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Evangelista JL, Kay MS. BracketMaker: Visualization and optimization of chemical protein synthesis. Protein Sci 2024; 33:e5174. [PMID: 39276022 PMCID: PMC11401056 DOI: 10.1002/pro.5174] [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: 05/28/2024] [Revised: 08/26/2024] [Accepted: 08/28/2024] [Indexed: 09/16/2024]
Abstract
Chemical protein synthesis (CPS), in which custom peptide segments of ~20-60 aa are produced by solid-phase peptide synthesis and then stitched together through sequential ligation reactions, is an increasingly popular technique. The workflow of CPS is often depicted with a "bracket" style diagram detailing the starting segments and the order of all ligation, desulfurization, and/or deprotection steps to obtain the product protein. Brackets are invaluable tools for comparing multiple possible synthetic approaches and serve as blueprints throughout a synthesis. Drawing CPS brackets by hand or in standard graphics software, however, is a painstaking and error-prone process. Furthermore, the CPS field lacks a standard bracket format, making side-by-side comparisons difficult. To address these problems, we developed BracketMaker, an open-source Python program with built-in graphic user interface (GUI) for the rapid creation and analysis of CPS brackets. BracketMaker contains a custom graphics engine which converts a text string (a protein sequence annotated with reaction steps, introduced herein as a standardized format for brackets) into a high-quality vector or PNG image. To aid with new syntheses, BracketMaker's "AutoBracket" tool automatically performs retrosynthetic analysis on a set of segments to draft and rank all possible ligation orders using standard native chemical ligation, protection, and desulfurization techniques. AutoBracket, in conjunction with an improved version of our previously reported Automated Ligator (Aligator) program, provides a pipeline to rapidly develop synthesis plans for a given protein sequence. We demonstrate the application of both programs to develop a blueprint for 65 proteins of the minimal Escherichia coli ribosome.
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Affiliation(s)
| | - Michael S. Kay
- Department of BiochemistryUniversity of UtahSalt Lake CityUtahUSA
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2
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Liu H, Chow HY, Liu J, Shi P, Li X. Prior disulfide bond-mediated Ser/Thr ligation. Chem Sci 2024:d4sc04825c. [PMID: 39170718 PMCID: PMC11333947 DOI: 10.1039/d4sc04825c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
In this work, we developed a novel strategy, prior disulfide bond-mediated Ser/Thr ligation (PD-STL), for the chemical synthesis of peptides and proteins. This approach combines disulfide bond-forming chemistry with Ser/Thr ligation (STL), converting intermolecular STL into intramolecular STL to effectively proceed regardless of concentrations. We demonstrated the effectiveness of PD-STL under high dilution conditions, even for the relatively inert C-terminal proline at the ligation site. Additionally, we applied this method to synthesize the N-terminal cytoplasmic domain (2-104) of caveolin-1 and its Tyr14 phosphorylated form.
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Affiliation(s)
- Heng Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Hoi Yee Chow
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Jiamei Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Pengfei Shi
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Hong Kong SAR P. R. China
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3
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Novacek A, Ugaz B, Stephanopoulos N. Templating Peptide Chemistry with Nucleic Acids: Toward Artificial Ribosomes, Cell-Specific Therapeutics, and Novel Protein-Mimetic Architectures. Biomacromolecules 2024; 25:3865-3876. [PMID: 38860980 DOI: 10.1021/acs.biomac.4c00372] [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: 06/12/2024]
Abstract
In biology, nanomachines like the ribosome use nucleic acid templates to synthesize polymers in a sequence-specific, programmable fashion. Researchers have long been interested in using the programmable properties of nucleic acids to enhance chemical reactions via colocalization of reagents using complementary nucleic acid handles. In this review, we describe progress in using nucleic acid templates, handles, or splints to enhance the covalent coupling of peptides to other peptides or oligonucleotides. We discuss work in several areas: creating ribosome-mimetic systems, synthesizing bioactive peptides on DNA or RNA templates, linking peptides into longer molecules and bioactive antibody mimics, and scaffolding peptides to build protein-mimetic architectures. We close by highlighting the challenges that must be overcome in nucleic acid-templated peptide chemistry in two areas: making full-length, functional proteins from synthetic peptides and creating novel protein-mimetic architectures not possible through macromolecular folding alone.
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Affiliation(s)
- Alexandra Novacek
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
| | - Bryan Ugaz
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
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4
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Peng J, Hughes GR, Müller MM, Seebeck FP. Enzymatic Fluoromethylation as a Tool for ATP-Independent Ligation. Angew Chem Int Ed Engl 2024; 63:e202312104. [PMID: 37955592 PMCID: PMC10952888 DOI: 10.1002/anie.202312104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
S-adenosylmethionine-dependent methyltransferases are involved in countless biological processes, including signal transduction, epigenetics, natural product biosynthesis, and detoxification. Only a handful of carboxylate methyltransferases have evolved to participate in amide bond formation. In this report we show that enzyme-catalyzed F-methylation of carboxylate substrates produces F-methyl esters that readily react with N- or S-nucleophiles under physiological conditions. We demonstrate the applicability of this approach to the synthesis of small amides, hydroxamates, and thioesters, as well as to site-specific protein modification and native chemical ligation.
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Affiliation(s)
- Jiaming Peng
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
| | - Gregory R. Hughes
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Manuel M. Müller
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Florian P. Seebeck
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
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5
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Peng J, Hughes GR, Müller MM, Seebeck FP. Enzymatic Fluoromethylation as a Tool for ATP-Independent Ligation. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 136:e202312104. [PMID: 38516647 PMCID: PMC10952241 DOI: 10.1002/ange.202312104] [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: 08/18/2023] [Indexed: 03/23/2024]
Abstract
S-adenosylmethionine-dependent methyltransferases are involved in countless biological processes, including signal transduction, epigenetics, natural product biosynthesis, and detoxification. Only a handful of carboxylate methyltransferases have evolved to participate in amide bond formation. In this report we show that enzyme-catalyzed F-methylation of carboxylate substrates produces F-methyl esters that readily react with N- or S-nucleophiles under physiological conditions. We demonstrate the applicability of this approach to the synthesis of small amides, hydroxamates, and thioesters, as well as to site-specific protein modification and native chemical ligation.
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Affiliation(s)
- Jiaming Peng
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
| | - Gregory R. Hughes
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Manuel M. Müller
- Department of ChemistryKing's College LondonBritannia House7 Trinity StreetSE1 1DBLondonUK
| | - Florian P. Seebeck
- Department of ChemistryUniversity of BaselMattenstrasse 24a4002BaselSwitzerland
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6
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Javid H, Oryani MA, Rezagholinejad N, Esparham A, Tajaldini M, Karimi‐Shahri M. RGD peptide in cancer targeting: Benefits, challenges, solutions, and possible integrin-RGD interactions. Cancer Med 2024; 13:e6800. [PMID: 38349028 PMCID: PMC10832341 DOI: 10.1002/cam4.6800] [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: 06/28/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 02/15/2024] Open
Abstract
RGD peptide can be found in cell adhesion and signaling proteins, such as fibronectin, vitronectin, and fibrinogen. RGD peptides' principal function is to facilitate cell adhesion by interacting with integrin receptors on the cell surface. They have been intensively researched for use in biotechnology and medicine, including incorporation into biomaterials, conjugation to medicinal molecules or nanoparticles, and labeling with imaging agents. RGD peptides can be utilized to specifically target cancer cells and the tumor vasculature by engaging with these integrins, improving drug delivery efficiency and minimizing adverse effects on healthy tissues. RGD-functionalized drug carriers are a viable option for cancer therapy as this focused approach has demonstrated promise in the future. Writing a review on the RGD peptide can significantly influence how drugs are developed in the future by improving our understanding of the peptide, finding knowledge gaps, fostering innovation, and making drug design easier.
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Affiliation(s)
- Hossein Javid
- Department of Medical Laboratory SciencesVarastegan Institute for Medical SciencesMashhadIran
- Department of Clinical Biochemistry, Faculty of MedicineMashhad University of Medical SciencesMashhadIran
- Surgical Oncology Research CenterMashhad University of Medical SciencesMashhadIran
| | - Mahsa Akbari Oryani
- Department of Pathology, School of MedicineMashhad University of Medical SciencesMashhadIran
| | | | - Ali Esparham
- Student Research Committee, Faculty of MedicineMashhad University of Medical SciencesMashhadIran
| | - Mahboubeh Tajaldini
- Ischemic Disorder Research CenterGolestan University of Medical SciencesGorganIran
| | - Mehdi Karimi‐Shahri
- Department of Pathology, School of MedicineMashhad University of Medical SciencesMashhadIran
- Department of Pathology, School of MedicineGonabad University of Medical SciencesGonabadIran
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7
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Harrison K, Mackay AS, Kambanis L, Maxwell JWC, Payne RJ. Synthesis and applications of mirror-image proteins. Nat Rev Chem 2023; 7:383-404. [PMID: 37173596 DOI: 10.1038/s41570-023-00493-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 05/15/2023]
Abstract
The homochirality of biomolecules in nature, such as DNA, RNA, peptides and proteins, has played a critical role in establishing and sustaining life on Earth. This chiral bias has also given synthetic chemists the opportunity to generate molecules with inverted chirality, unlocking valuable new properties and applications. Advances in the field of chemical protein synthesis have underpinned the generation of numerous 'mirror-image' proteins (those comprised entirely of D-amino acids instead of canonical L-amino acids), which cannot be accessed using recombinant expression technologies. This Review seeks to highlight recent work on synthetic mirror-image proteins, with a focus on modern synthetic strategies that have been leveraged to access these complex biomolecules as well as their applications in protein crystallography, drug discovery and the creation of mirror-image life.
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Affiliation(s)
- Katriona Harrison
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Angus S Mackay
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Joshua W C Maxwell
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia.
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8
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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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9
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Digal LD, Kirkeby EK, Austin MJ, Roberts AG. Design and Evaluation of Ambiphilic Aryl Thiol-Iminium-Based Molecules for Organocatalyzed Thioacyl Aminolysis. ACS OMEGA 2023; 8:9319-9325. [PMID: 36936301 PMCID: PMC10018527 DOI: 10.1021/acsomega.2c07586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Progress toward the design and synthesis of ambiphilic aryl thiol-iminium-based small molecules for organocatalyzed thioacyl aminolysis is reported. Here we describe the synthesis of a novel tetrahydroisoquinoline-derived scaffold, bearing both thiol and iminium functionalities, capable of promoting the transthioesterification and subsequent amine capture reactions necessary to achieve organocatalyzed thioacyl aminolysis. Model studies demonstrate the ability of this designed organocatalyst to deliver critical intermediates capable of undergoing these individual reactions necessary for the proposed process. Future design improvements and directions toward cysteine-independent organocatalyzed native chemical ligation are discussed.
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10
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Sharma K, Sharma KK, Sharma A, Jain R. Peptide-based drug discovery: Current status and recent advances. Drug Discov Today 2023; 28:103464. [PMID: 36481586 DOI: 10.1016/j.drudis.2022.103464] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The progressive development of peptides from reaction vessels to life-saving drugs via rigorous preclinical and clinical assessments is fascinating. Peptide therapeutics have gained momentum with the evolution of techniques in peptide chemistry, such as microwave irradiation in solid- and solution-phase synthesis, ligation chemistry, recombinant synthesis, and amalgamation with synthetic tools, including metal catalysis. Diverse emerging technologies, such as DNA-encoded libraries (DELs) and display techniques, are changing the status quo in the discovery of peptide therapeutics. In this review, we analyzed US Food and Drug Administration (FDA)-approved peptide drugs and those in clinical trials, highlighting recent advances in peptide-based drug discovery.
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Affiliation(s)
- Komal Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Krishna K Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Anku Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India.
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11
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Ollivier N, Sénéchal M, Desmet R, Snella B, Agouridas V, Melnyk O. A biomimetic electrostatic assistance for guiding and promoting N-terminal protein chemical modification. Nat Commun 2022; 13:6667. [PMID: 36335111 PMCID: PMC9637170 DOI: 10.1038/s41467-022-34392-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
The modification of protein electrostatics by phosphorylation is a mechanism used by cells to promote the association of proteins with other biomolecules. In this work, we show that introducing negatively charged phosphoserines in a reactant is a powerful means for directing and accelerating the chemical modification of proteins equipped with oppositely charged arginines. While the extra charged amino acid residues induce no detectable affinity between the reactants, they bring site-selectivity to a reaction that is otherwise devoid of such a property. They also enable rate accelerations of four orders of magnitude in some cases, thereby permitting chemical processes to proceed at the protein level in the low micromolar range, using reactions that are normally too slow to be useful in such dilute conditions.
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Affiliation(s)
- Nathalie Ollivier
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Magalie Sénéchal
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Rémi Desmet
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Benoît Snella
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Vangelis Agouridas
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France ,Centrale Lille, F-59000 Lille, France
| | - Oleg Melnyk
- grid.410463.40000 0004 0471 8845Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017; Center for Infection and Immunity of Lille, F-59000 Lille, France
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12
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Diemer V, Firstova O, Agouridas V, Melnyk O. Pedal to the Metal: The Homogeneous Catalysis of the Native Chemical Ligation Reaction. Chemistry 2022; 28:e202104229. [PMID: 35048443 DOI: 10.1002/chem.202104229] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Indexed: 11/08/2022]
Abstract
The native chemical ligation reaction of peptide thioesters with cysteinyl peptides is a pivotal chemical process in the production of native or modified peptides and proteins, and well beyond in the preparation of various biomolecule analogs and materials. To benefit from this reaction at its fullest and to access all the possible applications, the experimentalist needs to know the factors affecting its rate and how to control it. This concept article presents the fundamental principles underlying the rate of the native chemical ligation and its homogeneous catalysis by nucleophiles. It has been prepared to serve as a quick guide in the search for an appropriate catalyst.
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Affiliation(s)
- Vincent Diemer
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -, UMR 9017 -, CIIL -, Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Olga Firstova
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -, UMR 9017 -, CIIL -, Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Vangelis Agouridas
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -, UMR 9017 -, CIIL -, Center for Infection and Immunity of Lille, 59000, Lille, France.,Centrale Lille, 59000, Lille, France
| | - Oleg Melnyk
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 -, UMR 9017 -, CIIL -, Center for Infection and Immunity of Lille, 59000, Lille, France
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13
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Fersing C, Masurier N, Rubira L, Deshayes E, Lisowski V. AAZTA-Derived Chelators for the Design of Innovative Radiopharmaceuticals with Theranostic Applications. Pharmaceuticals (Basel) 2022; 15:234. [PMID: 35215346 PMCID: PMC8879111 DOI: 10.3390/ph15020234] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 02/06/2023] Open
Abstract
With the development of 68Ga and 177Lu radiochemistry, theranostic approaches in modern nuclear medicine enabling patient-centered personalized medicine applications have been growing in the last decade. In conjunction with the search for new relevant molecular targets, the design of innovative chelating agents to easily form stable complexes with various radiometals for theranostic applications has gained evident momentum. Initially conceived for magnetic resonance imaging applications, the chelating agent AAZTA features a mesocyclic seven-membered diazepane ring, conferring some of the properties of both acyclic and macrocyclic chelating agents. Described in the early 2000s, AAZTA and its derivatives exhibited interesting properties once complexed with metals and radiometals, combining a fast kinetic of formation with a slow kinetic of dissociation. Importantly, the extremely short coordination reaction times allowed by AAZTA derivatives were particularly suitable for short half-life radioelements (i.e., 68Ga). In view of these particular characteristics, the scope of this review is to provide a survey on the design, synthesis, and applications in the nuclear medicine/radiopharmacy field of AAZTA-derived chelators.
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Affiliation(s)
- Cyril Fersing
- Nuclear Medicine Department, Institut Régional du Cancer de Montpellier (ICM), University Montpellier, 34298 Montpellier, France; (L.R.); (E.D.)
- IBMM, University Montpellier, CNRS, ENSCM, 34293 Montpellier, France; (N.M.); (V.L.)
| | - Nicolas Masurier
- IBMM, University Montpellier, CNRS, ENSCM, 34293 Montpellier, France; (N.M.); (V.L.)
| | - Léa Rubira
- Nuclear Medicine Department, Institut Régional du Cancer de Montpellier (ICM), University Montpellier, 34298 Montpellier, France; (L.R.); (E.D.)
| | - Emmanuel Deshayes
- Nuclear Medicine Department, Institut Régional du Cancer de Montpellier (ICM), University Montpellier, 34298 Montpellier, France; (L.R.); (E.D.)
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer de Montpellier (ICM), University of Montpellier, 34298 Montpellier, France
| | - Vincent Lisowski
- IBMM, University Montpellier, CNRS, ENSCM, 34293 Montpellier, France; (N.M.); (V.L.)
- Department of Pharmacy, Lapeyronie Hospital, CHU Montpellier, 191 Av. du Doyen Gaston Giraud, 34295 Montpellier, France
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14
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Wang S, Zhou Q, Li Y, Wei B, Liu X, Zhao J, Ye F, Zhou Z, Ding B, Wang P. Quinoline-Based Photolabile Protection Strategy Facilitates Efficient Protein Assembly. J Am Chem Soc 2022; 144:1232-1242. [PMID: 35034454 DOI: 10.1021/jacs.1c10324] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Native chemical ligation (NCL) provides a powerful solution to assemble proteins with precise chemical features, which enables a detailed investigation of the protein structure-function relationship. As an extension to NCL, the discovery of desulfurization and expressed protein ligation (EPL) techniques has greatly expanded the efficient access to large or challenging protein sequences via chemical ligations. Despite its superior reliability, the NCL-desulfurization protocol requires orthogonal protection strategies to allow selective desulfurization in the presence of native Cys, which is crucial to its synthetic application. In contrast to traditional thiol protecting groups, photolabile protecting groups (PPGs), which are removed upon irradiation, simplify protein assembly and therefore provide minimal perturbation to the peptide scaffold. However, current PPG strategies are mainly limited to nitro-benzyl derivatives, which are incompatible with NCL-desulfurization. Herein, we present for the first time that quinoline-based PPG for cysteine can facilitate various ligation strategies, including iterative NCL and EPL-desulfurization methods. 7-(Piperazin-1-yl)-2-(methyl)quinolinyl (PPZQ) caging of multiple cysteine residues within the protein sequence can be readily introduced via late-stage modification, while the traceless removal of PPZQ is highly efficient via photolysis in an aqueous buffer. In addition, the PPZQ group is compatible with radical desulfurization. The efficiency of this strategy has been highlighted by the synthesis of γ-synuclein and phosphorylated cystatin-S via one-pot iterative ligation and EPL-desulfurization methods. Besides, successful sextuple protection and deprotection of the expressed Interleukin-34 fragment demonstrate the great potential of this strategy in protein caging/uncaging investigations.
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Affiliation(s)
- Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qingqing Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yunxue Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Bingcheng Wei
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xinliang Liu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jie Zhao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Farong Ye
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zhongneng Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Bei Ding
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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15
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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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16
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Houska R, Stutz MB, Seitz O. Expanding the scope of native chemical ligation - templated small molecule drug synthesis via benzanilide formation. Chem Sci 2021; 12:13450-13457. [PMID: 34777764 PMCID: PMC8528049 DOI: 10.1039/d1sc00513h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/10/2021] [Indexed: 12/15/2022] Open
Abstract
We describe a reaction system that enables the synthesis of Bcr–Abl tyrosine kinase inhibitors (TKI) via benzanilide formation in water. The reaction is based on native chemical ligation (NCL). In contrast to previous applications, we used the NCL chemistry to establish aromatic rather than aliphatic amide bonds in coupling reactions between benzoyl and o-mercaptoaniline fragments. The method was applied for the synthesis of thiolated ponatinib and GZD824 derivatives. Acid treatment provided benzothiazole structures, which opens opportunities for diversification. Thiolation affected the affinity for Abl1 kinase only moderately. Of note, a ponatinib-derived benzothiazole also showed nanomolar affinity. NCL-enabled benzanilide formation may prove useful for fragment-based drug discovery. To show that benzanilide synthesis can be put under the control of a template, we connected the benzoyl and o-mercaptoaniline fragments to DNA and peptide nucleic acid (PNA) oligomers. Complementary RNA templates enabled adjacent binding of reactive conjugates triggering a rapid benzoyl transfer from a thioester-linked DNA conjugate to an o-mercaptoaniline-DNA or -PNA conjugate. We evaluated the influence of linker length and unpaired spacer nucleotides within the RNA template on the product yield. The data suggest that nucleic acid-templated benzanilide formation could find application in the establishment of DNA-encoded combinatorial libraries (DEL). The templated native chemical ligation between benzoyl thioesters and o-mercaptoaniline fragments proceeds in water and provides benzanilides that have nanomolar affinity for Abl1 kinase.![]()
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Affiliation(s)
- Richard Houska
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Marvin Björn Stutz
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
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17
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Chung CZ, Krahn N, Crnković A, Söll D. Intein-based Design Expands Diversity of Selenocysteine Reporters. J Mol Biol 2021; 434:167199. [PMID: 34411545 PMCID: PMC8847544 DOI: 10.1016/j.jmb.2021.167199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 12/27/2022]
Abstract
The presence of selenocysteine in a protein confers many unique properties that make the production of recombinant selenoproteins desirable. Targeted incorporation of Sec into a protein of choice is possible by exploiting elongation factor Tu-dependent reassignment of UAG codons, a strategy that has been continuously improved by a variety of means. Improving selenoprotein yield by directed evolution requires selection and screening markers that are titratable, have a high dynamic range, enable high-throughput screening, and can discriminate against nonspecific UAG decoding. Current screening techniques are limited to a handful of reporters where a cysteine (Cys) or Sec residue normally affords activity. Unfortunately, these existing Cys/Sec-dependent reporters lack the dynamic range of more ubiquitous reporters or suffer from other limitations. Here we present a versatile strategy to adapt established reporters for specific Sec incorporation. Inteins are intervening polypeptides that splice themselves from the precursor protein in an autocatalytic splicing reaction. Using an intein that relies exclusively on Sec for splicing, we show that this intein cassette can be placed in-frame within selection and screening markers, affording reporter activity only upon successful intein splicing. Furthermore, because functional splicing can only occur when a catalytic Sec is present, the amount of synthesized reporter directly measures UAG-directed Sec incorporation. Importantly, we show that results obtained with intein-containing reporters are comparable to the Sec incorporation levels determined by mass spectrometry of isolated recombinant selenoproteins. This result validates the use of these intein-containing reporters to screen for evolved components of a translation system yielding increased selenoprotein amounts.
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Affiliation(s)
- Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA; Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511, USA.
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18
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Li Y, Liu J, Zhou Q, Zhao J, Wang P. Preparation of Peptide Selenoesters from Their Corresponding Acyl Hydrazides
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yunxue Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University Shanghai 200240 China
| | - Jiazhi Liu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University Shanghai 200240 China
| | - Qingqing Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University Shanghai 200240 China
| | - Jie Zhao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University Shanghai 200240 China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University Shanghai 200240 China
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19
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Zheng J, Chen X, Yang Y, Tan CSH, Tian R. Mass Spectrometry-Based Protein Complex Profiling in Time and Space. Anal Chem 2020; 93:598-619. [DOI: 10.1021/acs.analchem.0c04332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiong Chen
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yun Yang
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Chris Soon Heng Tan
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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