1
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Bachelart T, Kumar S, Jouin A, Yousef M, Kieffer B, Torbeev V. Design, Synthesis and Catalytic Activity of Protein Containing Thiotyrosine as an Active Site Residue. Chembiochem 2024; 25:e202400148. [PMID: 38629812 DOI: 10.1002/cbic.202400148] [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: 02/18/2024] [Revised: 04/16/2024] [Indexed: 06/05/2024]
Abstract
Native chemical ligation is a key reaction in the toolbox of chemical methods for the synthesis of native and modified proteins. The catalysis of ligation is commonly performed by using small aryl-thiol molecules added at high concentrations. In this work, we incorporated thiotyrosine, a non-canonical amino acid containing an aryl-thiol moiety, into a designed cyclic protein « sans queue ni tête ». Importantly, the protein environment reduced the pKa of the thiol group to 5.8-5.9, which is significantly lower than the previously reported value for thiotyrosine in a short peptide (pKa 6.4). Furthermore, we demonstrated the catalytic activity of this protein both as hydrolase and in native chemical ligation of peptides. These results will be useful for the development of efficient protein catalysts (enzymes) for protein synthesis and modification.
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Affiliation(s)
- Thomas Bachelart
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Shailesh Kumar
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Alexis Jouin
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Mo'ath Yousef
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
| | - Bruno Kieffer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 1258, University of Strasbourg, 67400, Illkirch, France
| | - Vladimir Torbeev
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400, Illkirch, France
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2
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Alešković M, Šekutor M. Overcoming barriers with non-covalent interactions: supramolecular recognition of adamantyl cucurbit[ n]uril assemblies for medical applications. RSC Med Chem 2024; 15:433-471. [PMID: 38389878 PMCID: PMC10880950 DOI: 10.1039/d3md00596h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 02/24/2024] Open
Abstract
Adamantane, a staple in medicinal chemistry, recently became a cornerstone of a supramolecular host-guest drug delivery system, ADA/CB[n]. Owing to a good fit between the adamantane cage and the host cavity of the cucurbit[n]uril macrocycle, formed strong inclusion complexes find applications in drug delivery and controlled drug release. Note that the cucurbit[n]uril host is not solely a delivery vehicle of the ADA/CB[n] system but rather influences the bioactivity and bioavailability of drug molecules and can tune drug properties. Namely, as host-guest interactions are capable of changing the intrinsic properties of the guest molecule, inclusion complexes can become more soluble, bioavailable and more resistant to metabolic conditions compared to individual non-complexed molecules. Such synergistic effects have implications for practical bioapplicability of this complex system and provide a new viewpoint to therapy, beyond the traditional single drug molecule approach. By achieving a balance between guest encapsulation and release, the ADA/CB[n] system has also found use beyond just drug delivery, in fields like bioanalytics, sensing assays, bioimaging, etc. Thus, chemosensing in physiological conditions, indicator displacement assays, in vivo diagnostics and hybrid nanostructures are just some recent examples of the ADA/CB[n] applicability, be it for displacements purposes or as cargo vehicles.
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Affiliation(s)
- Marija Alešković
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute Bijenička 54 10 000 Zagreb Croatia
| | - Marina Šekutor
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute Bijenička 54 10 000 Zagreb Croatia
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3
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Zhao F, Frandsen M, Capodaglio S, Sleiman HF. DNA-Mediated Peptide Assembly into Protein Mimics. J Am Chem Soc 2024; 146:1946-1956. [PMID: 38226787 DOI: 10.1021/jacs.3c08984] [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: 01/17/2024]
Abstract
The design of new protein structures is challenging due to their vast sequence space and the complexity of protein folding. Here, we report a new modular DNA-templated strategy to construct protein mimics. We achieve the spatial control of multiple peptide units by conjugation with DNA and hybridization to a branched DNA trimer template followed by covalent stapling of the preorganized peptides into a single unit. A library of protein mimics with different lengths, sequences, and heptad registers has been efficiently constructed. DNA-templated protein mimics show an α-helix or coiled-coil motif formation even when they are constructed from weakly interacting peptide units. Their attached DNA handles can be used to exert dynamic control over the protein mimics' secondary and tertiary structures. This modular strategy will facilitate the development of DNA-encoded protein libraries for the rapid discovery of new therapeutics, enzymes, and antibody mimics.
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Affiliation(s)
- Fangzhou Zhao
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Martin Frandsen
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, Aarhus 8000, Denmark
| | - Sabrina Capodaglio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma I-43124, Italy
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
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4
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Kim H, Choi H, Min KS, Han WJ, Park JW, Kim KT. Riboflavin-catalyzed templated reaction to translate nucleic acid cues into signals of rhodamine derivatives. Chem Commun (Camb) 2022; 58:13743-13746. [PMID: 36416038 DOI: 10.1039/d2cc05447g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We report a templated reaction for the facile translation of nucleic acid cues into signals of universal rhodamine derivatives based on the riboflavin-catalyzed oxidation of dihydrorhodamine compounds. The rhodamine-signaling operation enabled us to design a highly sequence-selective fluorescent sensor that can detect as little as 500 pM of the target nucleic acid in 90 min or to present a rhodamine antibody that can be further applied to immunoassays.
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Affiliation(s)
- Hokyung Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Hayeon Choi
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Kyeong Su Min
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Woo Joo Han
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Jae Woo Park
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Ki Tae Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea.
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5
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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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6
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Assembly of Biologically Functional Structures by Nucleic Acid Templating: Implementation of a Strategy to Overcome Inhibition by Template Excess. Molecules 2022; 27:molecules27206831. [PMID: 36296424 PMCID: PMC9610079 DOI: 10.3390/molecules27206831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022] Open
Abstract
Delivery of therapeutic molecules to pathogenic cells is often hampered by unintended toxicity to normal cells. In principle, this problem can be circumvented if the therapeutic effector molecule is split into two inactive components, and only assembled on or within the target cell itself. Such an in situ process can be realized by exploiting target-specific molecules as templates to direct proximity-enhanced assembly. Modified nucleic acids carrying inert precursor fragments can be designed to co-hybridize on a target-specific template nucleic acid, such that the enforced proximity accelerates assembly of a functional molecule for antibody recognition. We demonstrate the in vitro feasibility of this adaptation of nucleic acid-templated synthesis (NATS) using oligonucleotides bearing modified peptides (“haplomers”), for templated assembly of a mimotope recognized by the therapeutic antibody trastuzumab. Enforced proximity promotes mimotope assembly via traceless native chemical ligation. Nevertheless, titration of participating haplomers through template excess is a potential limitation of trimolecular NATS. In order to overcome this problem, we devised a strategy where haplomer hybridization can only occur in the presence of target, without being subject to titration effects. This generalizable NATS modification may find future applications in enabling directed targeting of pathological cells.
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7
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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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8
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McLoughlin NM, Kuepper A, Neubacher S, Grossmann TN. Synergistic DNA- and Protein-Based Recognition Promote an RNA-Templated Bio-orthogonal Reaction. Chemistry 2021; 27:10477-10483. [PMID: 33914384 PMCID: PMC8362040 DOI: 10.1002/chem.202101103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 12/28/2022]
Abstract
Biomolecular assemblies composed of proteins and oligonucleotides play a central role in biological processes. While in nature, oligonucleotides and proteins usually assemble via non-covalent interactions, synthetic conjugates have been developed which covalently link both modalities. The resulting peptide-oligonucleotide conjugates have facilitated novel biological applications as well as the design of functional supramolecular systems and materials. However, despite the importance of concerted protein/oligonucleotide recognition in nature, conjugation approaches have barely utilized the synergistic recognition abilities of such complexes. Herein, the structure-based design of peptide-DNA conjugates that bind RNA through Watson-Crick base pairing combined with peptide-mediated major groove recognition is reported. Two distinct conjugate families with tunable binding characteristics have been designed to adjacently bind a particular RNA sequence. In the resulting ternary complex, their peptide elements are located in proximity, a feature that was used to enable an RNA-templated click reaction. The introduced structure-based design approach opens the door to novel functional biomolecular assemblies.
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Affiliation(s)
- Niall M. McLoughlin
- Department of Chemistry and Pharmaceutical SciencesVrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck SocietyDortmund44227Germany
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical SciencesVrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical SciencesVrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS)Vrije Universiteit AmsterdamAmsterdam1081 HZThe Netherlands
- Chemical Genomics Centre of the Max Planck SocietyDortmund44227Germany
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9
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Koo B, Yoo H, Choi HJ, Kim M, Kim C, Kim KT. Visible Light Photochemical Reactions for Nucleic Acid-Based Technologies. Molecules 2021; 26:556. [PMID: 33494512 PMCID: PMC7865461 DOI: 10.3390/molecules26030556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 12/16/2022] Open
Abstract
The expanding scope of chemical reactions applied to nucleic acids has diversified the design of nucleic acid-based technologies that are essential to medicinal chemistry and chemical biology. Among chemical reactions, visible light photochemical reaction is considered a promising tool that can be used for the manipulations of nucleic acids owing to its advantages, such as mild reaction conditions and ease of the reaction process. Of late, inspired by the development of visible light-absorbing molecules and photocatalysts, visible light-driven photochemical reactions have been used to conduct various molecular manipulations, such as the cleavage or ligation of nucleic acids and other molecules as well as the synthesis of functional molecules. In this review, we describe the recent developments (from 2010) in visible light photochemical reactions involving nucleic acids and their applications in the design of nucleic acid-based technologies including DNA photocleaving, DNA photoligation, nucleic acid sensors, the release of functional molecules, and DNA-encoded libraries.
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Affiliation(s)
| | | | | | - Min Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Korea; (B.K.); (H.Y.); (H.J.C.)
| | - Cheoljae Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Korea; (B.K.); (H.Y.); (H.J.C.)
| | - Ki Tae Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Korea; (B.K.); (H.Y.); (H.J.C.)
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10
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Baranda Pellejero L, Mahdifar M, Ercolani G, Watson J, Brown T, Ricci F. Using antibodies to control DNA-templated chemical reactions. Nat Commun 2020; 11:6242. [PMID: 33288745 PMCID: PMC7721721 DOI: 10.1038/s41467-020-20024-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/11/2020] [Indexed: 11/09/2022] Open
Abstract
DNA-templated synthesis takes advantage of the programmability of DNA-DNA interactions to accelerate chemical reactions under diluted conditions upon sequence-specific hybridization. While this strategy has proven advantageous for a variety of applications, including sensing and drug discovery, it has been so far limited to the use of nucleic acids as templating elements. Here, we report the rational design of DNA templated synthesis controlled by specific IgG antibodies. Our approach is based on the co-localization of reactants induced by the bivalent binding of a specific IgG antibody to two antigen-conjugated DNA templating strands that triggers a chemical reaction that would be otherwise too slow under diluted conditions. This strategy is versatile, orthogonal and adaptable to different IgG antibodies and can be employed to achieve the targeted synthesis of clinically-relevant molecules in the presence of specific IgG biomarker antibodies.
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Affiliation(s)
- Lorena Baranda Pellejero
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Malihe Mahdifar
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Gianfranco Ercolani
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Jonathan Watson
- ATDBio Ltd, Magdalen Centre, Oxford Science Park, Robert Robinson Avenue, Oxford, OX4 4GA, UK
| | - Tom Brown
- ATDBio Ltd, Magdalen Centre, Oxford Science Park, Robert Robinson Avenue, Oxford, OX4 4GA, UK
| | - Francesco Ricci
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy.
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11
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Smith JD, Scanlan MM, Chen AN, Ashberry HM, Skrabalak SE. Kinetically Controlled Sequential Seeded Growth: A General Route to Crystals with Different Hierarchies. ACS NANO 2020; 14:15953-15961. [PMID: 33119253 DOI: 10.1021/acsnano.0c07384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The organization of natural materials into hierarchical structures accounts for the amazing properties of many biological systems; however, translating the structural motifs present in such natural materials to synthetic systems remains difficult. Inspired by how nature creates materials, this work demonstrates that kinetically controlled sequential seeded growth is a general bottom-up strategy to prepare hierarchical inorganic crystals with distinct compositions and nanostructured forms. Specifically, 85 distinct hierarchical crystals with different shape-controlled features, compositions, and overall symmetries were readily achieved by altering the kinetics of metal deposition in sequential rounds of seeded growth. These modifications in the deposition kinetics were achieved through simple changes to the reaction conditions (e.g., pH or halide concentration) and dictate whether concave or convex features are produced at specific seed locations, much in the manner that the changing atmospheric conditions account for the hierarchical and symmetrical structures of snow crystals. As such, this work provides a general paradigm for the bottom-up synthesis of hierarchical crystals regardless of inorganic material class.
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Affiliation(s)
- Joshua D Smith
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Mattea M Scanlan
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alexander N Chen
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Hannah M Ashberry
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Sara E Skrabalak
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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12
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Wagh SB, Maslivetc V, La Clair JJ, Kornienko A. A fluorescent target-guided Paal-Knorr reaction. RSC Adv 2020; 10:37035-37039. [PMID: 34262697 PMCID: PMC8276889 DOI: 10.1039/d0ra06962k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
It has become increasingly apparent that high-diversity chemical reactions play a significant role in the discovery of bioactive small molecules. Here, we describe an expanse of this paradigm, combining a 'target-guided synthesis' concept with Paal-Knorr chemistry applied to the preparation of fluorescent ligands for human prostaglandin-endoperoxide synthase (COX-2).
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Affiliation(s)
- Sachin B Wagh
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos 78666, USA
| | - Vladimir Maslivetc
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos 78666, USA
| | | | - Alexander Kornienko
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos 78666, USA
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13
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Jin S, Brea RJ, Rudd AK, Moon SP, Pratt MR, Devaraj NK. Traceless native chemical ligation of lipid-modified peptide surfactants by mixed micelle formation. Nat Commun 2020; 11:2793. [PMID: 32493905 PMCID: PMC7270136 DOI: 10.1038/s41467-020-16595-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/07/2020] [Indexed: 12/04/2022] Open
Abstract
Biology utilizes multiple strategies, including sequestration in lipid vesicles, to raise the rate and specificity of chemical reactions through increases in effective molarity of reactants. We show that micelle-assisted reaction can facilitate native chemical ligations (NCLs) between a peptide-thioester – in which the thioester leaving group contains a lipid-like alkyl chain – and a Cys-peptide modified by a lipid-like moiety. Hydrophobic lipid modification of each peptide segment promotes the formation of mixed micelles, bringing the reacting peptides into close proximity and increasing the reaction rate. The approach enables the rapid synthesis of polypeptides using low concentrations of reactants without the need for thiol catalysts. After NCL, the lipid moiety is removed to yield an unmodified ligation product. This micelle-based methodology facilitates the generation of natural peptides, like Magainin 2, and the derivatization of the protein Ubiquitin. Formation of mixed micelles from lipid-modified reactants shows promise for accelerating chemical reactions in a traceless manner. Sequestration of reactants in lipid vesicles is a strategy prevalent in biological systems to raise the rate and specificity of chemical reactions. Here, the authors show that micelle-assisted reactions facilitate native chemical ligation between a peptide-thioester and a Cys-peptide modified by a lipid-like moiety.
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Affiliation(s)
- Shuaijiang Jin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Roberto J Brea
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Andrew K Rudd
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Stuart P Moon
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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14
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Yeldell SB, Seitz O. Nucleic acid constructs for the interrogation of multivalent protein interactions. Chem Soc Rev 2020; 49:6848-6865. [DOI: 10.1039/d0cs00518e] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sequence-programmed self-assembly provides multivalent nucleic acid–ligand constructs used as tailor-made probes for unravelling and exploiting the mechanisms of multivalency-enhanced interactions on protein receptors.
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Affiliation(s)
- Sean B. Yeldell
- Department of Chemistry
- Humboldt-Universität zu Berlin
- Brook-Taylor-Str. 2
- 12489 Berlin
- Germany
| | - Oliver Seitz
- Department of Chemistry
- Humboldt-Universität zu Berlin
- Brook-Taylor-Str. 2
- 12489 Berlin
- Germany
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15
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Seitz O. Templated chemistry for bioorganic synthesis and chemical biology. J Pept Sci 2019; 25:e3198. [PMID: 31309674 PMCID: PMC6771651 DOI: 10.1002/psc.3198] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 12/24/2022]
Abstract
In light of the 2018 Max Bergmann Medal, this review discusses advancements on chemical biology-driven templated chemistry developed in the author's laboratories. The focused review introduces the template categories applied to orient functional units such as functional groups, chromophores, biomolecules, or ligands in space. Unimolecular templates applied in protein synthesis facilitate fragment coupling of unprotected peptides. Templating via bimolecular assemblies provides control over proximity relationships between functional units of two molecules. As an instructive example, the coiled coil peptide-templated labelling of receptor proteins on live cells will be shown. Termolecular assemblies provide the opportunity to put the proximity of functional units on two (bio)molecules under the control of a third party molecule. This allows the design of conditional bimolecular reactions. A notable example is DNA/RNA-triggered peptide synthesis. The last section shows how termolecular and multimolecular assemblies can be used to better characterize and understand multivalent protein-ligand interactions.
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Affiliation(s)
- Oliver Seitz
- Department of ChemistryHumboldt University BerlinBerlinGermany
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