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Martí-Rujas J, Famulari A. Polycatenanes Formed of Self-Assembled Metal-Organic Cages. Angew Chem Int Ed Engl 2024; 63:e202407626. [PMID: 38837637 DOI: 10.1002/anie.202407626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024]
Abstract
Poly-[n]-catenanes (PCs) self-assembled of three-dimensional (3D) metal organic cages (MOCs) (hereafter referred to as PCs-MOCs) are a relatively new class of mechanically interlocked molecules (MIMs) that combine the properties of MOCs and polymers. The synthesis of PCs-MOCs is challenging because of the difficulties associated with interlocking MOCs, the occurrence of multiple weak supramolecular electrostatic interactions between cages, and the importance of solvent templating effects. The high density of mechanical bonds interlocking the MOCs endows the MOCs with mechanical and physical properties such as enhanced stability, responsive dynamic behavior and low solubility, which can unlock new functional properties. In this Minireview, we highlight the benefit of interlocking MOCs in the formation of PCs-MOCs structures as well as the synthetic approaches exploited in their preparation, from thermodynamic to kinetic methods, both in the solution and solid-states. Examples of PCs-MOCs self-assembled from various types of nanosized cages (i.e., tetrahedral, trigonal prismatic, octahedral and icosahedral) are described in this article, providing an overview of the research carried out in this area. The focus is on the structure-property relationship with examples of functional applications such as electron conductivity, X-ray attenuation, gas adsorption and molecular sensing. We believe that the structural and functional aspects of the reviewed PCs-MOCs will attract chemists in this research field with great potential as new functional materials in nanotechnological disciplines such as gas adsorption, sensing and photophysical properties such as X-ray attenuation or electron conductivity.
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Affiliation(s)
- Javier Martí-Rujas
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milan, Italy)
| | - Antonino Famulari
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milan, Italy)
- INSTM Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali, 50121, Florence, Italy
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2
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Kurita T, Higashi M, Gimenez-Dejoz J, Fujita S, Uji H, Sato H, Numata K. Synthesis of All-Peptide-Based Rotaxane from a Proline-Containing Cyclic Peptide. Biomacromolecules 2024; 25:3661-3670. [PMID: 38807574 DOI: 10.1021/acs.biomac.4c00257] [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: 05/30/2024]
Abstract
Rotaxane cross-linkers enhance the toughness of the resulting rotaxane cross-linked polymers through a stress dispersion effect, which is attributed to the mobility of the interlocked structure. To date, the compositional diversity of rotaxane cross-linkers has been limited, and the poor compatibility of these cross-linkers with peptides and proteins has made their use in such materials challenging. The synthesis of a rotaxane composed of peptides may result in a biodegradable cross-linker that is compatible with peptides and proteins, allowing the fortification of polypeptides and proteins and ultimately leading to the development of innovative materials that possess excellent mechanical properties and biodegradability. However, the chemical synthesis of all-peptide-based rotaxanes has remained elusive because of the absence of strong binding motifs in peptides, which prevents an axial peptide from penetrating a cyclic peptide. Here, we synthesized all-peptide-based rotaxanes using an active template method for proline-containing cyclic peptides. The results of molecular dynamics simulations suggested that cyclic peptides with an expansive inner cavity and carbonyl oxygens oriented toward the center are favorable for rotaxane synthesis. This rotaxane synthesis method is expected to accelerate the synthesis of peptides and proteins with mechanically interlocked structures, potentially leading to the development of peptide- and protein-based materials with unprecedented functionalities.
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Affiliation(s)
- Taichi Kurita
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masahiro Higashi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Joan Gimenez-Dejoz
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 31, 08034 Barcelona, Spain
| | - Seiya Fujita
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hirotaka Uji
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano-Nishibiraki-cho 34-4, Sakyou-ku, Kyoto 606-8103, Japan
| | - Keiji Numata
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Institute for Advanced Biosciences, Keio University, Nipponkoku 403-1, Daihouji, Tsuruoka, Yamagata 997-0017, Japan
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3
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Baquero F, Beis K, Craik DJ, Li Y, Link AJ, Rebuffat S, Salomón R, Severinov K, Zirah S, Hegemann JD. The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide. Nat Prod Rep 2024; 41:469-511. [PMID: 38164764 DOI: 10.1039/d3np00046j] [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: 01/03/2024]
Abstract
Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, 4072 Brisbane, Queensland, Australia
| | - Yanyan Li
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - A James Link
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Raúl Salomón
- Instituto de Química Biológica "Dr Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany.
- Department of Pharmacy, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
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4
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Cringoli MC, Marchesan S. Cysteine Redox Chemistry in Peptide Self-Assembly to Modulate Hydrogelation. Molecules 2023; 28:4970. [PMID: 37446630 DOI: 10.3390/molecules28134970] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Cysteine redox chemistry is widely used in nature to direct protein assembly, and in recent years it has inspired chemists to design self-assembling peptides too. In this concise review, we describe the progress in the field focusing on the recent advancements that make use of Cys thiol-disulfide redox chemistry to modulate hydrogelation of various peptide classes.
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Affiliation(s)
- Maria Cristina Cringoli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy
| | - Silvia Marchesan
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy
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5
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Qu Z, Fang J, Wang YX, Sun Y, Liu Y, Wu WH, Zhang WB. A single-domain green fluorescent protein catenane. Nat Commun 2023; 14:3480. [PMID: 37311944 DOI: 10.1038/s41467-023-39233-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 06/05/2023] [Indexed: 06/15/2023] Open
Abstract
Natural proteins exhibit rich structural diversity based on the folds of an invariably linear chain. Macromolecular catenanes that cooperatively fold into a single domain do not belong to the current protein universe, and their design and synthesis open new territories in chemistry. Here, we report the design, synthesis, and properties of a single-domain green fluorescent protein catenane via rewiring the connectivity of GFP's secondary motifs. The synthesis could be achieved in two steps via a pseudorotaxane intermediate or directly via expression in cellulo. Various proteins-of-interest may be inserted at the loop regions to give fusion protein catenanes where the two subunits exhibit enhanced thermal resilience, thermal stability, and mechanical stability due to strong conformational coupling. The strategy can be applied to other proteins with similar fold, giving rise to a family of single-domain fluorescent proteins. The results imply that there may be multiple protein topological variants with desirable functional traits beyond their corresponding linear protein counterparts, which are now made accessible and fully open for exploration.
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Affiliation(s)
- Zhiyu Qu
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Yu-Xiang Wang
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Yibin Sun
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Beijing, P. R. China.
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Peking University, Beijing, P. R. China.
- Center for Soft Matter Science and Engineering, Peking University, Beijing, P. R. China.
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China.
- Beijing Academy of Artificial Intelligence, Beijing, P. R. China.
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6
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Guo X, Wu M, Deng Y, Liu Y, Liu Y, Xu J. Redox-Responsive Lipidic Prodrug Nano-Delivery System Improves Antitumor Effect of Curcumin Derivative C210. Pharmaceutics 2023; 15:pharmaceutics15051546. [PMID: 37242789 DOI: 10.3390/pharmaceutics15051546] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
The poor bioavailability of curcumin and its derivatives limits their antitumor efficacy and clinical translation. Although curcumin derivative C210 has more potent antitumor activity than curcumin, it has a similar deficiency to curcumin. In order to improve its bioavailability and accordingly enhance its antitumor activity in vivo, we developed a redox-responsive lipidic prodrug nano-delivery system of C210. Briefly, we synthesized three conjugates of C210 and oleyl alcohol (OA) via different linkages containing single sulfur/disulfide/carbon bonds and prepared their nanoparticles using a nanoprecipitation method. The prodrugs required only a very small amount of DSPE-PEG2000 as a stabilizer to self-assemble in aqueous solution to form nanoparticles (NPs) with a high drug loading capacity (~50%). Among them, the prodrug (single sulfur bond) nanoparticles (C210-S-OA NPs) were the most sensitive to the intracellular redox level of cancer cells; therefore, they could rapidly release C210 in cancer cells and thus had the strongest cytotoxicity to cancer cells. Furthermore, C210-S-OA NPs exerted a dramatic improvement in its pharmacokinetic behavior; that is, the area under the curve (AUC), mean retention time and accumulation in tumor tissue were 10, 7 and 3 folds that of free C210, respectively. Thus, C210-S-OA NPs exhibited the strongest antitumor activity in vivo than C210 or other prodrug NPs in mouse models of breast cancer and liver cancer. The results demonstrated that the novel prodrug self-assembled redox-responsive nano-delivery platform was able to improve the bioavailability and antitumor activity of curcumin derivative C210, which provides a basis for further clinical applications of curcumin and its derivatives.
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Affiliation(s)
- Xin Guo
- The School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
- Fujian Provincial Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University, Fuzhou 350122, China
| | - Min Wu
- The School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
- Fujian Provincial Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University, Fuzhou 350122, China
| | - Yanping Deng
- The School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
- Fujian Provincial Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University, Fuzhou 350122, China
| | - Yan Liu
- The School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
- Fujian Provincial Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University, Fuzhou 350122, China
| | - Yanpeng Liu
- The School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
- Fujian Provincial Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University, Fuzhou 350122, China
| | - Jianhua Xu
- The School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
- Fujian Provincial Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University, Fuzhou 350122, China
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7
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Lu Y, Dutschke PD, Kinas J, Hepp A, Jin GX, Hahn FE. Organometallic Borromean Rings and [2]Catenanes Featuring Di-NHC Ligands. Angew Chem Int Ed Engl 2023; 62:e202217681. [PMID: 36629746 DOI: 10.1002/anie.202217681] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/27/2022] [Accepted: 01/11/2023] [Indexed: 01/12/2023]
Abstract
We report herein a series of organometallic Borromean rings (BRs) and [2]catenanes prepared from benzobiscarbene ligands. The reaction of dinickel complexes of the benzobiscarbenes 1 a-1 c with a thiazolothiazole bridged bipyridyl ligand L2 led by self-assembly to a series of organometallic BRs. Solvophobic effects played a crucial role in the formation and stability of the interlocked species. The stability of BRs is related to the N-alkyl substituents at the precursors 1 a-1 c, where longer alkyl substitutes improve stability and inter-ring interactions. Solvophobic effects are also important for the stability of [2]catenanes prepared from 1 a-1 c and a flexible bipyridyl ligand L3 . In solution, an equilibrium between the [2]catenanes and their macrocyclic building blocks was observed. High proportions of [2]catenanes were obtained in concentrated solutions or polar solvents. The proportion of [2]catenanes in solution could be further enhanced by lengthening of the N-alkyl substitutes.
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Affiliation(s)
- Ye Lu
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 30, 48149, Münster, Germany
| | - Patrick D Dutschke
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 30, 48149, Münster, Germany
| | - Jenny Kinas
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 30, 48149, Münster, Germany
| | - Alexander Hepp
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 30, 48149, Münster, Germany
| | - Guo-Xin Jin
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Department of Chemistry, Fudan University, Shanghai, 200438, P. R. China
| | - F Ekkehardt Hahn
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 30, 48149, Münster, Germany
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8
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Shao L, Ma J, Prelesnik JL, Zhou Y, Nguyen M, Zhao M, Jenekhe SA, Kalinin SV, Ferguson AL, Pfaendtner J, Mundy CJ, De Yoreo JJ, Baneyx F, Chen CL. Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction. Chem Rev 2022; 122:17397-17478. [PMID: 36260695 DOI: 10.1021/acs.chemrev.2c00220] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature's own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and "smart" architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.
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Affiliation(s)
- Li Shao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jinrong Ma
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Jesse L Prelesnik
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mary Nguyen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Samson A Jenekhe
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sergei V Kalinin
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Jim Pfaendtner
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher J Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - François Baneyx
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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9
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Liu Y, Bai X, Lyu C, Fang J, Zhang F, Wu WH, Wei W, Zhang WB. Mechano-bioconjugation Strategy Empowering Fusion Protein Therapeutics with Aggregation Resistance, Prolonged Circulation, and Enhanced Antitumor Efficacy. J Am Chem Soc 2022; 144:18387-18396. [PMID: 36178288 DOI: 10.1021/jacs.2c06532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bioconjugation is a powerful protein modification strategy to improve protein properties. Herein, we report mechano-bioconjugation as a novel approach to empower fusion protein therapeutics and demonstrate its utility by a protein heterocatenane (cat-IFN-ABD) containing interferon-α2b (IFN) mechanically interlocked with a consensus albumin-binding domain (ABD). The conjugate was selectively synthesized in cellulo following a cascade of post-translational events using a pair of heterodimerizing p53dim variants and two orthogonal split-intein reactions. The catenane topology was proven by combined techniques of LC-MS, SDS-PAGE, SEC, and controlled proteolytic digestion. Not only did cat-IFN-ABD retain activities comparable to those of the wild-type IFN and ABD, the conjugate also exhibited enhanced aggregation resistance and prolonged circulation time over the simple linear and cyclic fusions. Consequently, cat-IFN-ABD potently inhibited tumor growth in the mouse xenograft model. Therefore, mechano-bioconjugation by catenation accomplishes function integration with additional benefits, providing an alternative pathway for developing advanced protein therapeutics.
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Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
| | - Xilin Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
| | - Chengliang Lyu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
| | - Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
| | - Wei Wei
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
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10
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Greń BA, Dabrowski-Tumanski P, Niemyska W, Sulkowska JI. Lasso Proteins-Unifying Cysteine Knots and Miniproteins. Polymers (Basel) 2021; 13:3988. [PMID: 34833285 PMCID: PMC8621785 DOI: 10.3390/polym13223988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Complex lasso proteins are a recently identified class of biological compounds that are present in considerable fraction of proteins with disulfide bridges. In this work, we look at complex lasso proteins as a generalization of well-known cysteine knots and miniproteins (lasso peptides). In particular, we show that complex lasso proteins with the same crucial topological features-cysteine knots and lasso peptides-are antimicrobial proteins, which suggests that they act as a molecular plug. Based on an analysis of the stability of the lasso piercing residue, we also introduce a method to determine which lasso motif is potentially functional. Using this method, we show that the lasso motif in antimicrobial proteins, as well in that in cytokines, is functionally relevant. We also study the evolution of lasso motifs, their conservation, and the usefulness of the lasso fingerprint, which extracts all topologically non-triviality concerning covalent loops. The work is completed by the presentation of extensive statistics on complex lasso proteins to analyze, in particular, the strange propensity for "negative" piercings. We also identify 21 previously unknown complex lasso proteins with an ester and a thioester bridge.
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Affiliation(s)
- Bartosz Ambroży Greń
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; (B.A.G.); (P.D.-T.)
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | | | - Wanda Niemyska
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland;
| | - Joanna Ida Sulkowska
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; (B.A.G.); (P.D.-T.)
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11
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Wu WH, Bai X, Shao Y, Yang C, Wei J, Wei W, Zhang WB. Higher Order Protein Catenation Leads to an Artificial Antibody with Enhanced Affinity and In Vivo Stability. J Am Chem Soc 2021; 143:18029-18040. [PMID: 34664942 DOI: 10.1021/jacs.1c06169] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The chemical topology is a unique dimension for protein engineering, yet the topological diversity and architectural complexity of proteins remain largely untapped. Herein, we report the biosynthesis of complex topological proteins using a rationally engineered, cross-entwining peptide heterodimer motif derived from p53dim (an entangled homodimeric mutant of the tetramerization domain of the tumor suppressor protein p53). The incorporation of an electrostatic interaction at specific sites converts the p53dim homodimer motif into a pair of heterodimer motifs with high specificity for directing chain entanglement upon folding. Its combination with split-intein-mediated ligation and/or SpyTag/SpyCatcher chemistry facilitates the programmed synthesis of protein heterocatenane or [n]catenanes in cells, leading to a general and modular approach to complex protein catenanes containing various proteins of interest. Concatenation enhances not only the target protein's affinity but also the in vivo stability as shown by its prolonged circulation time in blood. As a proof of concept, artificial antibodies have been developed by embedding a human epidermal growth factor receptor 2-specific affibody onto the [n]catenane scaffolds and shown to exhibit a higher affinity and a better pharmacokinetic profile than the wild-type affibody. These results suggest that topology engineering holds great promise in the development of therapeutic proteins.
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Affiliation(s)
- Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xilin Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yu Shao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Chao Yang
- College of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang, Henan 455000, P. R. China
| | - Jingjing Wei
- College of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang, Henan 455000, P. R. China
| | - Wei Wei
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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12
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Wang M, Fage CD, He Y, Mi J, Yang Y, Li F, An X, Fan H, Song L, Zhu S, Tong Y. Recent Advances and Perspectives on Expanding the Chemical Diversity of Lasso Peptides. Front Bioeng Biotechnol 2021; 9:741364. [PMID: 34631682 PMCID: PMC8498205 DOI: 10.3389/fbioe.2021.741364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/13/2021] [Indexed: 12/16/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing family of natural products that exhibit a range of structures and bioactivities. Initially assembled from the twenty proteinogenic amino acids in a ribosome-dependent manner, RiPPs assume their peculiar bioactive structures through various post-translational modifications. The essential modifications representative of each subfamily of RiPP are performed on a precursor peptide by the so-called processing enzymes; however, various tailoring enzymes can also embellish the precursor peptide or processed peptide with additional functional groups. Lasso peptides are an interesting subfamily of RiPPs characterized by their unique lariat knot-like structure, wherein the C-terminal tail is inserted through a macrolactam ring fused by an isopeptide bond between the N-terminal amino group and an acidic side chain. Until recently, relatively few lasso peptides were found to be tailored with extra functional groups. Nevertheless, the development of new routes to diversify lasso peptides and thus introduce novel or enhanced biological, medicinally relevant, or catalytic properties is appealing. In this review, we highlight several strategies through which lasso peptides have been successfully modified and provide a brief overview of the latest findings on the tailoring of these peptides. We also propose future directions for lasso peptide tailoring as well as potential applications for these peptides in hybrid catalyst design.
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Affiliation(s)
- Mengjiao Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Christopher D Fage
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
| | - Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jinhui Mi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yang Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Fei Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,Clinical Laboratory Center, Taian City Central Hospital, Taian, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shaozhou Zhu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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13
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Schröder HV, Zhang Y, Link AJ. Dynamic covalent self-assembly of mechanically interlocked molecules solely made from peptides. Nat Chem 2021; 13:850-857. [PMID: 34426684 PMCID: PMC8446321 DOI: 10.1038/s41557-021-00770-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022]
Abstract
Mechanically interlocked molecules (MIMs), such as rotaxanes and catenanes, have captured the attention of chemists both from a synthetic perspective and because of their role as simple prototypes of molecular machines. Although examples exist in nature, most synthetic MIMs are made from artificial building blocks and assembled in organic solvents. Synthesis of MIMs from natural biomolecules remains highly challenging. Here we report on a synthesis strategy for interlocked molecules solely made from peptides—mechanically interlocked peptides (MIPs). Fully peptidic, cysteine-decorated building blocks were self-assembled in water to generate disulfide-bonded dynamic combinatorial libraries consisting of multiple different rotaxanes, catenanes and daisy chains as well as more exotic structures. Detailed NMR spectroscopy and mass spectrometry characterization of a [2]catenane comprised of two peptide macrocycles revealed that this structure has rich conformational dynamics reminiscent of protein folding. Thus, MIPs can serve as a bridge between fully synthetic MIMs and those found in nature.
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Affiliation(s)
- Hendrik V Schröder
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Yi Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA. .,Department of Chemistry, Princeton University, Princeton, NJ, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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14
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15
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Phan N, Shear TA, Zakharov LN, Johnson DW. An Efficient Route to Symmetrical and Unsymmetrical Disulfide, Thioether, and Hydrocarbon Cyclophanes. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ngoc‐Minh Phan
- Department of Chemistry & Biochemistry and Materials Science Institute University of Oregon 97403‐1253 Eugene Oregon USA
| | - Trevor A. Shear
- Department of Chemistry & Biochemistry and Materials Science Institute University of Oregon 97403‐1253 Eugene Oregon USA
| | - Lev N. Zakharov
- CAMCOR Center for Advanced Materials Characterization in Oregon University of Oregon 97403‐1443 Eugene OR USA
| | - Darren W. Johnson
- Department of Chemistry & Biochemistry and Materials Science Institute University of Oregon 97403‐1253 Eugene Oregon USA
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16
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Liu Y, Wu W, Hong S, Fang J, Zhang F, Liu G, Seo J, Zhang W. Lasso Proteins: Modular Design, Cellular Synthesis, and Topological Transformation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Wen‐Hao Wu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Sumin Hong
- Department of Chemistry Pohang University of Science and Technology (POSTECH) Pohang 37673 Republic of Korea
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Geng‐Xin Liu
- Center for Advanced Low-dimension Materials State Key Laboratory for Modification of Chemical Fibers and Polymer Materials College of Material Science and Engineering Donghua University Shanghai 201620 China
| | - Jongcheol Seo
- Department of Chemistry Pohang University of Science and Technology (POSTECH) Pohang 37673 Republic of Korea
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
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17
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How to harness biosynthetic gene clusters of lasso peptides. ACTA ACUST UNITED AC 2020; 47:703-714. [DOI: 10.1007/s10295-020-02292-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023]
Abstract
Abstract
Lasso peptides produced by bacteria have a very unique cyclic structure (“lasso” structure) and are resistant to protease. To date, a number of lasso peptides have been isolated from proteobacteria and actinobacteria. Many lasso peptides exhibit various biological activities, such as antibacterial activity, and are expected to have various applications. Based on study of genome mining, large numbers of biosynthetic gene cluster of lasso peptides are revealed to distribute over genomes of proteobacteria and actinobacteria. However, the biosynthetic gene clusters are cryptic in most cases. Therefore, the combination of genome mining and heterologous production is efficient method for the production of lasso peptides. To utilize lasso peptide as fine chemical, there have been several attempts to add new function to lasso peptide by genetic engineering. Currently, a more efficient lasso peptide production system is being developed to harness cryptic biosynthetic gene clusters of lasso peptide. In this review, the overview of lasso peptide study is discussed.
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18
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Fuwa H, Hemmi H, Kaweewan I, Kozaki I, Honda H, Kodani S. Heterologous production of new lasso peptide koreensin based on genome mining. J Antibiot (Tokyo) 2020; 74:42-50. [PMID: 32855516 DOI: 10.1038/s41429-020-00363-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 11/09/2022]
Abstract
Lasso peptides are a class of ribosomally biosynthesized and posttranslationally modified peptides with a knot structure as a common motif. Based on a genome search, a new biosynthetic gene cluster of lasso peptide was found in the genome of the proteobacterium Sphingomonas koreensis. Interestingly, the amino acid sequence of the precursor peptide gene includes two cell adhesion motif sequences (KGD and DGR). Heterologous production of the new lasso peptide was performed using the cryptic biosynthetic gene cluster of S. koreensis. As a result, a new lasso peptide named koreensin was produced by the gene expression system in the host strain Sphingomonas subterranea. The structure of koreensin was determined by NMR and ESI-MS analysis. The three-dimensional structure of koreensin was obtained based on an NOE experiment and the coupling constants. A variant peptide (koreensin-RGD), which had RGD instead of KGD, was produced by heterologous production with site-directed mutagenesis experiment. Koreensin and koreensin-RGD did not show cell adhesion inhibitory activity, although the molecules possessed cell adhesion motifs. The possible presence of a salt bridge between the motifs in koreensin was indicated, and it may prevent the cell adhesion motif from functioning.
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Affiliation(s)
- Hiroki Fuwa
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hikaru Hemmi
- Food Research Institute, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Issara Kaweewan
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Ikko Kozaki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Hiroyuki Honda
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan. .,Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan. .,Academic Institute, Shizuoka University, Shizuoka, Japan.
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19
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Liu Y, Wu WH, Hong S, Fang J, Zhang F, Liu GX, Seo J, Zhang WB. Lasso Proteins: Modular Design, Cellular Synthesis, and Topological Transformation. Angew Chem Int Ed Engl 2020; 59:19153-19161. [PMID: 32602613 DOI: 10.1002/anie.202006727] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/30/2020] [Indexed: 02/06/2023]
Abstract
Entangled proteins have attracted significant research interest. Herein, we report the first rationally designed lasso proteins, or protein [1]rotaxanes, by using a p53dim-entwined dimer for intramolecular entanglement and a SpyTag-SpyCatcher reaction for side-chain ring closure. The lasso structures were confirmed by proteolytic digestion, mutation, NMR spectrometry, and controlled ligation. Their dynamic properties were probed by experiments such as end-capping, proteolytic digestion, and heating/cooling. As a versatile topological intermediate, a lasso protein could be converted to a rotaxane, a heterocatenane, and a "slide-ring" network. Being entirely genetically encoded, this robust and modular lasso-protein motif is a valuable addition to the topological protein repertoire and a promising candidate for protein-based biomaterials.
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Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Sumin Hong
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Geng-Xin Liu
- Center for Advanced Low-dimension Materials, State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Jongcheol Seo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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20
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Cheung-Lee WL, Parry ME, Zong C, Cartagena AJ, Darst SA, Connell ND, Russo R, Link AJ. Discovery of Ubonodin, an Antimicrobial Lasso Peptide Active against Members of the Burkholderia cepacia Complex. Chembiochem 2020; 21:1335-1340. [PMID: 31765515 PMCID: PMC7205569 DOI: 10.1002/cbic.201900707] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Indexed: 11/09/2022]
Abstract
We report the heterologous expression, structure, and antimicrobial activity of a lasso peptide, ubonodin, encoded in the genome of Burkholderia ubonensis. The topology of ubonodin is unprecedented amongst lasso peptides, with 18 of its 28 amino acids found in the mechanically bonded loop segment. Ubonodin inhibits RNA polymerase in vitro and has potent antimicrobial activity against several pathogenic members of the Burkholderia genus, most notably B. cepacia and B. multivorans, causative agents of lung infections in cystic fibrosis patients.
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Affiliation(s)
- Wai Ling Cheung-Lee
- Department of Chemical and Biological Engineering, Princeton University, 207 Hoyt Laboratory, Princeton, NJ, 08544, USA
| | - Madison E Parry
- Department of Chemical and Biological Engineering, Princeton University, 207 Hoyt Laboratory, Princeton, NJ, 08544, USA
| | - Chuhan Zong
- Department of Chemistry, Princeton University, 207 Hoyt Laboratory, Princeton, NJ, 08544, USA
| | - Alexis Jaramillo Cartagena
- Laboratory of Molecular Biophysics and, Tri-Institutional Training Program in Chemical Biology, Rockefeller University, 1230 York Ave., New York, NY, 10065, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics and, Tri-Institutional Training Program in Chemical Biology, Rockefeller University, 1230 York Ave., New York, NY, 10065, USA
| | - Nancy D Connell
- Center for Health Security, Johns Hopkins Bloomberg School of Public Health, 621 E. Pratt St. Suite 210, Baltimore, MD, 21202, USA
| | - Riccardo Russo
- Center for Emerging Pathogens, Division of Infectious Disease, New Jersey Medical School, Rutgers Biomedical and Health Sciences University, 185 South Orange Ave., Newark, NJ, 07103, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, 207 Hoyt Laboratory, Princeton, NJ, 08544, USA
- Department of Chemistry, Princeton University, 207 Hoyt Laboratory, Princeton, NJ, 08544, USA
- Department of Molecular Biology, Princeton University, 207 Hoyt Laboratory, Princeton, NJ, 08544, USA
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21
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Zhang G, Zhang J. Topological catenation induced swelling of ring polymers revealed by molecular dynamics simulation. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Singh J, Kim DH, Kim EH, Kim H, Hadiputra R, Jung J, Chi KW. The First Quantitative Synthesis of a Closed Three-Link Chain (613) Using Coordination and Noncovalent Interactions-Driven Self-Assembly. J Am Chem Soc 2020; 142:9327-9336. [DOI: 10.1021/jacs.0c01406] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jatinder Singh
- Department of Chemistry, University of Ulsan, Ulsan 44776, Republic of Korea
- Energy Materials Laboratory, Korea Institute of Energy Research, Daejeon 34129, Republic of Korea
| | - Dong Hwan Kim
- Department of Chemistry, University of Ulsan, Ulsan 44776, Republic of Korea
| | - Eun-Hee Kim
- Center for Research Equipments, Korea Basic Science Institute, Ochang, Chungbuk 28119, Republic of Korea
| | - Hyunuk Kim
- Energy Materials Laboratory, Korea Institute of Energy Research, Daejeon 34129, Republic of Korea
| | - Rizky Hadiputra
- Department of Chemistry, University of Ulsan, Ulsan 44776, Republic of Korea
| | - Jaehoon Jung
- Department of Chemistry, University of Ulsan, Ulsan 44776, Republic of Korea
| | - Ki-Whan Chi
- Department of Chemistry, University of Ulsan, Ulsan 44776, Republic of Korea
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23
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Orlandini G, Casimiro L, Bazzoni M, Cogliati B, Credi A, Lucarini M, Silvi S, Arduini A, Secchi A. Synthesis and properties of a redox-switchable calix[6]arene-based molecular lasso. Org Chem Front 2020. [DOI: 10.1039/c9qo01379b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A self-complexing lasso-like molecule has been synthesised as the first example of a calix[6]arene-based [1]pseudorotaxane. This artificial molecular lasso can be switched between self-threaded and dethreaded structures by redox stimulation.
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Affiliation(s)
- Guido Orlandini
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università di Parma
- I-43124 Parma
- Italy
| | - Lorenzo Casimiro
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Italy
| | - Margherita Bazzoni
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università di Parma
- I-43124 Parma
- Italy
| | - Beatrice Cogliati
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università di Parma
- I-43124 Parma
- Italy
| | - Alberto Credi
- Istituto per la Sintesi Organica e la Fotoreattività
- Consiglio Nazionale delle Ricerche
- I-40129 Bologna
- Italy
- Dipartimento di Chimica Industriale “Toso Montanari”
| | - Marco Lucarini
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Italy
| | - Serena Silvi
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Italy
| | - Arturo Arduini
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università di Parma
- I-43124 Parma
- Italy
| | - Andrea Secchi
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università di Parma
- I-43124 Parma
- Italy
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24
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Hegemann JD. Factors Governing the Thermal Stability of Lasso Peptides. Chembiochem 2019; 21:7-18. [DOI: 10.1002/cbic.201900364] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Julian D. Hegemann
- Technische Universität BerlinInstitute of Chemistry Strasse des 17. Juni 124/TC2 10623 Berlin Germany
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25
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Phan NM, Choy EPKL, Zakharov LN, Johnson DW. Self-sorting in dynamic disulfide assembly: new biphenyl-bridged "nanohoops" and unsymmetrical cyclophanes. Chem Commun (Camb) 2019; 55:11840-11843. [PMID: 31517340 DOI: 10.1039/c9cc06503b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We expand on our approach combining dynamic covalent self-assembly and sulfur extrusion to synthesize new biphenyl-linked disulfide and thioether macrocycles, which are variants of the venerable phenyl-bridged paracyclophanes. We then advance this strategy further to use two different thiols in tandem to provide new, elusive unsymmetrical disulfides which can also be trapped as unsymmetrical thioether "nanohoops". This approach enables substantial amplification of two unsymmetrical trimers out of a library of at least 21 possible macrocycles of various sizes.
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Affiliation(s)
- Ngoc-Minh Phan
- Department of Chemistry & Biochemistry and Materials Science Institute, University of Oregon, Eugene, Oregon, 97403-1253, USA.
| | - Emma P K L Choy
- Department of Chemistry & Biochemistry and Materials Science Institute, University of Oregon, Eugene, Oregon, 97403-1253, USA.
| | - Lev N Zakharov
- CAMCOR - Center for Advanced Materials Characterization in Oregon, University of Oregon, Eugene, OR 97403-1443, USA
| | - Darren W Johnson
- Department of Chemistry & Biochemistry and Materials Science Institute, University of Oregon, Eugene, Oregon, 97403-1253, USA.
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26
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Sumida T, Dubiley S, Wilcox B, Severinov K, Tagami S. Structural Basis of Leader Peptide Recognition in Lasso Peptide Biosynthesis Pathway. ACS Chem Biol 2019; 14:1619-1627. [PMID: 31188556 DOI: 10.1021/acschembio.9b00348] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) with a unique 3D-interlocked structure, in which an N-terminal macrolactam ring is threaded by a linear C-terminal part. The unique structure of lasso peptides is introduced into ribosomally translated precursor peptides by lasso peptide synthetase encompassing proteins B and C or B1, B2, and C when the B enzyme is split into two distinct proteins. The B1 protein recognizes the leader sequence of the precursor peptide, and then the B2 protein cleaves it. The C protein catalyzes the formation of the macrolactam ring. However, the detailed mechanism of lasso peptide maturation has remained elusive, due to the lack of structural information about the responsible proteins. Here we report the crystal structure of the B1 protein from the thermophilic actinobacteria, Thermobifida fusca (TfuB1), complexed with the leader peptide (TfuA-Leader), which revealed the detailed mechanism of leader peptide recognition. The structure of TfuB1 consists of an N-terminal β-sheet and three C-terminal helices. The leader peptide is docked on one edge of the N-terminal β-sheet of TfuB1, as an additional β strand. Three conserved amino acid residues of the leader peptide (TfuA Tyr-17, Pro-14, and Leu-12) fit well on the hydrophobic cleft between the β-sheet and adjacent helices. Biochemical analysis demonstrated that these conserved residues are essential for affinity between TfuB1 and the TfuA-Leader. Furthermore, we found that TfuB1 and the leader peptide jointly form a hydrophobic patch on the β-sheet, which includes the highly conserved TfuA Phe-6 and TfuB1 Tyr33. Homology modeling and mutational analysis of the B1 protein from a firmicute, Bacillus pseudomycoides (PsmB1), revealed that the hydrophobic patch is conserved in a wide range of species and involved in the cleavage activity of the B2 protein, indicating it forms the interaction surface for the B2 protein or the core part of the precursor peptide.
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Affiliation(s)
- Tomomi Sumida
- Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Svetlana Dubiley
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
- Institute of Gene Biology, Russian Academy of Science, Moscow 119334, Russia
| | - Brendan Wilcox
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
| | - Konstantin Severinov
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia
- Institute of Gene Biology, Russian Academy of Science, Moscow 119334, Russia
- Waksman Institute for Microbiology, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
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Hegemann JD, Bobeica SC, Walker MC, Bothwell IR, van der Donk WA. Assessing the Flexibility of the Prochlorosin 2.8 Scaffold for Bioengineering Applications. ACS Synth Biol 2019; 8:1204-1214. [PMID: 31042373 PMCID: PMC6525029 DOI: 10.1021/acssynbio.9b00080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclization is a common strategy to confer proteolytic resistance to peptide scaffolds. Thus, cyclic peptides have been the focus of extensive bioengineering efforts. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a superfamily of peptidic natural products that often contain macrocycles. In the RiPP family of lanthipeptides, macrocyclization is accomplished through formation of thioether cross-links between cysteines and dehydrated serines/threonines. The recent production of lanthipeptide libraries and development of methods to display lanthipeptides on yeast or phage highlights their potential for bioengineering and synthetic biology. In this regard, the prochlorosins are especially promising as the corresponding class II lanthipeptide synthetase ProcM matures numerous precursor peptides with diverse core peptide sequences. To facilitate future bioengineering projects, one of its native substrates, ProcA2.8, was subjected in this study to in-depth mutational analysis to test the limitations of ProcM-mediated cyclization. Alanine scan mutagenesis was performed on all residues within the two rings, and multiple prolines were introduced at various positions. Moreover, mutation, deletion, and insertion of residues in the region linking the two lanthionine rings was tested. Additional residues were also introduced or deleted from either ring, and inversion of ring forming residues was attempted to generate diastereomers. The findings were used for epitope grafting of the RGD integrin binding epitope within prochlorosin 2.8, resulting in a low nanomolar affinity binder of the αvβ3 integrin that was more stable toward proteolysis and displayed higher affinity than the linear counterpart.
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Affiliation(s)
- Julian D. Hegemann
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Silvia C. Bobeica
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Mark C. Walker
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Ian R. Bothwell
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois 61801, United States
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28
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Dabrowski-Tumanski P, Gren B, Sulkowska JI. Statistical Properties of Lasso-Shape Polymers and Their Implications for Complex Lasso Proteins Function. Polymers (Basel) 2019; 11:E707. [PMID: 30999683 PMCID: PMC6523798 DOI: 10.3390/polym11040707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/19/2022] Open
Abstract
The shape and properties of closed loops depend on various topological factors. One of them is loop-threading, which is present in complex lasso proteins. In this work, we analyze the probability of loop-threading by the tail and its influence on the shape of the loop measured by the radius of gyration, distention, asphericity, and prolateness. In particular, we show that the probability of a trivial lasso for phantom polymer is non-zero even for an infinite structure, as well as that the threading flattens the loop by restricting its motion in one dimension. These results are further used to show that there are fewer non-trivial protein lassos than expected and select potentially functional complex lasso proteins.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
| | - Bartosz Gren
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland.
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
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29
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Li H, Zhang S, Yu X, Feng X, Yamamoto Y, Bao M. Rhodium(iii)-catalyzed aromatic C–H cyanation with dimethylmalononitrile as a cyanating agent. Chem Commun (Camb) 2019; 55:1209-1212. [DOI: 10.1039/c8cc08930b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Safe, bench-stable, and commercially available DMMN was used as a cyanating reagent in Rh(iii)-catalyzed aromatic C–H bond direct cyanation in the presence of copper oxide as a promotor.
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Affiliation(s)
- He Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology
- Dalian 116023
- China
| | - Sheng Zhang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology
- Dalian 116023
- China
| | - Xiaoqiang Yu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology
- Dalian 116023
- China
| | - Xiujuan Feng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology
- Dalian 116023
- China
| | - Yoshinori Yamamoto
- State Key Laboratory of Fine Chemicals, Dalian University of Technology
- Dalian 116023
- China
- WPI-Advanced Institute for Materials Research, Tohoku University
- Sendai 980-8577
| | - Ming Bao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology
- Dalian 116023
- China
- School of Petroleum and Chemical Engineering, Dalian University of Technology
- Panjin 124221
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30
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Singh J, Kim DH, Kim EH, Singh N, Kim H, Hadiputra R, Jung J, Chi KW. Selective and quantitative synthesis of a linear [3]catenane by two component coordination-driven self-assembly. Chem Commun (Camb) 2019; 55:6866-6869. [DOI: 10.1039/c9cc03336j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Coordination-driven self-assembly and synergistic non-covalent intercycler interactions (π–π, CH–π and CH–N) for the selective formation of a linear [3]catenane.
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Affiliation(s)
- Jatinder Singh
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
| | - Dong Hwan Kim
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
| | - Eun-Hee Kim
- Protein Structure Group
- Korea Basic Science Institute
- Ochang
- Chungbuk 28119
- Republic of Korea
| | - Nem Singh
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
| | - Hyunuk Kim
- Energy Materials Laboratory
- Korea Institute of Energy Research
- Daejeon 34129
- Republic of Korea
| | - Rizky Hadiputra
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
| | - Jaehoon Jung
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
| | - Ki-Whan Chi
- Department of Chemistry
- University of Ulsan
- Ulsan 44610
- Republic of Korea
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31
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Wang XW, Zhang WB. Chemical Topology and Complexity of Protein Architectures. Trends Biochem Sci 2018; 43:806-817. [DOI: 10.1016/j.tibs.2018.07.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/01/2018] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
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32
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Wang J, Du R, Zhang X. Thermoresponsive Polyrotaxane Aerogels: Converting Molecular Necklaces into Tough Porous Monoliths. ACS APPLIED MATERIALS & INTERFACES 2018; 10:1468-1473. [PMID: 29299915 DOI: 10.1021/acsami.7b18741] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Polyrotaxanes (PRs) are supramolecular systems that combine with several cyclic molecules threaded on a linear molecule, and have been widely applied in molecular abacus, stimuli-responsive systems, self-healing materials, etc. The fabrication of macroscopic porous PR monoliths, which is expected to impart more functions, has not been realized yet. PR aerogels featuring with high specific surface area (232 m2/g), high strength (74.7 MPa), and temperature-responsiveness have been synthesized in this work by introducing poly(N-isopropylacrylamide) to the molecular necklaces followed by chemical cross-linking with a rigid cross-linker and supercritical fluid drying in sequence, which might open a new door toward smart macroscopic porous materials.
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Affiliation(s)
- Jin Wang
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123, P. R. China
| | - Ran Du
- Physical Chemistry, Technische Universität Dresden , Bergstrasse 66b, Dresden 01062, Germany
| | - Xuetong Zhang
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123, P. R. China
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33
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Wang J, Ferguson AL. A Study of the Morphology, Dynamics, and Folding Pathways of Ring Polymers with Supramolecular Topological Constraints Using Molecular Simulation and Nonlinear Manifold Learning. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b01684] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jiang Wang
- Department
of Physics, ‡Department of Materials Science and Engineering, and §Department of
Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Department
of Physics, ‡Department of Materials Science and Engineering, and §Department of
Chemical and Biomolecular Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
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34
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Martin-Gómez H, Tulla-Puche J. Lasso peptides: chemical approaches and structural elucidation. Org Biomol Chem 2018; 16:5065-5080. [DOI: 10.1039/c8ob01304g] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The diverse functionality and the extraordinary stability of lasso peptides make these molecules attractive scaffolds for drug discovery. The ability to generate lasso peptides chemically remains a challenging endeavor.
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Affiliation(s)
| | - Judit Tulla-Puche
- Department of Inorganic and Organic Chemistry – Organic Chemistry Section
- University of Barcelona
- Barcelona
- Spain
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35
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36
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Zong C, Wu MJ, Qin JZ, Link AJ. Lasso Peptide Benenodin-1 Is a Thermally Actuated [1]Rotaxane Switch. J Am Chem Soc 2017; 139:10403-10409. [PMID: 28696674 DOI: 10.1021/jacs.7b04830] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mechanically interlocked molecules that change their conformation in response to stimuli have been developed by synthetic chemists as building blocks for molecular machines. Here we describe a natural product, the lasso peptide benenodin-1, which exhibits conformational switching between two distinct threaded conformers upon actuation by heat. We have determined the structures of both conformers and have characterized the kinetics and energetics of the conformational switch. Single amino acid substitutions to benenodin-1 generate peptides that are biased to a single conformer, showing that the switching behavior is potentially an evolvable trait in these peptides. Lasso peptides such as benenodin-1 can be recognized and cleaved by enzymes called lasso peptide isopeptidases. We show that only the native conformer of benenodin-1 is cleaved by its cognate isopeptidase. Thus, thermally induced conformational switching of benenodin-1 may also be relevant to the biological function of these molecules.
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Affiliation(s)
- Chuhan Zong
- Department of Chemistry, ‡Department of Molecular Biology, and §Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
| | - Michelle J Wu
- Department of Chemistry, ‡Department of Molecular Biology, and §Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
| | - Jason Z Qin
- Department of Chemistry, ‡Department of Molecular Biology, and §Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
| | - A James Link
- Department of Chemistry, ‡Department of Molecular Biology, and §Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
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37
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Synthesis of spiro quasi[1]catenanes and quasi[1]rotaxanes via a templated backfolding strategy. Nat Commun 2017; 8:15392. [PMID: 28541349 PMCID: PMC5458513 DOI: 10.1038/ncomms15392] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/27/2017] [Indexed: 12/15/2022] Open
Abstract
Due to their well-defined three-dimensional geometry, spiro compounds are widely utilized in drug research. From the central tetrahedral carbon atom, besides the regular structure, an inverted spiro connectivity may be envisioned. Here we disclose the synthesis of this molecule class that we have coined quasi[1]catenanes. Next to their fascinating and aesthetic shape, the higher compactness as compared to regular spiro bicycles is noteworthy. To enable synthetic access to compact entangled multimacrocyclic molecules, we have developed a new strategy. The key element is a template, which is covalently connected to the linear precursors, and spatially directs the sterically congested backfolding macrocyclizations that are required to give quasi[1]catenanes. Similarly, quasi[1]rotaxanes are made. Spiro compounds contain two or more rings linked together through one common atom. Here the authors provide a method to backfold both rings, producing spiro quasi[1]catenanes, via a strategy of temporarily linking the linear intermediates with covalent bonds.
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