1
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Shao C, Tang B, Chu JCH, Lau KM, Wong WT, Che CM, Tai WCS, Wong WT, Wong CTT. Macrophage-engaging peptidic bispecific antibodies (pBsAbs) for immunotherapy via a facile bioconjugation strategy. Chem Sci 2024; 15:11272-11278. [PMID: 39055004 PMCID: PMC11268508 DOI: 10.1039/d4sc00851k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/29/2024] [Indexed: 07/27/2024] Open
Abstract
Bispecific antibodies are artificial molecules that fuse two different antigen-binding sites of monoclonal antibodies into one single entity. They have emerged as a promising next-generation anticancer treatment. Despite the fascinating applications of bispecific antibodies, the design and production of bispecific antibodies remain tedious and challenging, leading to a long R&D process and high production costs. We herein report an unprecedented strategy to cyclise and conjugate tumour-targeting peptides on the surface of a monoclonal antibody to form a novel type of bispecific antibody, namely the peptidic bispecific antibody (pBsAb). Such design combines the merits of highly specific monoclonal antibodies and serum-stable cyclic peptides that endows an additional tumour-targeting ability to the monoclonal antibody for binding with two different antigens. Our results show that the novel pBsAb, which comprises EGFR-binding cyclic peptides and an anti-SIRP-α monoclonal antibody, could serve as a macrophage-engaging bispecific antibody to initiate enhanced macrophage-cancer cell interaction and block the "don't eat me" signal between CD47-SIRP-α, as well as promoting antibody-dependent cellular phagocytosis and 3D cell spheroid infiltration. These findings give rise to a new type of bispecific antibody and a new platform for the rapid generation of new bispecific antibodies for research and potential therapeutic uses.
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Affiliation(s)
- Chihao Shao
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Bo Tang
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Jacky C H Chu
- Laboratory for Synthetic Chemistry and Chemical Biology Limited Units 1503-1511, 15/F, Building 17W, Hong Kong Science Park New Territories Hong Kong China
| | - Kwai Man Lau
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Wai-Ting Wong
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Chi-Ming Che
- Laboratory for Synthetic Chemistry and Chemical Biology Limited Units 1503-1511, 15/F, Building 17W, Hong Kong Science Park New Territories Hong Kong China
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - William C S Tai
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Wing-Tak Wong
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
| | - Clarence T T Wong
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chemical Biology and Drug Discovery, Hong Kong Polytechnic University Kowloon Hong Kong China
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2
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Sonnentag SJ, Jenne F, Orian-Rousseau V, Nesterov-Mueller A. High-throughput screening for cell binding and repulsion peptides on multifunctionalized surfaces. Commun Biol 2024; 7:870. [PMID: 39020032 PMCID: PMC11255233 DOI: 10.1038/s42003-024-06541-7] [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: 10/11/2023] [Accepted: 07/03/2024] [Indexed: 07/19/2024] Open
Abstract
The adhesion of cells to the extracellular matrix engages cell surface receptors such as integrins, proteoglycans and other types of cell adhesion molecules such as CD44. To closely examine the determinants of cell adhesion, herein we describe the generation of high-density peptide arrays and test the growth of cells on these multifunctionalized surfaces. The peptide library used consists of over 11,000 different sequences, either random or derived from existing proteins. By applying this screen to SW620 mCherry colorectal cancer cells, we select for peptides with both maximum cell adhesion and maximum cell repulsion. All of these extreme properties are based on unique combinations of amino acids. Here, we identify peptides with maximum cell repulsion on secreted frizzled- and Dickkopf-related proteins. Peptides with strong cell repulsion are found at the poles of the TNF-alpha homotrimer. The formation of cellular patterns on alternating highly repulsive and adhesive peptides are examined. Our screen allows the identification of peptides suitable for biomedical and tissue engineering applications.
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Affiliation(s)
- Steffen J Sonnentag
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany
| | - Felix Jenne
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany
| | - Véronique Orian-Rousseau
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany.
| | - Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany.
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3
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Cugudda A, La Manna S, Marasco D. Are peptidomimetics the compounds of choice for developing new modulators of the JAK-STAT pathway? Front Immunol 2024; 15:1406886. [PMID: 38983855 PMCID: PMC11232365 DOI: 10.3389/fimmu.2024.1406886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
Protein-protein interactions (PPIs) play critical roles in a wide range of biological processes including the dysregulation of cellular pathways leading to the loss of cell function, which in turn leads to diseases. The dysfunction of several signaling pathways is linked to the insurgence of pathological processes such as inflammation, cancer development and neurodegeneration. Thus, there is an urgent need for novel chemical modulators of dysregulated PPIs to drive progress in targeted therapies. Several PPIs have been targeted by bioactive compounds, and, often, to properly cover interacting protein regions and improve the biological activities of modulators, a particular focus concerns the employment of macrocycles as proteomimetics. Indeed, for their physicochemical properties, they occupy an intermediate space between small organic molecules and macromolecular proteins and are prominent in the drug discovery process. Peptide macrocycles can modulate fundamental biological mechanisms and here we will focus on peptidomimetics active on the Janus kinase/signal transducers and activators of transcription (JAK-STAT) pathways.
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Affiliation(s)
| | | | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
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4
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Kobayashi M, Onozawa N, Matsuda K, Wakimoto T. Chemoenzymatic tandem cyclization for the facile synthesis of bicyclic peptides. Commun Chem 2024; 7:67. [PMID: 38548970 PMCID: PMC10978974 DOI: 10.1038/s42004-024-01147-w] [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: 10/31/2023] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
Bicyclic peptides exhibit improved metabolic stabilities and target specificities when compared to their linear or mono-cyclic counterparts; however, efficient and straightforward synthesis remains challenging due to their intricate architectures. Here, we present a highly selective and operationally simple one-pot chemoenzymatic tandem cyclization approach to synthesize bicyclic peptides with small to medium ring sizes. Penicillin-binding protein-type thioesterases (PBP-type TEs) efficiently cyclized azide/alkyne-containing peptides in a head-to-tail manner. Successive copper (I)-catalyzed azide-alkyne cycloaddition generated bicyclic peptides in one-pot, thus omitting the purification of monocyclic intermediates. This chemoenzymatic strategy enabled the facile synthesis of bicyclic peptides bearing hexa-, octa-, and undecapeptidyl head-to-tail cyclic scaffolds.
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Affiliation(s)
- Masakazu Kobayashi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Naho Onozawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
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5
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He J, Ghosh P, Nitsche C. Biocompatible strategies for peptide macrocyclisation. Chem Sci 2024; 15:2300-2322. [PMID: 38362412 PMCID: PMC10866349 DOI: 10.1039/d3sc05738k] [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: 10/27/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Peptides are increasingly important drug candidates, offering numerous advantages over conventional small molecules. However, they face significant challenges related to stability, cellular uptake and overall bioavailability. While individual modifications may not address all these challenges, macrocyclisation stands out as a single modification capable of enhancing affinity, selectivity, proteolytic stability and membrane permeability. The recent successes of in situ peptide modifications during screening in combination with genetically encoded peptide libraries have increased the demand for peptide macrocyclisation reactions that can occur under biocompatible conditions. In this perspective, we aim to distinguish biocompatible conditions from those well-known examples that are fully bioorthogonal. We introduce key strategies for biocompatible peptide macrocyclisation and contextualise them within contemporary screening methods, providing an overview of available transformations.
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Affiliation(s)
- Junming He
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Pritha Ghosh
- Research School of Chemistry, Australian National University Canberra ACT Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University Canberra ACT Australia
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6
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Kern K, Delaroque N, Boysen A, Puder M, Wendt R, Kölsch A, Ehrentreich-Förster E, Stærk K, Andersen TE, Andersen K, Lund L, Szardenings M. Glycosylation of bacterial antigens changes epitope patterns. Front Immunol 2023; 14:1258136. [PMID: 37954588 PMCID: PMC10637626 DOI: 10.3389/fimmu.2023.1258136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/21/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction Unlike glycosylation of proteins expressed in mammalian systems, bacterial glycosylation is often neglected in the development of recombinant vaccines. Methods Here, we compared the effects of glycosylation of YghJ, an Escherichia coli protein important for mucus attachment of bacteria causing in urinary tract infections (UTIs). A novel method based on statistical evaluation of phage display for the identification and comparison of epitopes and mimotopes of anti-YghJ antibodies in the sera was used. This is the first time that the effect of glycosylation of a recombinant bacterial antigen has been studied at the peptide epitope level. Results The study identifies differences in the immune response for (non)-glycosylated antigens in rabbits and pigs and compares them to a large group of patients with UTI, which have been diagnosed as positive for various bacterial pathogens. We identified glycosylation-specific peptide epitopes, a large immunological similarity between different UTI pathogens, and a broad peptide epitope pattern in patients and animals, which could result in a variable response in patients upon vaccination. Discussion This epitope analysis indicates that the vaccination of rabbits and pigs raises antibodies that translate well into the human immune system. This study underlines the importance of glycosylation in bacterial vaccines and provides detailed immune diagnostic methods to understand individual immune responses to vaccines.
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Affiliation(s)
- Karolin Kern
- Ligand Development Unit, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
- Epitopic, Leipzig, Germany
| | - Nicolas Delaroque
- Ligand Development Unit, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | | | | | - Ralph Wendt
- Department of Nephrology, St. Georg Hospital Leipzig, Leipzig, Germany
| | - Andreas Kölsch
- MicroDiagnostics Unit, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
| | - Eva Ehrentreich-Förster
- Molekulare und Zelluläre Bioanalytik Unit, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Golm, Germany
| | - Kristian Stærk
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Thomas Emil Andersen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Karin Andersen
- Department of Urology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lars Lund
- Department of Urology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Michael Szardenings
- Ligand Development Unit, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
- Epitopic, Leipzig, Germany
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7
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Todaro B, Ottalagana E, Luin S, Santi M. Targeting Peptides: The New Generation of Targeted Drug Delivery Systems. Pharmaceutics 2023; 15:1648. [PMID: 37376097 DOI: 10.3390/pharmaceutics15061648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Peptides can act as targeting molecules, analogously to oligonucleotide aptamers and antibodies. They are particularly efficient in terms of production and stability in physiological environments; in recent years, they have been increasingly studied as targeting agents for several diseases, from tumors to central nervous system disorders, also thanks to the ability of some of them to cross the blood-brain barrier. In this review, we will describe the techniques employed for their experimental and in silico design, as well as their possible applications. We will also discuss advancements in their formulation and chemical modifications that make them even more stable and effective. Finally, we will discuss how their use could effectively help to overcome various physiological problems and improve existing treatments.
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Affiliation(s)
- Biagio Todaro
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Elisa Ottalagana
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- Fondazione Pisana per la Scienza, Via Ferruccio Giovannini 13, San Giuliano Terme, 56017 Pisa, Italy
| | - Stefano Luin
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Melissa Santi
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
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8
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Davies LJ, Shuttleworth LM, Zhang X, Peng S, Nitsche C. Bioorthogonal Peptide Macrocyclization Using Oxime Ligation. Org Lett 2023; 25:2806-2809. [PMID: 37053571 DOI: 10.1021/acs.orglett.3c00695] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The biocompatible synthesis of constrained peptides is challenging. Oxime ligation is a bioorthogonal technique frequently used for protein bioconjugation. We report a straightforward method to install N-terminal ketones and aminooxy side chains during standard solid-phase peptide synthesis. Cyclization occurs spontaneously after acidic cleavage or in aqueous buffer. We demonstrate the facile synthesis of protease inhibitors with varying conformational constraint. The most constrained peptide displayed an activity 2 orders of magnitude higher than its linear analog.
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Affiliation(s)
- Lani J Davies
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Laura M Shuttleworth
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Xiaobai Zhang
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Sherry Peng
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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9
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Li B, Wan Z, Zheng H, Cai S, Tian HW, Tang H, Chu X, He G, Guo DS, Xue XS, Chen G. Construction of Complex Macromulticyclic Peptides via Stitching with Formaldehyde and Guanidine. J Am Chem Soc 2022; 144:10080-10090. [PMID: 35639413 DOI: 10.1021/jacs.2c04620] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is a growing interest in constructing multicyclic peptide structures to expand the chemical space of peptides. Conventional strategies for constructing large peptide structures are limited by the typical reliance on the inflexible coupling between premade templates equipped with fixed reactive handles and peptide substrates via cysteine anchors. Herein, we report the development of a facile three-component condensation reaction of primary alkyl amine, formaldehyde, and guanidine for construction of complex macromulticyclic peptides with novel topologies via lysine anchors. Moreover, the reaction sequences can be orchestrated in different anchor combinations and spatial arrangements to generate various macrocyclic structures crosslinked by distinct fused tetrahydrotriazine linkages. The macrocyclization reactions are selective, efficient, versatile, and workable in both organic and aqueous media. Thus, the condensation reaction provides a smart tool for stitching native peptides in situ using simple methylene threads and guanidine joints in a flexible and programmable manner.
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Affiliation(s)
- Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhao Wan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hanliang Zheng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Shaokun Cai
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Han-Wen Tian
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xin Chu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Dong-Sheng Guo
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiao-Song Xue
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.,Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.,Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
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10
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Resemblance-Ranking Peptide Library to Screen for Binders to Antibodies on a Peptidomic Scale. Int J Mol Sci 2022; 23:ijms23073515. [PMID: 35408876 PMCID: PMC8999133 DOI: 10.3390/ijms23073515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
A novel resemblance-ranking peptide library with 160,000 10-meric peptides was designed to search for selective binders to antibodies. The resemblance-ranking principle enabled the selection of sequences that are most similar to the human peptidome. The library was synthesized with ultra-high-density peptide arrays. As proof of principle, screens for selective binders were performed for the therapeutic anti-CD20 antibody rituximab. Several features in the amino acid composition of antibody-binding peptides were identified. The selective affinity of rituximab increased with an increase in the number of hydrophobic amino acids in a peptide, mainly tryptophan and phenylalanine, while a total charge of the peptide remained relatively small. Peptides with a higher affinity exhibited a lower sum helix propensity. For the 30 strongest peptide binders, a substitutional analysis was performed to determine dissociation constants and the invariant amino acids for binding to rituximab. The strongest selective peptides had a dissociation constant in the hundreds of the nano-molar range. The substitutional analysis revealed a specific hydrophobic epitope for rituximab. To show that conformational binders can, in principle, be detected in array format, cyclic peptide substitutions that are similar to the target of rituximab were investigated. Since the specific binders selected via the resemblance-ranking peptide library were based on the hydrophobic interactions that are widespread in the world of biomolecules, the library can be used to screen for potential linear epitopes that may provide information about the cross-reactivity of antibodies.
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11
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Tomassi S, Dimmito MP, Cai M, D’Aniello A, Del Bene A, Messere A, Liu Z, Zhu T, Hruby VJ, Stefanucci A, Cosconati S, Mollica A, Di Maro S. CLIPSing Melanotan-II to Discover Multiple Functionally Selective hMCR Agonists. J Med Chem 2022; 65:4007-4017. [DOI: 10.1021/acs.jmedchem.1c01848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Stefano Tomassi
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, Naples 80131, Italy
| | - Marilisa Pia Dimmito
- Dipartimento di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Minying Cai
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Antonia D’Aniello
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Alessandra Del Bene
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Anna Messere
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Zekun Liu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Tingyi Zhu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Victor J. Hruby
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Azzurra Stefanucci
- Dipartimento di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Adriano Mollica
- Dipartimento di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Salvatore Di Maro
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
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12
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Oppewal TR, Jansen ID, Hekelaar J, Mayer C. A Strategy to Select Macrocyclic Peptides Featuring Asymmetric Molecular Scaffolds as Cyclization Units by Phage Display. J Am Chem Soc 2022; 144:3644-3652. [PMID: 35171585 PMCID: PMC8895403 DOI: 10.1021/jacs.1c12822] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Macrocyclic peptides (MPs) have positioned themselves as a privileged class of compounds for the discovery of therapeutics and development of chemical probes. Aided by the development of powerful selection strategies, high-affinity binders against biomolecular targets can readily be elicited from massive, genetically encoded libraries by affinity selection. For example, in phage display, MPs are accessed on the surface of whole bacteriophages via disulfide formation, the use of (symmetric) crosslinkers, or the incorporation of non-canonical amino acids. To facilitate a straightforward cyclization of linear precursors with asymmetric molecular scaffolds, which are often found at the core of naturally occurring MPs, we report an efficient two-step strategy to access MPs via the programmed modification of a unique cysteine residue and an N-terminal amine. We demonstrate that this approach yields MPs featuring asymmetric cyclization units from both synthetic peptides and when linear precursors are appended onto a phage-coat protein. Finally, we showcase that our cyclization strategy is compatible with traditional phage-display protocols and enables the selection of MP binders against a model target protein from naïve libraries. By enabling the incorporation of non-peptidic moieties that (1) can serve as cyclization units, (2) provide interactions for binding, and/or (3) tailor pharmacological properties, our head-to-side-chain cyclization strategy provides access to a currently under-explored chemical space for the development of chemical probes and therapeutics.
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Affiliation(s)
- Titia Rixt Oppewal
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
| | - Ivar D Jansen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
| | - Johan Hekelaar
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
| | - Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
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13
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Dengler S, Mandal PK, Allmendinger L, Douat C, Huc I. Conformational interplay in hybrid peptide-helical aromatic foldamer macrocycles. Chem Sci 2021; 12:11004-11012. [PMID: 34522297 PMCID: PMC8386670 DOI: 10.1039/d1sc03640h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/26/2021] [Indexed: 12/28/2022] Open
Abstract
Macrocyclic peptides are an important class of bioactive substances. When inserting an aromatic foldamer segment in a macrocyclic peptide, the strong folding propensity of the former may influence the conformation and alter the properties of the latter. Such an insertion is relevant because some foldamer-peptide hybrids have recently been shown to be tolerated by the ribosome, prior to forming macrocycles, and can thus be produced using an in vitro translation system. We have investigated the interplay of peptide and foldamer conformations in such hybrid macrocycles. We show that foldamer helical folding always prevails and stands as a viable means to stretch, i.e. unfold, peptides in a solvent dependent manner. Conversely, the peptide systematically has a reciprocal influence and gives rise to strong foldamer helix handedness bias as well as foldamer helix stabilisation. The hybrid macrocycles also show resistance towards proteolytic degradation.
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Affiliation(s)
- Sebastian Dengler
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität Butenandtstraße 5-13 D-81377 Munich Germany
| | - Pradeep K Mandal
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität Butenandtstraße 5-13 D-81377 Munich Germany
| | - Lars Allmendinger
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität Butenandtstraße 5-13 D-81377 Munich Germany
| | - Céline Douat
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität Butenandtstraße 5-13 D-81377 Munich Germany
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität Butenandtstraße 5-13 D-81377 Munich Germany
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14
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Bechtler C, Lamers C. Macrocyclization strategies for cyclic peptides and peptidomimetics. RSC Med Chem 2021; 12:1325-1351. [PMID: 34447937 PMCID: PMC8372203 DOI: 10.1039/d1md00083g] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Peptides are a growing therapeutic class due to their unique spatial characteristics that can target traditionally "undruggable" protein-protein interactions and surfaces. Despite their advantages, peptides must overcome several key shortcomings to be considered as drug leads, including their high conformational flexibility and susceptibility to proteolytic cleavage. As a general approach for overcoming these challenges, macrocyclization of a linear peptide can usually improve these characteristics. Their synthetic accessibility makes peptide macrocycles very attractive, though traditional synthetic methods for macrocyclization can be challenging for peptides, especially for head-to-tail cyclization. This review provides an updated summary of the available macrocyclization chemistries, such as traditional lactam formation, azide-alkyne cycloadditions, ring-closing metathesis as well as unconventional cyclization reactions, and it is structured according to the obtained functional groups. Keeping peptide chemistry and screening in mind, the focus is given to reactions applicable in solution, on solid supports, and compatible with contemporary screening methods.
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Affiliation(s)
- Clément Bechtler
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
| | - Christina Lamers
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
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15
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Toplak A, Teixeira de Oliveira EF, Schmidt M, Rozeboom HJ, Wijma HJ, Meekels LKM, de Visser R, Janssen DB, Nuijens T. From thiol-subtilisin to omniligase: Design and structure of a broadly applicable peptide ligase. Comput Struct Biotechnol J 2021; 19:1277-1287. [PMID: 33717424 PMCID: PMC7921005 DOI: 10.1016/j.csbj.2021.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/01/2021] [Accepted: 02/01/2021] [Indexed: 11/05/2022] Open
Abstract
Omniligase-1 is a broadly applicable enzyme for peptide bond formation between an activated acyl donor peptide and a non-protected acyl acceptor peptide. The enzyme is derived from an earlier subtilisin variant called peptiligase by several rounds of protein engineering aimed at increasing synthetic yields and substrate range. To examine the contribution of individual mutations on S/H ratio and substrate scope in peptide synthesis, we selected peptiligase variant M222P/L217H as a starting enzyme and introduced successive mutations. Mutation A225N in the S1′ pocket and F189W of the S2′ pocket increased the synthesis to hydrolysis (S/H) ratio and overall coupling efficiency, whereas the I107V mutation was added to S4 pocket to increase the reaction rate. The final omniligase variants appeared to have a very broad substrate range, coupling more than 250 peptides in a 400-member library of acyl acceptors, as indicated by a high-throughput FRET assay. Crystal structures and computational modelling could rationalize the exceptional properties of omniligase-1 in peptide synthesis
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Affiliation(s)
- Ana Toplak
- EnzyPep B.V., Brightlands Campus Urmonderbaan 22, 6167 RD Geleen, The Netherlands
| | - Eduardo F Teixeira de Oliveira
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marcel Schmidt
- EnzyPep B.V., Brightlands Campus Urmonderbaan 22, 6167 RD Geleen, The Netherlands
| | - Henriëtte J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Linda K M Meekels
- EnzyPep B.V., Brightlands Campus Urmonderbaan 22, 6167 RD Geleen, The Netherlands
| | - Rowin de Visser
- EnzyPep B.V., Brightlands Campus Urmonderbaan 22, 6167 RD Geleen, The Netherlands
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Timo Nuijens
- EnzyPep B.V., Brightlands Campus Urmonderbaan 22, 6167 RD Geleen, The Netherlands
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16
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Small and Simple, yet Sturdy: Conformationally Constrained Peptides with Remarkable Properties. Int J Mol Sci 2021; 22:ijms22041611. [PMID: 33562633 PMCID: PMC7915549 DOI: 10.3390/ijms22041611] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
The sheer size and vast chemical space (i.e., diverse repertoire and spatial distribution of functional groups) underlie peptides’ ability to engage in specific interactions with targets of various structures. However, the inherent flexibility of the peptide chain negatively affects binding affinity and metabolic stability, thereby severely limiting the use of peptides as medicines. Imposing conformational constraints to the peptide chain offers to solve these problems but typically requires laborious structure optimization. Alternatively, libraries of constrained peptides with randomized modules can be screened for specific functions. Here, we present the properties of conformationally constrained peptides and review rigidification chemistries/strategies, as well as synthetic and enzymatic methods of producing macrocyclic peptides. Furthermore, we discuss the in vitro molecular evolution methods for the development of constrained peptides with pre-defined functions. Finally, we briefly present applications of selected constrained peptides to illustrate their exceptional properties as drug candidates, molecular recognition probes, and minimalist catalysts.
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17
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Pineda-Castañeda HM, Insuasty-Cepeda DS, Niño-Ramírez VA, Curtidor H, Rivera-Monroy ZJ. Designing Short Peptides: A Sisyphean Task? CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999200910094034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Over the last few years, short peptides have become a powerful tool in basic and
applied research, with different uses like diagnostic, antimicrobial peptides, human health
promoters or bioactive peptides, therapeutic treatments, templates for peptidomimetic design,
and peptide-based vaccines. In this endeavor, different approaches and technologies
have been explored, such as bioinformatics, large-scale peptide synthesis, omics sciences,
structure-activity relationship studies, and a biophysical approach, among others, seeking to
obtain the shortest sequence with the best activity. The advantage of short peptides lies in
their stability, ease of production, safety, and low cost. There are many strategies for designing
short peptides with biomedical and industrial applications (targeting the structure, length,
charge, or polarity) or as a starting point for improving their properties (sequence data base,
de novo sequences, templates, or organic scaffolds). In peptide design, it is necessary to keep in mind factors
such as the application (peptidomimetic, immunogen, antimicrobial, bioactive, or protein-protein interaction
inhibitor), the expected target (membrane cell, nucleus, receptor proteins, or immune system), and particular
characteristics (shorter, conformationally constrained, cycled, charged, flexible, polymerized, or pseudopeptides).
This review summarizes the different synthetic approaches and strategies used to design new peptide analogs,
highlighting the achievements, constraints, and advantages of each.
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Affiliation(s)
| | | | - Víctor A. Niño-Ramírez
- Chemistry Department, Sciences Faculty, Universidad Nacional de Colombia, Bogota, Colombia
| | | | - Zuly J. Rivera-Monroy
- Chemistry Department, Sciences Faculty, Universidad Nacional de Colombia, Bogota, Colombia
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18
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Meuleman TJ, Cowton VM, Patel AH, Liskamp RM. Improving the aqueous solubility of HCV-E2 glycoprotein epitope mimics by cyclization using POLAR hinges. J Pept Sci 2020; 26:e3222. [PMID: 31984607 PMCID: PMC7050536 DOI: 10.1002/psc.3222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 12/20/2022]
Abstract
In this research we describe the improvement of the water-solubility of cyclic epitope mimics based on the HCV E2 glycoprotein by incorporation of suitable polar hinges. The poor solubility of epitope mimics based on peptide sequences in the envelope (E2) protein hampered their synthesis and purification and made it very difficult to prepare the molecular constructs for evaluation of their bioactivity. Since changes in the amino acid composition are hardly possible in these epitope mimics in order to increase water-solubility, a polar cyclization hinge may offer a remedy leading to a significant increase of polarity and therefore water solubility. These polar hinges were applied in the synthesis of better water-soluble HCV-E2 epitopes. An azide functionality in the polar hinges allowed attachment of a tetraethylene glycol linker by Cu-catalyzed azide-alkyne cyclo-addition (CuAAC) for a convenient conjugation to ELISA plates in order to evaluate the bio-activity of the epitope mimics. The immunoassays showed that the use of more polar cyclization hinges still supported anti-HCV antibody recognition and did not negatively influence their binding. This significantly increased solubility induced by polar hinges should therefore allow for the molecular construction and ultimate evaluation of synthetic vaccine molecules.
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Affiliation(s)
- Theodorus J. Meuleman
- School of Chemistry, University of GlasgowJoseph Black Building, University AvenueGlasgowG12 8QQUK
| | - Vanessa M. Cowton
- MRC‐University of Glasgow Centre for Virus ResearchGarscube Campus, Sir Michael Stoker Building, 464 Bearsden RoadGlasgowG61 1QHUK
| | - Arvind H. Patel
- MRC‐University of Glasgow Centre for Virus ResearchGarscube Campus, Sir Michael Stoker Building, 464 Bearsden RoadGlasgowG61 1QHUK
| | - Rob M.J. Liskamp
- School of Chemistry, University of GlasgowJoseph Black Building, University AvenueGlasgowG12 8QQUK
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19
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Duflocq S, Zhou J, Huguenot F, Vidal M, Liu WQ. One-pot oxime ligation from peptides bearing thiazolidine and aminooxyacetyl groups. RSC Adv 2020; 10:17681-17685. [PMID: 35515616 PMCID: PMC9053634 DOI: 10.1039/d0ra03235b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 11/25/2022] Open
Abstract
One-pot oxime ligation under mild conditions using Pd(ii) as a shared catalyst from an aldehyde precursor (Thz) and a protected aminooxyacetyl group (Proc-Aoa) is reported. Two complementary metal-free protocols using unmasked Aoa-peptide are also described. Acetoxime-peptide can proceed to the desired oxime through an additional transoximation step. Pd(ii), acidic hydrolysis and iodine lead to one-pot oxime ligation from peptides bearing thiazolidine and aminooxyacetyl groups.![]()
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Affiliation(s)
| | - Jingjing Zhou
- Université de Paris
- CiTCoM
- 8038 CNRS
- U 1268 INSERM
- F-75006 Paris
| | | | - Michel Vidal
- Université de Paris
- CiTCoM
- 8038 CNRS
- U 1268 INSERM
- F-75006 Paris
| | - Wang-Qing Liu
- Université de Paris
- CiTCoM
- 8038 CNRS
- U 1268 INSERM
- F-75006 Paris
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20
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Nuijens T, Toplak A, Schmidt M, Ricci A, Cabri W. Natural Occurring and Engineered Enzymes for Peptide Ligation and Cyclization. Front Chem 2019; 7:829. [PMID: 31850317 PMCID: PMC6895249 DOI: 10.3389/fchem.2019.00829] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022] Open
Abstract
The renaissance of peptides as prospective therapeutics has fostered the development of novel strategies for their synthesis and modification. In this context, besides the development of new chemical peptide ligation approaches, especially the use of enzymes as a versatile tool has gained increased attention. Nowadays, due to their inherent properties such as excellent regio- and chemoselectivity, enzymes represent invaluable instruments in both academic and industrial laboratories. This mini-review focuses on natural- and engineered peptide ligases that can form a new peptide (amide) bond between the C-terminal carboxy and N-terminal amino group of a peptide and/or protein. The pro's and cons of several enzyme classes such as Sortases, Asparaginyl Endoproteases, Trypsin related enzymes and as a central focus subtilisin-derived variants are summarized. Most recent developments with regards to ligation and cyclization are highlighted.
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Affiliation(s)
- Timo Nuijens
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | - Ana Toplak
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | - Marcel Schmidt
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | | | - Walter Cabri
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
- Fresenius Kabi iPSUM Srl, Villadose, Italy
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21
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Abstract
Subtiligase-catalyzed peptide ligation is a powerful approach for site-specific protein bioconjugation, synthesis and semisynthesis of proteins and peptides, and chemoproteomic analysis of cellular N termini. Here, we provide a comprehensive review of the subtiligase technology, including its development, applications, and impacts on protein science. We highlight key advantages and limitations of the tool and compare it to other peptide ligase enzymes. Finally, we provide a perspective on future applications and challenges and how they may be addressed.
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Affiliation(s)
- Amy M Weeks
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94143, United States
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