering. The three-dimensional (3D) protein/peptide-based polymeric scaffolds are promising in vitro biomaterials to replicate the in vivo microenvironment mimicking the extracellular matrix (ECM) for cell differentiation and subsequent tissue formation. Among different strategies in the fabrication of scaffolds, bioorthogonal enzymatic reactions for rapid in situ zero-length cross-linking are advantageous. Peptide ligases as a novel toolbox have the potentiality to enzymatically cross-link natural/synthetic protein/peptide-based polymeric chains for a wide range of biomedical applications. Although natural peptide ligases, such as sortases and butelase 1 are known cysteine proteases with ligase activity, some serine proteases, such as trypsin and subtilisin, are protein engineered to form trypsiligase and subtiligase, respectively, which exhibited efficient ligase activity by linking proteins/peptides with a great variety of molecules. Peptide ligase activity by these engineered proteases is more efficient than the hydrolysis of peptide bonds (peptidase activity). Peptide esters form acyl-enzyme intermediate with serine/cysteine residues of these proteases, with subsequent aminolysis forming covalent peptide bond with N-terminal residue of another polymeric chain. In addition, peptide ligases have the potential to conjugate with cell-adhesive ECM proteins or motifs and growth factors to (bio)polymeric networks to enhance cell attachment, growth, and differentiation. Here, we review the potential and limitations of natural and engineered peptide ligases as an enzyme toolbox with a focus on sortases (classes A-D), butelase 1, trypsiligase, and subtilisin variants, and the mechanisms for their zero-length cross-linking of (bio)polymeric scaffolds for various tissue engineering and regenerative applications.
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Affiliation(s)
- Kannan Badri Narayanan
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| | - Sung Soo Han
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
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27
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Zhang D, Wang Z, Hu S, Chan NY, Liew HT, Lescar J, Tam JP, Liu CF. Asparaginyl Endopeptidase-Mediated Protein C-Terminal Hydrazinolysis for the Synthesis of Bioconjugates. Bioconjug Chem 2022; 33:238-247. [PMID: 34985285 DOI: 10.1021/acs.bioconjchem.1c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Asparaginyl endopeptidases (AEPs) are cysteinyl enzymes naturally catalyzing the hydrolysis and transpeptidation reactions at Asx-Xaa bonds. These reactions go by a common acyl-enzyme thioester intermediate, which is either attacked by water (for a protease-AEP) or by a peptidic amine nucleophile (for a ligase-AEP) to form the respective hydrolysis or aminolysis product. Herein, we show that hydrazine and hydroxylamine, two α-effect nucleophiles, are capable of resolving the thioester intermediate to yield peptide and protein products containing a C-terminal hydrazide and hydroxamic acid functionality, respectively. The hydrazinolysis reaction exhibits very high efficiency and can be completed in minutes at a low enzyme-to-substrate ratio. We further show the utility of the so-formed asparaginyl hydrazide in native chemical ligation and hydrazone conjugation. Using an EGFR-targeting affibody as a model protein, we have showcased our methodology in the preparation of a number of protein ligation or conjugation products, which are decorated with various functional moieties. The ZEGFR affibody-doxorubicin conjugate shows high selective binding and cytotoxicity toward the EGFR-positive A431 cells. Our results demonstrate the advantages of AEP-mediated protein hydrazinolysis as a simple and straightforward strategy for the precision manufacturing of protein bioconjugates.
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Affiliation(s)
- Dingpeng Zhang
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Zhen Wang
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Side Hu
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Ning-Yu Chan
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Heng Tai Liew
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Julien Lescar
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - James P Tam
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Chuan-Fa Liu
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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28
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Handley TNG, Jackson MA, Craik DJ. Scalable and Efficient In Planta Biosynthesis of Sunflower Trypsin Inhibitor-1 (SFTI) Peptide Therapeutics. Methods Mol Biol 2022; 2371:117-142. [PMID: 34596846 DOI: 10.1007/978-1-0716-1689-5_7] [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: 12/17/2023]
Abstract
Sunflower trypsin inhibitor-1 (SFTI-1) is a 14 amino acid cyclic peptide which has been effectively employed as a scaffold for engineering a range of peptide therapeutic candidates. Typically, synthesis of SFTI-1-based therapeutics is performed via solid-phase peptide synthesis and native chemical ligation, with significant financial and environmental costs associated. In planta synthesis of SFTI-1 based therapeutics serves as a greener approach for environmentally sustainable production. Here, we detail the methods for the transient expression, production, and purification of SFTI-1-based therapeutic peptides in Nicotiana benthamiana using a scalable and high-throughput approach. We demonstrate that a prerequisite for this is the co-expression of specialized asparaginyl endopeptidases (AEPs) that perform the backbone cyclization of SFTI-1. In our founding study, we were able to achieve in planta yields of a plasmin inhibitor SFTI-1 peptide at yields of ~60 μg/g of dried plant material.
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Affiliation(s)
- Thomas N G Handley
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia
| | - Mark A Jackson
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, Australia.
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29
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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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30
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Jiang H, Chen W, Wang J, Zhang R. Selective N-terminal modification of peptides and proteins: Recent progresses and applications. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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31
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Zhang D, Wang Z, Hu S, Lescar J, Tam JP, Liu CF. Vypal2: A Versatile Peptide Ligase for Precision Tailoring of Proteins. Int J Mol Sci 2021; 23:ijms23010458. [PMID: 35008882 PMCID: PMC8745061 DOI: 10.3390/ijms23010458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/19/2022] Open
Abstract
The last two decades have seen an increasing demand for new protein-modification methods from the biotech industry and biomedical research communities. Owing to their mild aqueous reaction conditions, enzymatic methods based on the use of peptide ligases are particularly desirable. In this regard, the recently discovered peptidyl Asx-specific ligases (PALs) have emerged as powerful biotechnological tools in recent years. However, as a new class of peptide ligases, their scope and application remain underexplored. Herein, we report the use of a new PAL, VyPAL2, for a diverse range of protein modifications. We successfully showed that VyPAL2 was an efficient biocatalyst for protein labelling, inter-protein ligation, and protein cyclization. The labelled or cyclized protein ligands remained functionally active in binding to their target receptors. We also demonstrated on-cell labelling of protein ligands pre-bound to cellular receptors and cell-surface engineering via modifying a covalently anchored peptide substrate pre-installed on cell-surface glycans. Together, these examples firmly establish Asx-specific ligases, such as VyPAL2, as the biocatalysts of the future for site-specific protein modification, with a myriad of applications in basic research and drug discovery.
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32
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Cao Y, Bi X. Butelase-1 as the Prototypical Peptide Asparaginyl Ligase and Its Applications: A Review. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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33
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Tran HNT, Tran P, Deuis JR, McMahon KL, Yap K, Craik DJ, Vetter I, Schroeder CI. Evaluation of Efficient Non-reducing Enzymatic and Chemical Ligation Strategies for Complex Disulfide-Rich Peptides. Bioconjug Chem 2021; 32:2407-2419. [PMID: 34751572 PMCID: PMC10167913 DOI: 10.1021/acs.bioconjchem.1c00452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Double-knotted peptides identified in venoms and synthetic bivalent peptide constructs targeting ion channels are emerging tools for the study of ion channel pharmacology and physiology. These highly complex and disulfide-rich peptides contain two individual cystine knots, each comprising six cysteines and three disulfide bonds. Until now, native double-knotted peptides, such as Hi1a and DkTx, have only been isolated from venom or produced recombinantly, whereas engineered double-knotted peptides have successfully been produced through enzymatic ligation using sortase A to form a seamless amide bond at the ligation site between two knotted toxins, and by alkyne/azide click chemistry, joining two peptide knots via a triazole linkage. To further pursue these double-knotted peptides as pharmacological tools or probes for therapeutically relevant ion channels, we sought to identify a robust methodology resulting in a high yield product that lends itself to rapid production and facile mutational studies. In this study, we evaluated the ligation efficiency of enzymatic (sortase A5°, butelase 1, wild-type OaAEP 1, C247A-OaAEP 1, and peptiligase) and mild chemical approaches (α-ketoacid-hydroxylamine, KAHA) for forming a native amide bond linking the toxins while maintaining the native disulfide connectivity of each pre-folded peptide. We used two NaV1.7 inhibitors: PaurTx3, a spider-derived gating modifier peptide, and KIIIA, a small cone snail-derived pore blocker peptide, which have previously been shown to increase affinity and inhibitory potency on hNaV1.7 when ligated together. Correctly folded peptides were successfully ligated in varying yields, without disulfide bond shuffling or reduction, with sortase A5° being the most efficient, resulting in 60% ligation conversion within 15 min. In addition, electrophysiology studies demonstrated that for these two peptides, the amino acid composition of the linker did not affect the activity of the double-knotted peptides. This study demonstrates the powerful application of enzymes in efficiently ligating complex disulfide-rich peptides, paving the way for facile production of double-knotted peptides.
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Affiliation(s)
- Hue N T Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Poanna Tran
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jennifer R Deuis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kirsten L McMahon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Irina Vetter
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,School of Pharmacy, The University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Christina I Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
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34
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Chen Y, Zhang D, Zhang X, Wang Z, Liu CF, Tam JP. Site-Specific Protein Modifications by an Engineered Asparaginyl Endopeptidase from Viola canadensis. Front Chem 2021; 9:768854. [PMID: 34746098 PMCID: PMC8568951 DOI: 10.3389/fchem.2021.768854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/06/2021] [Indexed: 12/04/2022] Open
Abstract
Asparaginyl endopeptidases (AEPs) or legumains are Asn/Asp (Asx)-specific proteases that break peptide bonds, but also function as peptide asparaginyl ligases (PALs) that make peptide bonds. This ligase activity can be used for site-specific protein modifications in biochemical and biotechnological applications. Although AEPs are common, PALs are rare. We previously proposed ligase activity determinants (LADs) of these enzymes that could determine whether they catalyze formation or breakage of peptide bonds. LADs are key residues forming the S2 and S1' substrate-binding pockets flanking the S1 active site. Here, we build on the LAD hypothesis with the engineering of ligases from proteases by mutating the S2 and S1' pockets of VcAEP, an AEP from Viola canadensis. Wild type VcAEP yields <5% cyclic product from a linear substrate at pH 6.5, whereas the single mutants VcAEP-V238A (Vc1a) and VcAEP-Y168A (Vc1b) targeting the S2 and S1' substrate-binding pockets yielded 34 and 61% cyclic products, respectively. The double mutant VcAEP-V238A/Y168A (Vc1c) targeting both the S2 and S1' substrate-binding pockets yielded >90% cyclic products. Vc1c had cyclization efficiency of 917,759 M-1s-1, which is one of the fastest rates for ligases yet reported. Vc1c is useful for protein engineering applications, including labeling of DARPins and cell surface MCF-7, as well as producing cyclic protein sfGFP. Together, our work validates the importance of LADs for AEP ligase activity and provides valuable tools for site-specific modification of proteins and biologics.
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Affiliation(s)
- Yu Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Dingpeng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Zhen Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
- Nanyang Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
- Nanyang Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
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35
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Haim A, Neubacher S, Grossmann TN. Protein Macrocyclization for Tertiary Structure Stabilization. Chembiochem 2021; 22:2672-2679. [PMID: 34060202 PMCID: PMC8453710 DOI: 10.1002/cbic.202100111] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/26/2021] [Indexed: 12/30/2022]
Abstract
Proteins possess unique molecular recognition capabilities and enzymatic activities, features that are usually tied to a particular tertiary structure. To make use of proteins for biotechnological and biomedical purposes, it is often required to enforce their tertiary structure in order to ensure sufficient stability under the conditions inherent to the application of interest. The introduction of intramolecular crosslinks has proven efficient in stabilizing native protein folds. Herein, we give an overview of methods that allow the macrocyclization of expressed proteins, discussing involved reaction mechanisms and structural implications.
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Affiliation(s)
- Anissa Haim
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
- Incircular B.V.De Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
- Amsterdam Institute of Molecular and Life SciencesVU University AmsterdamAmsterdamThe Netherlands
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36
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Mogilevsky CS, Lobba MJ, Brauer DD, Marmelstein AM, Maza JC, Gleason JM, Doudna JA, Francis MB. Synthesis of Multi-Protein Complexes through Charge-Directed Sequential Activation of Tyrosine Residues. J Am Chem Soc 2021; 143:13538-13547. [PMID: 34382787 DOI: 10.1021/jacs.1c03079] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Site-selective protein-protein coupling has long been a goal of chemical biology research. In recent years, that goal has been realized to varying degrees through a number of techniques, including the use of tyrosinase-based coupling strategies. Early publications utilizing tyrosinase from Agaricus bisporus(abTYR) showed the potential to convert tyrosine residues into ortho-quinone functional groups, but this enzyme is challenging to produce recombinantly and suffers from some limitations in substrate scope. Initial screens of several tyrosinase candidates revealed that the tyrosinase from Bacillus megaterium (megaTYR) is an enzyme that possesses a broad substrate tolerance. We use the expanded substrate preference as a starting point for protein design experiments and show that single point mutants of megaTYR are capable of activating tyrosine residues in various sequence contexts. We leverage this new tool to enable the construction of protein trimers via a charge-directed sequential activation of tyrosine residues (CDSAT).
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Affiliation(s)
- Casey S Mogilevsky
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Marco J Lobba
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Daniel D Brauer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Alan M Marmelstein
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Johnathan C Maza
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jamie M Gleason
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States.,Gladstone Institutes, San Francisco, California 94158, United States.,Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States.,Innovative Genomics Institute, University of California, Berkeley, California 94720, United States
| | - Matthew B Francis
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720, United States
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37
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Tang TMS, Luk LYP. Asparaginyl endopeptidases: enzymology, applications and limitations. Org Biomol Chem 2021; 19:5048-5062. [PMID: 34037066 PMCID: PMC8209628 DOI: 10.1039/d1ob00608h] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/12/2021] [Indexed: 12/15/2022]
Abstract
Asparaginyl endopeptidases (AEP) are cysteine proteases found in mammalian and plant cells. Several AEP isoforms from plant species were found to exhibit transpeptidase activity which is integral for the key head-to-tail cyclisation reaction during the biosynthesis of cyclotides. Since many plant AEPs exhibit excellent enzyme kinetics for peptide ligation via a relatively short substrate recognition sequence, they have become appealing tools for peptide and protein modification. In this review, research focused on the enzymology of AEPs and their applications in polypeptide cyclisation and labelling will be presented. Importantly, the limitations of using AEPs and opportunities for future research and innovation will also be discussed.
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Affiliation(s)
- T M Simon Tang
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK.
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK. and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
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38
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Zhang D, Wang Z, Hu S, Balamkundu S, To J, Zhang X, Lescar J, Tam JP, Liu CF. pH-Controlled Protein Orthogonal Ligation Using Asparaginyl Peptide Ligases. J Am Chem Soc 2021; 143:8704-8712. [PMID: 34096285 DOI: 10.1021/jacs.1c02638] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptide asparaginyl ligases (PALs) catalyze transpeptidation at the Asn residue of a short Asn-Xaa1-Xaa2 tripeptide motif. Due to their high catalytic activity toward the P1-Asn substrates at around neutral pH, PALs have been used extensively for peptide ligation at asparaginyl junctions. PALs also bind to aspartyl substrates, but only when the γCOOH of P1-Asp remains in its neutral, protonated form, which usually requires an acidic pH. However, this limits the availability of the amine nucleophile and, consequently, the ligation efficiency at aspartyl junctions. Because of this perceived inefficiency, the use of PALs for Asp-specific ligation remains largely unexplored. We found that PAL enzymes, such as VyPAL2, display appreciable catalytic activities toward P1-Asp substrates at pH 4-5, which are at least 2 orders of magnitude higher than that of sortase A, making them practically useful for both intra- and intermolecular ligations. This also allows sequential ligations, first at Asp and then at Asn junctions, because the newly formed aspartyl peptide bond is resistant to the ligase at the pH used for asparaginyl ligation in the second step. Using this pH-controlled orthogonal ligation method, we dually labeled truncated sfGFP with a cancer-targeting peptide and a doxorubicin derivative at the respective N- and C-terminal ends in the N-to-C direction. In addition, a fluorescein tag and doxorubicin derivative were tagged to an EGFR-targeting affibody in the C-to-N direction. This study shows that the pH-dependent catalytic activity of PAL enzymes can be exploited to prepare multifunction protein biologics for pharmacological applications.
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Affiliation(s)
- Dingpeng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Zhen Wang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | | | - Janet To
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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39
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De Rosa L, Di Stasi R, Romanelli A, D’Andrea LD. Exploiting Protein N-Terminus for Site-Specific Bioconjugation. Molecules 2021; 26:3521. [PMID: 34207845 PMCID: PMC8228110 DOI: 10.3390/molecules26123521] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022] Open
Abstract
Although a plethora of chemistries have been developed to selectively decorate protein molecules, novel strategies continue to be reported with the final aim of improving selectivity and mildness of the reaction conditions, preserve protein integrity, and fulfill all the increasing requirements of the modern applications of protein conjugates. The targeting of the protein N-terminal alpha-amine group appears a convenient solution to the issue, emerging as a useful and unique reactive site universally present in each protein molecule. Herein, we provide an updated overview of the methodologies developed until today to afford the selective modification of proteins through the targeting of the N-terminal alpha-amine. Chemical and enzymatic strategies enabling the selective labeling of the protein N-terminal alpha-amine group are described.
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Affiliation(s)
- Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy; (L.D.R.); (R.D.S.)
| | - Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy; (L.D.R.); (R.D.S.)
| | - Alessandra Romanelli
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Via Venezian 21, 20133 Milano, Italy;
| | - Luca Domenico D’Andrea
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR Via M. Bianco 9, 20131 Milano, Italy
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40
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Zhao J, Fan R, Jia F, Huang Y, Huang Z, Hou Y, Hu SQ. Enzymatic Properties of Recombinant Ligase Butelase-1 and Its Application in Cyclizing Food-Derived Angiotensin I-Converting Enzyme Inhibitory Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5976-5985. [PMID: 34003638 DOI: 10.1021/acs.jafc.1c01755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Butelase-1 is an efficient ligase from Clitoria ternatea with wide applications in the food and biopharmaceutical fields. This research aimed to achieve high-efficiency expression of butelase-1 and explore its application in food-derived angiotensin I-converting enzyme (ACE) inhibitory peptides. The recombinant butelase-1 zymogen was prepared at a yield of 100 mg/L in Escherichia coli and successfully activated at pH 4.5, resulting in a 6973.8 U/L yield of activated butelase-1 with a specific activity of 348.69 U/mg and a catalytic efficiency of 9956 M-1 s-1. Activated butelase-1 exhibited considerable resistance to Tween-20, Triton X-100, and methanol. The "traceless" cyclization of ACE inhibitory peptides was realized using activated butelase-1, which resulted in higher stability and ACE inhibitory activity than those of the linear peptides. Our work proposed an efficient method for the preparation of butelase-1 and provided a promising model for its application in food fields.
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Affiliation(s)
- Jinsong Zhao
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Renshui Fan
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Feng Jia
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yanbo Huang
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Zhiqiang Huang
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yi Hou
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Song-Qing Hu
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
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41
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Hayes HC, Luk LYP, Tsai YH. Approaches for peptide and protein cyclisation. Org Biomol Chem 2021; 19:3983-4001. [PMID: 33978044 PMCID: PMC8114279 DOI: 10.1039/d1ob00411e] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/01/2021] [Indexed: 12/26/2022]
Abstract
The cyclisation of polypeptides can play a crucial role in exerting biological functions, maintaining stability under harsh conditions and conferring proteolytic resistance, as demonstrated both in nature and in the laboratory. To date, various approaches have been reported for polypeptide cyclisation. These approaches range from the direct linkage of N- and C- termini to the connection of amino acid side chains, which can be applied both in reaction vessels and in living systems. In this review, we categorise the cyclisation approaches into chemical methods (e.g. direct backbone cyclisation, native chemical ligation, aldehyde-based ligations, bioorthogonal reactions, disulphide formation), enzymatic methods (e.g. subtiligase variants, sortases, asparaginyl endopeptidases, transglutaminases, non-ribosomal peptide synthetases) and protein tags (e.g. inteins, engineered protein domains for isopeptide bond formation). The features of each approach and the considerations for selecting an appropriate method of cyclisation are discussed.
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Affiliation(s)
- Heather C Hayes
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT.
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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42
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Westerlund K, Myrhammar A, Tano H, Gestin M, Karlström AE. Stability Enhancement of a Dimeric HER2-Specific Affibody Molecule through Sortase A-Catalyzed Head-to-Tail Cyclization. Molecules 2021; 26:2874. [PMID: 34066245 PMCID: PMC8150554 DOI: 10.3390/molecules26102874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 11/16/2022] Open
Abstract
Natural backbone-cyclized proteins have an increased thermostability and resistance towards proteases, characteristics that have sparked interest in head-to-tail cyclization as a method to stability-enhance proteins used in diagnostics and therapeutic applications, for example. In this proof-of principle study, we have produced and investigated a head-to-tail cyclized and HER2-specific ZHER2:342 Affibody dimer. The sortase A-mediated cyclization reaction is highly efficient (>95%) under optimized conditions, and renders a cyclic ZHER3:342-dimer with an apparent melting temperature, Tm, of 68 °C, which is 3 °C higher than that of its linear counterpart. Circular dichroism spectra of the linear and cyclic dimers looked very similar in the far-UV range, both before and after thermal unfolding to 90 °C, which suggests that cyclization does not negatively impact the helicity or folding of the cyclic protein. The cyclic dimer had an apparent sub-nanomolar affinity (Kd ~750 pM) to the HER2-receptor, which is a ~150-fold reduction in affinity relative to the linear dimer (Kd ~5 pM), but the anti-HER2 Affibody dimer remained a high-affinity binder even after cyclization. No apparent difference in proteolytic stability was detected in an endopeptidase degradation assay for the cyclic and linear dimers. In contrast, in an exopeptidase degradation assay, the linear dimer was shown to be completely degraded after 5 min, while the cyclic dimer showed no detectable degradation even after 60 min. We further demonstrate that a site-specifically DyLight 594-labeled cyclic dimer shows specific binding to HER2-overexpressing cells. Taken together, the results presented here demonstrate that head-to-tail cyclization can be an effective strategy to increase the stability of an Affibody dimer.
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Affiliation(s)
| | | | | | | | - Amelie Eriksson Karlström
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden; (K.W.); (A.M.); (H.T.); (M.G.)
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43
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Nonis SG, Haywood J, Mylne JS. Plant asparaginyl endopeptidases and their structural determinants of function. Biochem Soc Trans 2021; 49:965-976. [PMID: 33666219 PMCID: PMC8106488 DOI: 10.1042/bst20200908] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Asparaginyl endopeptidases (AEPs) are versatile enzymes that in biological systems are involved in producing three different catalytic outcomes for proteins, namely (i) routine cleavage by bond hydrolysis, (ii) peptide maturation, including macrocyclisation by a cleavage-coupled intramolecular transpeptidation and (iii) circular permutation involving separate cleavage and transpeptidation reactions resulting in a major reshuffling of protein sequence. AEPs differ in their preference for cleavage or transpeptidation reactions, catalytic efficiency, and preference for asparagine or aspartate target residues. We look at structural analyses of various AEPs that have laid the groundwork for identifying important determinants of AEP function in recent years, with much of the research impetus arising from the potential biotechnological and pharmaceutical applications.
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Affiliation(s)
- Samuel G. Nonis
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Joshua S. Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
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44
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Rehm FBH, Tyler TJ, Xie J, Yap K, Durek T, Craik DJ. Asparaginyl Ligases: New Enzymes for the Protein Engineer's Toolbox. Chembiochem 2021; 22:2079-2086. [PMID: 33687132 DOI: 10.1002/cbic.202100071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/08/2021] [Indexed: 01/11/2023]
Abstract
Enzyme-catalysed site-specific protein modifications enable the precision manufacture of conjugates for the study of protein function and/or for therapeutic or diagnostic applications. Asparaginyl ligases are a class of highly efficient transpeptidases with the capacity to modify proteins bearing only a tripeptide recognition motif. Herein, we review the types of protein modification that are accessible using these enzymes, including N- and C-terminal protein labelling, head-to-tail cyclisation, and protein-protein conjugation. We describe the progress that has been made to engineer highly efficient ligases as well as efforts to chemically manipulate the enzyme reaction to favour product formation. These enzymes are powerful additions to the protein engineer's toolbox.
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Affiliation(s)
- Fabian B H Rehm
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Tristan J Tyler
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jing Xie
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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45
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Wang Z, Zhang D, Hemu X, Hu S, To J, Zhang X, Lescar J, Tam JP, Liu CF. Engineering protein theranostics using bio-orthogonal asparaginyl peptide ligases. Theranostics 2021; 11:5863-5875. [PMID: 33897886 PMCID: PMC8058723 DOI: 10.7150/thno.53615] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/18/2021] [Indexed: 12/19/2022] Open
Abstract
Background: Protein theranostics integrate both diagnostic and treatment functions on a single disease-targeting protein. However, the preparation of these multimodal agents remains a major challenge. Ideally, conventional recombinant proteins should be used as starting materials for modification with the desired detection and therapeutic functionalities, but simple chemical strategies that allow the introduction of two different modifications into a protein in a site-specific manner are not currently available. We recently discovered two highly efficient peptide ligases, namely butelase-1 and VyPAL2. Although both ligate at asparaginyl peptide bonds, these two enzymes are bio-orthogonal with distinguishable substrate specificities, which can be exploited to introduce distinct modifications onto a protein. Methods: We quantified substrate specificity differences between butelase-1 and VyPAL2, which provide orthogonality for a tandem ligation method for protein dual modifications. Recombinant proteins or synthetic peptides engineered with the preferred recognition motifs of butelase-1 and VyPAL2 at their respective C- and N-terminal ends could be modified consecutively by the action of the two ligases. Results: Using this method, we modified an EGFR-targeting affibody with a fluorescein tag and a mitochondrion-lytic peptide at its respective N- and C-terminal ends. The dual-labeled protein was found to be a selective bioimaging and cytotoxic agent for EGFR-positive A431 cancer cells. In addition, the method was used to prepare a cyclic form of the affibody conjugated with doxorubicin. Both modified affibodies showed increased cytotoxicity to A431 cells by 10- and 100-fold compared to unconjugated doxorubicin and the free peptide, respectively. Conclusion: Bio-orthogonal tandem ligation using two asparaginyl peptide ligases with differential substrate specificities is a straightforward approach for the preparation of multifunctional protein biologics as potential theranostics.
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46
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Zhang J, Yuan J, Li Z, Fu C, Xu M, Yang J, Jiang X, Zhou B, Ye X, Xu C. Exploring and exploiting plant cyclic peptides for drug discovery and development. Med Res Rev 2021; 41:3096-3117. [PMID: 33599316 DOI: 10.1002/med.21792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/10/2021] [Accepted: 01/31/2021] [Indexed: 01/07/2023]
Abstract
Ever since the discovery of insulin, natural peptides have become an important resource for therapeutic development. Decades of research has led to the discovery of a long list of peptide drugs with broad applications in clinics, from antibiotics to hypertension treatment to pain management. Many of these US FDA-approved peptide drugs are derived from microorganisms and animals. By contrast, the great potential of plant cyclic peptides as therapeutics remains largely unexplored. These macrocyclic peptides typically have rigid structures, good bioavailability and membrane permeability, making them appealing candidates for drug development and engineering. In this review, we introduce the three major classes of plant cyclic peptides and summarize their potential medical applications. We discuss how we can leverage the genome information of many different plants to quickly search for new cyclic peptides and how we can take advantage of the insights gained from their biosynthetic pathways to transform the process of production and drug development. These recent developments have provided a new angle for exploring and exploiting plant cyclic peptides, and we believe that many more peptide drugs derived from plants are about to come.
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Affiliation(s)
- Jingjing Zhang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong, China
| | - Jimin Yuan
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Zhijie Li
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Chunjin Fu
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Menglong Xu
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jing Yang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xin Jiang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Boping Zhou
- Department of Infectious Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xiufeng Ye
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Chengchao Xu
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
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47
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Bowen J, Schneible J, Bacon K, Labar C, Menegatti S, Rao BM. Screening of Yeast Display Libraries of Enzymatically Treated Peptides to Discover Macrocyclic Peptide Ligands. Int J Mol Sci 2021; 22:ijms22041634. [PMID: 33562883 PMCID: PMC7915732 DOI: 10.3390/ijms22041634] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/12/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
We present the construction and screening of yeast display libraries of post-translationally modified peptides wherein site-selective enzymatic treatment of linear peptides is achieved using bacterial transglutaminase. To this end, we developed two alternative routes, namely (i) yeast display of linear peptides followed by treatment with recombinant transglutaminase in solution; or (ii) intracellular co-expression of linear peptides and transglutaminase to achieve peptide modification in the endoplasmic reticulum prior to yeast surface display. The efficiency of peptide modification was evaluated via orthogonal detection of epitope tags integrated in the yeast-displayed peptides by flow cytometry, and via comparative cleavage of putative cyclic vs. linear peptides by tobacco etch virus (TEV) protease. Subsequently, yeast display libraries of transglutaminase-treated peptides were screened to isolate binders to the N-terminal region of the Yes-Associated Protein (YAP) and its WW domains using magnetic selection and fluorescence activated cell sorting (FACS). The identified peptide cyclo[E-LYLAYPAH-K] featured a KD of 1.75 μM for YAP and 0.68 μM for the WW domains of YAP as well as high binding selectivity against albumin and lysozyme. These results demonstrate the usefulness of enzyme-mediated cyclization in screening combinatorial libraries to identify cyclic peptide binders.
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Affiliation(s)
- John Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA; (J.B.); (J.S.); (K.B.)
| | - John Schneible
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA; (J.B.); (J.S.); (K.B.)
| | - Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA; (J.B.); (J.S.); (K.B.)
| | - Collin Labar
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA;
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA; (J.B.); (J.S.); (K.B.)
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC 27606, USA
- Correspondence: (S.M.); (B.M.R.)
| | - Balaji M. Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA; (J.B.); (J.S.); (K.B.)
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, 850 Oval Dr, Raleigh, NC 27606, USA
- Correspondence: (S.M.); (B.M.R.)
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Boto A, González CC, Hernández D, Romero-Estudillo I, Saavedra CJ. Site-selective modification of peptide backbones. Org Chem Front 2021. [DOI: 10.1039/d1qo00892g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Exciting developments in the site-selective modification of peptide backbones are allowing an outstanding fine-tuning of peptide conformation, folding ability, and physico-chemical and biological properties.
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Affiliation(s)
- Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Concepción C. González
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Iván Romero-Estudillo
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos. Av. Universidad 1001, Cuernavaca, Morelos 62209, Mexico
- Catedrático CONACYT-CIQ-UAEM, Mexico
| | - Carlos J. Saavedra
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
- Programa Agustín de Betancourt, Universidad de la Laguna, 38200 Tenerife, Spain
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Abstract
Historically, ligase activity by proteases was theoretically derived due to their catalyst nature, and it was experimentally observed as early as around 1900. Initially, the digestive proteases, such as pepsin, chymotrypsin, and trypsin were employed to perform in vitro syntheses of small peptides. Protease-catalyzed ligation is more efficient than peptide bond hydrolysis in organic solvents, representing control of the thermodynamic equilibrium. Peptide esters readily form acyl intermediates with serine and cysteine proteases, followed by peptide bond synthesis at the N-terminus of another residue. This type of reaction is under kinetic control, favoring aminolysis over hydrolysis. Although only a few natural peptide ligases are known, such as ubiquitin ligases, sortases, and legumains, the principle of proteases as general catalysts could be adapted to engineer some proteases accordingly. In particular, the serine proteases subtilisin and trypsin were converted to efficient ligases, which are known as subtiligase and trypsiligase. Together with sortases and legumains, they turned out to be very useful in linking peptides and proteins with a great variety of molecules, including biomarkers, sugars or building blocks with non-natural amino acids. Thus, these engineered enzymes are a promising branch for academic research and for pharmaceutical progress.
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Jackson MA, Nguyen LT, Gilding EK, Durek T, Craik DJ. Make it or break it: Plant AEPs on stage in biotechnology. Biotechnol Adv 2020; 45:107651. [DOI: 10.1016/j.biotechadv.2020.107651] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/02/2020] [Accepted: 10/20/2020] [Indexed: 12/11/2022]
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