1
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Zeng P, Wang H, Zhang P, Leung SSY. Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies. Biotechnol Adv 2024; 73:108371. [PMID: 38704105 DOI: 10.1016/j.biotechadv.2024.108371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Honglan Wang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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2
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Schiefelbein K, Lang J, Schuster M, Grigglestone CE, Striga R, Bigler L, Schuman MC, Zerbe O, Li Y, Hartrampf N. Merging Flow Synthesis and Enzymatic Maturation to Expand the Chemical Space of Lasso Peptides. J Am Chem Soc 2024; 146:17261-17269. [PMID: 38759637 PMCID: PMC11212047 DOI: 10.1021/jacs.4c03898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
Many peptidic natural products, such as lasso peptides, cyclic peptides, and cyclotides, are conformationally constrained and show biological stability, making them attractive scaffolds for drug development. Although many peptides can be synthesized and modified through chemical methods, knot-like lasso peptides such as microcin J25 (MccJ25) and their analogues remain elusive. As the chemical space of MccJ25 analogues accessible through purely biological methods is also limited, we proposed a hybrid approach: flow-based chemical synthesis of non-natural precursor peptides, followed by in vitro transformation with recombinant maturation enzymes, to yield a more diverse array of lasso peptides. Herein, we established the rapid, flow-based synthesis of chemically modified MccJ25 precursor peptides (57 amino acids). Heterologous expression of enzymes McjB and McjC was extensively optimized to improve yields and facilitate the synthesis of multiple analogues of MccJ25, including the incorporation of non-canonical tyrosine and histidine derivatives into the lasso scaffold. Finally, using our chemoenzymatic strategy, we produced a biologically active analogue containing three d-amino acids in the loop region and incorporated backbone N-methylations. Our method provides rapid access to chemically modified lasso peptides that could be used to investigate structure-activity relationships, epitope grafting, and the improvement of therapeutic properties.
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Affiliation(s)
- Kevin Schiefelbein
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jakob Lang
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department
of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthias Schuster
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Claire E. Grigglestone
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Robin Striga
- Laboratory
Molecules of Communication and Adaptation of Microorganisms (MCAM).
UMR7245, CNRS-Muséum National d’Histoire
Naturelle (MNHN), Alliance Sorbonne Université, 57 rue Cuvier, 75005 Paris, France
| | - Laurent Bigler
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Meredith C. Schuman
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department
of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Oliver Zerbe
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Yanyan Li
- Laboratory
Molecules of Communication and Adaptation of Microorganisms (MCAM).
UMR7245, CNRS-Muséum National d’Histoire
Naturelle (MNHN), Alliance Sorbonne Université, 57 rue Cuvier, 75005 Paris, France
| | - Nina Hartrampf
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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3
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Goles M, Daza A, Cabas-Mora G, Sarmiento-Varón L, Sepúlveda-Yañez J, Anvari-Kazemabad H, Davari MD, Uribe-Paredes R, Olivera-Nappa Á, Navarrete MA, Medina-Ortiz D. Peptide-based drug discovery through artificial intelligence: towards an autonomous design of therapeutic peptides. Brief Bioinform 2024; 25:bbae275. [PMID: 38856172 PMCID: PMC11163380 DOI: 10.1093/bib/bbae275] [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: 02/08/2024] [Revised: 04/23/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024] Open
Abstract
With their diverse biological activities, peptides are promising candidates for therapeutic applications, showing antimicrobial, antitumour and hormonal signalling capabilities. Despite their advantages, therapeutic peptides face challenges such as short half-life, limited oral bioavailability and susceptibility to plasma degradation. The rise of computational tools and artificial intelligence (AI) in peptide research has spurred the development of advanced methodologies and databases that are pivotal in the exploration of these complex macromolecules. This perspective delves into integrating AI in peptide development, encompassing classifier methods, predictive systems and the avant-garde design facilitated by deep-generative models like generative adversarial networks and variational autoencoders. There are still challenges, such as the need for processing optimization and careful validation of predictive models. This work outlines traditional strategies for machine learning model construction and training techniques and proposes a comprehensive AI-assisted peptide design and validation pipeline. The evolving landscape of peptide design using AI is emphasized, showcasing the practicality of these methods in expediting the development and discovery of novel peptides within the context of peptide-based drug discovery.
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Affiliation(s)
- Montserrat Goles
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
- Departamento de Ingeniería Química, Biotecnología y Materiales, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Anamaría Daza
- Centre for Biotechnology and Bioengineering, CeBiB, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Gabriel Cabas-Mora
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Lindybeth Sarmiento-Varón
- Centro Asistencial de Docencia e Investigación, CADI, Universidad de Magallanes, Av. Los Flamencos 01364, 6210005, Punta Arenas, Chile
| | - Julieta Sepúlveda-Yañez
- Facultad de Ciencias de la Salud, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Hoda Anvari-Kazemabad
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Roberto Uribe-Paredes
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, CeBiB, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Marcelo A Navarrete
- Centro Asistencial de Docencia e Investigación, CADI, Universidad de Magallanes, Av. Los Flamencos 01364, 6210005, Punta Arenas, Chile
- Escuela de Medicina, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - David Medina-Ortiz
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
- Centre for Biotechnology and Bioengineering, CeBiB, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
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4
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da Hora GCA, Oh M, Nguyen JDM, Swanson JMJ. One Descriptor to Fold Them All: Harnessing Intuition and Machine Learning to Identify Transferable Lasso Peptide Reaction Coordinates. J Phys Chem B 2024; 128:4063-4075. [PMID: 38568862 DOI: 10.1021/acs.jpcb.3c08492] [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: 04/05/2024]
Abstract
Identifying optimal reaction coordinates for complex conformational changes and protein folding remains an outstanding challenge. This study combines collective variable (CV) discovery based on chemical intuition and machine learning with enhanced sampling to converge the folding free energy landscape of lasso peptides, a unique class of natural products with knot-like tertiary structures. This knotted scaffold imparts remarkable stability, making lasso peptides resistant to proteolytic degradation, thermal denaturation, and extreme pH conditions. Although their direct synthesis would enable therapeutic design, it has not yet been possible due to the improbable occurrence of spontaneous lasso folding. Thus, simulations characterizing the folding propensity are needed to identify strategies for increasing access to the lasso architecture by stabilizing the pre-lasso ensemble before isopeptide bond formation. Herein, harmonic linear discriminant analysis (HLDA) is combined with metadynamics-enhanced sampling to discover CVs capable of distinguishing the pre-lasso fold and converging the folding propensity. Intuitive CVs are compared to iterative rounds of HLDA to identify CVs that not only accomplish these goals for one lasso peptide but also seem to be transferable to others, establishing a protocol for the identification of folding reaction coordinates for lasso peptides.
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Affiliation(s)
- Gabriel C A da Hora
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Myongin Oh
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - John D M Nguyen
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jessica M J Swanson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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5
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da Hora GCA, Oh M, Mifflin MC, Digal L, Roberts AG, Swanson JMJ. Lasso Peptides: Exploring the Folding Landscape of Nature's Smallest Interlocked Motifs. J Am Chem Soc 2024; 146:4444-4454. [PMID: 38166378 DOI: 10.1021/jacs.3c10126] [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: 01/04/2024]
Abstract
Lasso peptides make up a class of natural products characterized by a threaded structure. Given their small size and stability, chemical synthesis would offer tremendous potential for the development of novel therapeutics. However, the accessibility of the pre-folded lasso architecture has limited this advance. To better understand the folding process de novo, simulations are used herein to characterize the folding propensity of microcin J25 (MccJ25), a lasso peptide known for its antimicrobial properties. New algorithms are developed to unambiguously distinguish threaded from nonthreaded precursors and determine handedness, a key feature in natural lasso peptides. We find that MccJ25 indeed forms right-handed pre-lassos, in contrast to past predictions but consistent with all natural lasso peptides. Additionally, the native pre-lasso structure is shown to be metastable prior to ring formation but to readily transition to entropically favored unfolded and nonthreaded structures, suggesting that de novo lasso folding is rare. However, by altering the ring forming residues and appending thiol and thioester functionalities, we are able to increase the stability of pre-lasso conformations. Furthermore, conditions leading to protonation of a histidine imidazole side chain further stabilize the modified pre-lasso ensemble. This work highlights the use of computational methods to characterize lasso folding and demonstrates that de novo access to lasso structures can be facilitated by optimizing sequence, unnatural modifications, and reaction conditions like pH.
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Affiliation(s)
- Gabriel C A da Hora
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Myongin Oh
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Marcus C Mifflin
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Lori Digal
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Andrew G Roberts
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jessica M J Swanson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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6
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Gauthier M, Fournel-Marotte K, Clavel C, Waelès P, Laurent P, Coutrot F. An Interlocked Figure-of-Eight Molecular Shuttle. Angew Chem Int Ed Engl 2023; 62:e202310643. [PMID: 37594476 DOI: 10.1002/anie.202310643] [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: 07/25/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/19/2023]
Abstract
Here is reported the synthesis and characterization of an interlocked figure-of-eight rotaxane molecular shuttle from a dibenzo-24-crown-8 (DB24C8) derivative. This latter bears two molecular chains, whose extremities are able to react together by click chemistry. One of the two substituting chain holds an ammonium function aimed at driving the self-entanglement through the complexation of the DB24C8 moiety. In the targeted figure-of-eight rotaxane, shuttling of the DB24C8 along the threaded axle from the best ammonium station to the weaker binding site triazolium was performed through deprotonation or deprotonation-then-carbamoylation of the ammonium. This way, two discrete co-conformational states were obtained, in which the folding and size of the two loops could be changed.
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Affiliation(s)
- Maxime Gauthier
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Karine Fournel-Marotte
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Caroline Clavel
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Philip Waelès
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Philippe Laurent
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Frédéric Coutrot
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
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7
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Miranda KJ, Jaber S, Atoum D, Arjunan S, Ebel R, Jaspars M, Edrada-Ebel R. Pseudomonassin, a New Bioactive Ribosomally Synthesised and Post-Translationally Modified Peptide from Pseudomonas sp. SST3. Microorganisms 2023; 11:2563. [PMID: 37894221 PMCID: PMC10609385 DOI: 10.3390/microorganisms11102563] [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: 09/21/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Genome mining and metabolomics have become valuable tools in natural products research to evaluate and identify potential new chemistry from bacteria. In the search for new compounds from the deep-sea organism, Pseudomonas sp. SST3, from the South Shetland Trough, Antarctica, a co-cultivation with a second deep-sea Pseudomonas zhaodongensis SST2, was undertaken to isolate pseudomonassin, a ribosomally synthesised and post-translationally modified peptide (RiPP) that belongs to a class of RiPP called lasso peptides. Pseudomonassin was identified using a genome-mining approach and isolated by means of mass spectrometric guided isolation. Extensive metabolomics analysis of the co-cultivation of Pseudomonas sp. SST3 and P. zhaodongensis SST2, Pseudomonas sp. SST3 and Escherichia coli, and P. zhaodongensis SST2 and E. coli were performed using principal component analysis (PCA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA), which revealed potential new metabolites in the outlier regions of the co-cultivation, with other metabolites identified previously from other species of Pseudomonas. The sequence of pseudomonassin was completely deduced using high collision dissociation tandem mass spectrometry (HCD-MS/MS). Preliminary studies on its activity against the pathogenic P. aeruginosa and its biofilm formation have been assessed and produced a minimum inhibitory concentration (MIC) of 63 μg/mL and 28 μg/mL, respectively.
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Affiliation(s)
- Kevin Jace Miranda
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK; (S.A.); (R.E.); (M.J.)
- College of Pharmacy and Graduate School, Adamson University, 900 San Marcelino Street, Ermita, Manila 1000, Philippines
| | - Saif Jaber
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, John Arbuthnott Building, 161 Cathedral Street, Glasgow G4 0RE, UK; (S.J.); (R.E.-E.)
| | - Dana Atoum
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa 13133, Jordan;
| | - Subha Arjunan
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK; (S.A.); (R.E.); (M.J.)
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK; (S.A.); (R.E.); (M.J.)
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK; (S.A.); (R.E.); (M.J.)
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, John Arbuthnott Building, 161 Cathedral Street, Glasgow G4 0RE, UK; (S.J.); (R.E.-E.)
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8
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Duan Y, Niu W, Pang L, Mu DS, Du ZJ, Zhang Y, Bian X, Zhong G. Leader peptide removal in lasso peptide biosynthesis based on penultimate isoleucine residue. Front Microbiol 2023; 14:1181125. [PMID: 37497541 PMCID: PMC10368454 DOI: 10.3389/fmicb.2023.1181125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
Lasso peptides are ribosomally synthesized peptides that undergo post-translational modifications including leader peptide removal by B (or the segregated B1 and B2) proteins and core peptide macrolactamization by C proteins to form a unique lariat topology. A conserved threonine residue at the penultimate position of leader peptide is hitherto found in lasso peptide precursors and shown to be a critical recognition element for effective enzymatic processing. We identified a lasso peptide biosynthetic gene cluster (bsf) from Bradymonas sediminis FA350, a Gram-negative and facultatively prey-dependent bacterium that belongs to a novel bacterial order Bradymonadales in the class Deltaproteobacteria. The kinase BsfK specifically catalyzes the phosphorylation of the precursor peptide BsfA on the Ser3 residue. BsfB1 performs dual functions to accelerate the post-translational phosphorylation and assist BsfB2 in leader peptide removal. Most importantly, the penultimate residue of leader peptide is an isoleucine rather than the conserved threonine and this isoleucine has a marked impact on the phosphorylation of Ser3 as well as leader peptide removal, implying that BsfB1 and BsfB2 exhibit a new substrate selectivity for leader peptide binding and excision. This is the first experimentally validated penultimate isoleucine residue in a lasso peptide precursor to our knowledge. In silico analysis reveals that the leader peptide Ile/Val(-2) residue is rare but not uncommon in phosphorylated lasso peptides, as this residue is also discovered in Acidobacteriaceae and Sphingomonadales in addition to Bradymonadales.
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Affiliation(s)
- Yuwei Duan
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Weijing Niu
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Linlin Pang
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Da-Shuai Mu
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Marine College, Shandong University, Weihai, China
| | - Zong-Jun Du
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Marine College, Shandong University, Weihai, China
| | - Youming Zhang
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology and Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoying Bian
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guannan Zhong
- Helmholtz International Laboratory for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Suzhou Research Institute of Shandong University, Suzhou, China
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9
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Saura‐Sanmartin A, Schalley CA. The Mobility of Homomeric Lasso‐ and Daisy Chain‐Like Rotaxanes in Solution and in the Gas Phase as a means to Study Structure and Switching Behaviour. Isr J Chem 2023. [DOI: 10.1002/ijch.202300022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Adrian Saura‐Sanmartin
- Departamento de Química Orgánica Facultad de Química Universidad de Murcia Calle Campus Universitario, 5 30100 Murcia Spain
- Institut für Chemie und Biochemie Freie Universität Berlin Arnimallee 20 14195 Berlin Germany
| | - Christoph A. Schalley
- Institut für Chemie und Biochemie Freie Universität Berlin Arnimallee 20 14195 Berlin Germany
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10
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Zhong G, Wang ZJ, Yan F, Zhang Y, Huo L. Recent Advances in Discovery, Bioengineering, and Bioactivity-Evaluation of Ribosomally Synthesized and Post-translationally Modified Peptides. ACS BIO & MED CHEM AU 2023; 3:1-31. [PMID: 37101606 PMCID: PMC10125368 DOI: 10.1021/acsbiomedchemau.2c00062] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 04/28/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are of increasing interest in natural products as well as drug discovery. This empowers not only the unique chemical structures and topologies in natural products but also the excellent bioactivities such as antibacteria, antifungi, antiviruses, and so on. Advances in genomics, bioinformatics, and chemical analytics have promoted the exponential increase of RiPPs as well as the evaluation of biological activities thereof. Furthermore, benefiting from their relatively simple and conserved biosynthetic logic, RiPPs are prone to be engineered to obtain diverse analogues that exhibit distinct physiological activities and are difficult to synthesize. This Review aims to systematically address the variety of biological activities and/or the mode of mechanisms of novel RiPPs discovered in the past decade, albeit the characteristics of selective structures and biosynthetic mechanisms are briefly covered as well. Almost one-half of the cases are involved in anti-Gram-positive bacteria. Meanwhile, an increasing number of RiPPs related to anti-Gram-negative bacteria, antitumor, antivirus, etc., are also discussed in detail. Last but not least, we sum up some disciplines of the RiPPs' biological activities to guide genome mining as well as drug discovery and optimization in the future.
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Affiliation(s)
- Guannan Zhong
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
| | - Zong-Jie Wang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Fu Yan
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- CAS
Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liujie Huo
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
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11
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Zhu H, Tian F, Sun L, Zhu Y, Qiu Q, Dai L. Computational Design of Extraordinarily Stable Peptide Structures through Side-Chain-Locked Knots. J Phys Chem Lett 2022; 13:7741-7748. [PMID: 35969173 DOI: 10.1021/acs.jpclett.2c02385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Extraordinarily stable protein and peptide structures are critically demanded in many applications. Typical approaches to enhance protein and peptide stability are strengthening certain interactions. Here, we develop a very different approach: stabilizing peptide structures through side-chain-locked knots. More specifically, a peptide core consists of a knot, which is prevented from unknotting and unfolding by large side chains of amino acids at knot boundaries. These side chains impose free energy barriers for unknotting. The free energy barriers are quantified using all-atom and coarse-grained simulations. The barriers become infinitely high for large side chains and tight knot cores, resulting in stable peptide structures, which never unfold unless one chemical bond is broken. The extraordinary stability is essentially kinetic stability. Our new approach lifts the thermodynamic restriction in designing peptide structures, provides extra freedom in selecting sequence and structural motifs that are thermodynamically unstable, and should expand the functionality of peptides. This work also provides a bottom-up understanding of how knotting enhances protein stability.
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Affiliation(s)
- Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Yongjian Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Qiyuan Qiu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
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12
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Vilo C, Dong Q, Galetovic A, Gómez-Silva B. Metagenome-Assembled Genome of Cyanocohniella sp. LLY from the Cyanosphere of Llayta, an Edible Andean Cyanobacterial Macrocolony. Microorganisms 2022; 10:1517. [PMID: 35893575 PMCID: PMC9332814 DOI: 10.3390/microorganisms10081517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
Cyanobacterial macrocolonies known as Llayta are found in Andean wetlands and have been consumed since pre-Columbian times in South America. Macrocolonies of filamentous cyanobacteria are niches for colonization by other microorganisms. However, the microbiome of edible Llayta has not been explored. Based on a culture-independent approach, we report the presence, identification, and metagenomic genome reconstruction of Cyanocohniella sp. LLY associated to Llayta trichomes. The assembled genome of strain LLY is now available for further inquiries and may be instrumental for taxonomic advances concerning this genus. All known members of the Cyanocohniella genus have been isolated from salty European habitats. A biogeographic gap for the Cyanocohniella genus is partially filled by the existence of strain LLY in Andes Mountains wetlands in South America as a new habitat. This is the first genome available for members of this genus. Genes involved in primary and secondary metabolism are described, providing new insights regarding the putative metabolic capabilities of Cyanocohniella sp. LLY.
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Affiliation(s)
- Claudia Vilo
- Laboratory of Biochemistry, Biomedical Department, Health Sciences Faculty and Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta 1270300, Chile; (C.V.); (A.G.)
| | - Qunfeng Dong
- Center for Biomedical Informatics, Department of Medicine, Stritch School of Medicine, Loyola University of Chicago, Chicago, IL 60660, USA;
| | - Alexandra Galetovic
- Laboratory of Biochemistry, Biomedical Department, Health Sciences Faculty and Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta 1270300, Chile; (C.V.); (A.G.)
| | - Benito Gómez-Silva
- Laboratory of Biochemistry, Biomedical Department, Health Sciences Faculty and Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta 1270300, Chile; (C.V.); (A.G.)
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13
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Unusual Post-Translational Modifications in the Biosynthesis of Lasso Peptides. Int J Mol Sci 2022; 23:ijms23137231. [PMID: 35806232 PMCID: PMC9266682 DOI: 10.3390/ijms23137231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022] Open
Abstract
Lasso peptides are a subclass of ribosomally synthesized and post-translationally modified peptides (RiPPs) and feature the threaded, lariat knot-like topology. The basic post-translational modifications (PTMs) of lasso peptide contain two steps, including the leader peptide removal of the ribosome-derived linear precursor peptide by an ATP-dependent cysteine protease, and the macrolactam cyclization by an ATP-dependent macrolactam synthetase. Recently, advanced bioinformatic tools combined with genome mining have paved the way to uncover a rapidly growing number of lasso peptides as well as a series of PTMs other than the general class-defining processes. Despite abundant reviews focusing on lasso peptide discoveries, structures, properties, and physiological functionalities, few summaries concerned their unique PTMs. In this review, we summarized all the unique PTMs of lasso peptides uncovered to date, shedding light on the related investigations in the future.
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14
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Schröder HV, Stadlmeier M, Wühr M, Link AJ. The Shuttling Cascade in Lasso Peptide Benenodin-1 is Controlled by Non-Covalent Interactions. Chemistry 2022; 28:e202103615. [PMID: 34797593 PMCID: PMC8792204 DOI: 10.1002/chem.202103615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Indexed: 01/26/2023]
Abstract
The lasso peptide benenodin-1, a naturally occurring and bacterially produced [1]rotaxane, undergoes a reversible zip tie-like motion under heat activation, in which a peptidic wheel stepwise translates along a molecular thread in a cascade of "tail/loop pulling" equilibria. Conformational and structural analyses of four translational isomers, in solution and in the gas phase, reveal that the equilibrium distribution is controlled by mechanical and non-covalent forces within the lasso peptide. Furthermore, each dynamic pulling step is accompanied by a major restructuring of the intramolecular hydrogen bonding network between wheel and thread, which affects the peptide's physico-chemical properties.
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Affiliation(s)
- Hendrik V. Schröder
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Michael Stadlmeier
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Martin Wühr
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544,Department of Chemistry and Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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15
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Saura-Sanmartin A, Pastor A, Martinez-Cuezva A, Berna J. Maximizing the [ c2]daisy chain to lasso ratio through competitive self-templating clipping reactions. Chem Commun (Camb) 2021; 58:290-293. [PMID: 34881747 DOI: 10.1039/d1cc05942d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Self-templating two-component coupling reactions allowed the isolation of two threaded products with different molecular sizes: a lasso-type [1]rotaxane and a [c2]daisy chain rotaxane. Their distribution in the final reaction mixture varies as a factor of the concentration of the reactants. Through this methodology we obtained a large 84-membered cyclic multistation [2]rotaxane.
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Affiliation(s)
- Adrian Saura-Sanmartin
- Departamento de Química Orgánica, Facultad de Química, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, E-30100, Murcia, Spain.
| | - Aurelia Pastor
- Departamento de Química Orgánica, Facultad de Química, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, E-30100, Murcia, Spain.
| | - Alberto Martinez-Cuezva
- Departamento de Química Orgánica, Facultad de Química, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, E-30100, Murcia, Spain.
| | - Jose Berna
- Departamento de Química Orgánica, Facultad de Química, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, E-30100, Murcia, Spain.
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16
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Pilon S, Jørgensen SI, van Maarseveen JH. Covalent [2]Catenane and [2]Rotaxane Synthesis via a δ-Amino Acid Template. ACS ORGANIC & INORGANIC AU 2021; 1:37-42. [PMID: 34870280 PMCID: PMC8640993 DOI: 10.1021/acsorginorgau.1c00017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 11/29/2022]
Abstract
![]()
Despite the advances
in the synthesis of mechanically interlocked
molecules, a generally applicable approach to interlocked natural
products, such as lasso peptides, is yet to be formulated. While amino
acid sequences have been introduced into several rotaxanes, the key
structural components have always been dictated by the method used
for supramolecular preorganization. In this work, we report the use
of an ester-functionalized, aromatic δ-amino acid as the central
covalent templating unit in the synthesis of both a [2]catenane and
a [2]rotaxane from the same multimacrocyclic intermediate. This represents
a key step toward future synthetic peptide-based interlocked products.
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Affiliation(s)
- Simone Pilon
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Steen Ingemann Jørgensen
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Jan H. van Maarseveen
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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17
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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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18
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Gauthier M, Waelès P, Coutrot F. Post-Synthetic Macrocyclization of Rotaxane Building Blocks. Chempluschem 2021; 87:e202100458. [PMID: 34811956 DOI: 10.1002/cplu.202100458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/11/2021] [Indexed: 11/06/2022]
Abstract
Although not often encountered, cyclic interlocked molecules are appealing molecular targets because of their restrained tridimensional structure which is related to both the cyclic and interlocked shapes. Interlocked molecules such as rotaxane building blocks may be good candidates for post-synthetic intramolecular cyclization if the preservation of the mechanical bond ensures the interlocked architecture throughout the reaction. This is obviously the case if the modification does not involve the cleavage of either the macrocycle's main chain or the encircled part of the axle. However, among the post-synthetic reactions, the chemical linkage between two reactive sites belonging to embedded elements of rotaxanes still consists of an underexploited route to interlocked cyclic molecules. This Review lists the rare examples of macrocyclization through chemical connection between reactive sites belonging to a surrounding macrocycle and/or an encircled axle of interlocked rotaxanes.
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Affiliation(s)
- Maxime Gauthier
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Philip Waelès
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Frédéric Coutrot
- Supramolecular Machines and Architectures Team, IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
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19
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Silva-Carvalho AÉ, Cardoso MH, Alencar-Silva T, Bogéa GMR, Carvalho JL, Franco OL, Saldanha-Araujo F. Dissecting the relationship between antimicrobial peptides and mesenchymal stem cells. Pharmacol Ther 2021; 233:108021. [PMID: 34637839 DOI: 10.1016/j.pharmthera.2021.108021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/02/2021] [Accepted: 10/06/2021] [Indexed: 02/06/2023]
Abstract
Among the various biological properties presented by Mesenchymal Stem Cells (MSCs), their ability to control the immune response and fight pathogen infection through the production of antimicrobial peptides (AMPs) have been the subject of intense research in recent years. AMPs secreted by MSCs exhibit activity against a wide range of microorganisms, including bacteria, fungi, yeasts, and viruses. The main AMPs produced by these cells are hepcidin, cathelicidin LL-37, and β-defensin-2. In addition to acting against pathogens, those AMPs have also been shown to interact with MSCs to modulate MSC proliferation, migration, and regeneration, indicating that such peptides exert a more diverse biological effect than initially thought. In the present review, we discuss the production of AMPs by MSCs, revise the multiple functions of these peptides, including their influence over MSCs, and present an overview of clinical situations in which the antimicrobial properties of MSCs may be explored for therapy. Finally, we discuss possibilities of combining MSCs and AMPs to generate improved therapeutic strategies.
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Affiliation(s)
- Amandda Évelin Silva-Carvalho
- Laboratório de Hematologia e Células-Tronco, Departamento de Ciências da Saúde, Universidade de Brasília, Brasília, DF, Brazil
| | - Marlon Henrique Cardoso
- S-Inova Biotech, Universidade Católica Dom Bosco, Programa de Pós-Graduação em Biotecnologia, Campo Grande, MS, Brazil
| | - Thuany Alencar-Silva
- Programa de Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Gabriela Muller Reche Bogéa
- Laboratório de Hematologia e Células-Tronco, Departamento de Ciências da Saúde, Universidade de Brasília, Brasília, DF, Brazil
| | - Juliana Lott Carvalho
- Programa de Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Faculty of Medicine, University of Brasilia, Brasilia, DF, Brazil
| | - Octávio Luiz Franco
- S-Inova Biotech, Universidade Católica Dom Bosco, Programa de Pós-Graduação em Biotecnologia, Campo Grande, MS, Brazil; Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Felipe Saldanha-Araujo
- Laboratório de Hematologia e Células-Tronco, Departamento de Ciências da Saúde, Universidade de Brasília, Brasília, DF, Brazil.
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20
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Huang Y, Tu WL, Yao YQ, Cai YL, Ma LP. Construction of a Novel Gene-Based Model for Survival Prediction of Hepatitis B Virus Carriers With HCC Development. Front Genet 2021; 12:720888. [PMID: 34531900 PMCID: PMC8439286 DOI: 10.3389/fgene.2021.720888] [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: 06/09/2021] [Accepted: 07/30/2021] [Indexed: 11/14/2022] Open
Abstract
Despite the effectiveness of hepatitis B virus (HBV) vaccination in reducing the prevalence of chronic HBV infection as well as the incidence of acute hepatitis B, fulminant hepatitis, liver cirrhosis and hepatocellular carcinoma (HCC), there was still a large crowd of chronically infected populations at risk of developing cirrhosis or HCC. In this study, we established a comprehensive prognostic system covering multiple signatures to elevate the predictive accuracy for overall survival (OS) of hepatitis B virus carriers with HCC development. Weighted Gene Co-Expression Network Analysis (WGCNA), Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine Recursive Feature Elimination (SVM-RFE), and multivariate COX analysis, along with a suite of other online analyses were successfully applied to filtrate a three-gene signature model (TP53, CFL1, and UBA1). Afterward, the gene-based risk score was calculated based on the Cox coefficient of the individual gene, and the prognostic power was assessed by time-dependent receiver operating characteristic (tROC) and Kaplan–Meier (KM) survival analysis. Furthermore, the predictive power of the nomogram, integrated with the risk score and clinical parameters (age at diagnosis and TNM stage), was revealed by the calibration plot and tROC curves, which was verified in the validation set. Taken together, our study may be more effective in guiding the clinical decision-making of personalized treatment for HBV carriers.
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Affiliation(s)
- Yuan Huang
- Department of Biochemistry and Molecular Biology, School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Wen-Ling Tu
- Department of Genetics, School of Bioscience and Technology, Chengdu Medical College, Chengdu, China.,The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Yan-Qiu Yao
- Department of Biochemistry and Molecular Biology, School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Ye-Ling Cai
- Department of Biochemistry and Molecular Biology, School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Li-Ping Ma
- Department of Biochemistry and Molecular Biology, School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
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21
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van Maarseveen JH. Tying peptide ropes. Nat Chem 2021; 13:822-823. [PMID: 34426683 DOI: 10.1038/s41557-021-00771-6] [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)
- Jan H van Maarseveen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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22
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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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23
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Stariha LM, McCafferty DG. Discovery of the Class I Antimicrobial Lasso Peptide Arcumycin. Chembiochem 2021; 22:2632-2640. [PMID: 34133845 DOI: 10.1002/cbic.202100132] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/27/2021] [Indexed: 12/13/2022]
Abstract
Lasso peptides are a structurally diverse superfamily of conformationally constrained peptide natural products, of which a subset exhibits broad antimicrobial activity. Although advances in bioinformatics have increased our knowledge of strains harboring the biosynthetic machinery for lasso peptide production, relating peptide sequence to bioactivity remains a continuous challenge. To this end, genome mining investigation of Actinobacteria-produced antimicrobial lasso peptides was performed to correlate predicted structure with antibiotic activity. Bioinformatic evaluation revealed eight putative novel class I lasso peptide sequences. Fermentation of one of these hits, Streptomyces NRRL F-5639, resulted in the production of a novel class I lasso peptide, arcumycin. Arcumycin exhibited antibiotic activity against Gram-positive bacteria including Bacillus subtilis (4 μg/mL), Staphylococcus aureus (8 μg/mL), and Micrococcus luteus (8 μg/mL). Arcumycin treatment of B. subtilis liaI-β-gal promoter fusion reporter strain resulted in upregulation of the liaRS system by the promoter liaI, indicating arcumycin interferes with lipid II biosynthesis. Cumulatively, the results illustrate the relationship between phylogenetically related lasso peptides and their bioactivity as validated through the isolation, structural determination, and evaluation of bioactivity of the novel class I antimicrobial lasso peptide arcumycin.
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Affiliation(s)
- Lydia M Stariha
- Department of Chemistry, Duke University, Durham, NC, 27708-0346, USA
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24
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Schreiber CL, Zhai C, Smith BD. Chiral figure-eight molecular scaffold for fluorescent probe development. Org Biomol Chem 2021; 19:3213-3219. [PMID: 33885576 PMCID: PMC8075008 DOI: 10.1039/d1ob00306b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeted fluorescent molecular probes are useful for cell microscopy, diagnostics, and biological imaging. An emerging discovery paradigm is to screen libraries of fluorescent molecules and identify hit compounds with interesting targeting properties. However, a current limitation with this approach is the lack of fluorescent molecular scaffolds that can produce libraries of probe candidates with three dimensional globular shape, chiral centers, and constrained conformation. This study evaluated a new probe scaffold called squaraine figure-eight (SF8), a self-threaded molecular architecture that is comprised of an encapsulated deep-red fluorescent squaraine dye, surrounding tetralactam macrocycle, and peripheral loops. Easy synthetic variation of the loops produced four chiral isomeric SF8 probes, with the same log P values. Cell microscopy showed that subtle changes in the loop structure led to significant differences in intracellular targeting. Most notably, a comparison of enantiomeric probes revealed a large difference in mitochondrial accumulation, very likely due to differences in affinity for a chiral biomarker within the organelle. A tangible outcome of the research is a probe candidate that can be: (a) developed further as a bright and photostable, deep-red fluorescent probe for mitochondrial imaging, and (b) used as a molecular tool to identify the mitochondrial biomarker for selective targeting. It will be straightforward to expand the SF8 probe chemical space and produce structurally diverse probe libraries with high potential for selective targeting of a wide range of biomarkers.
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Affiliation(s)
- Cynthia L Schreiber
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
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25
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Liu T, Huang Z, Gui X, Xiang W, Jin Y, Chen J, Zhao J. Multi-omics Comparative Analysis of Streptomyces Mutants Obtained by Iterative Atmosphere and Room-Temperature Plasma Mutagenesis. Front Microbiol 2021; 11:630309. [PMID: 33584595 PMCID: PMC7876522 DOI: 10.3389/fmicb.2020.630309] [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: 11/17/2020] [Accepted: 12/28/2020] [Indexed: 11/13/2022] Open
Abstract
Sponges, the most primitive multicellular animals, contain a large number of unique microbial communities. Sponge-associated microorganisms, particularly actinomyces, have the potential to produce diverse active natural products. However, a large number of silent secondary metabolic gene clusters have failed to be revived under laboratory culture conditions. In this study, iterative atmospheric room-temperature plasma. (ARTP) mutagenesis coupled with multi-omics conjoint analysis was adopted to activate the inactive wild Streptomyces strain. The desirable exposure time employed in this study was 75 s to obtain the appropriate lethality rate (94%) and mutation positive rate (40.94%). After three iterations of ARTP mutagenesis, the proportion of mutants exhibiting antibacterial activities significantly increased by 75%. Transcriptome analysis further demonstrated that the differential gene expression levels of encoding type I lasso peptide aborycin had a significant upward trend in active mutants compared with wild-type strains, which was confirmed by LC-MS results with a relative molecular mass of 1082.43 ([M + 2H]2+ at m/z = 2164.86). Moreover, metabolome comparative analysis of the mutant and wild-type strains showed that four spectra or mass peaks presented obvious differences in terms of the total ion count or extracting ion current profiles with each peak corresponding to a specific compound exhibiting moderate antibacterial activity against Gram-positive indicators. Taken together, our data suggest that the ARTP treatment method coupled with multi-omics profiling analysis could be used to estimate the valid active molecules of metabolites from microbial crudes without requiring a time-consuming isolation process.
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Affiliation(s)
- Tan Liu
- College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Zhiyong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xi Gui
- College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Wei Xiang
- College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Yubo Jin
- College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jun Chen
- College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jing Zhao
- College of Ocean and Earth Science, Xiamen University, Xiamen, China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
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26
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Barnes NG, Nyandoro K, Jin H, Macmillan D. Rapid access to Asp/Glu sidechain hydrazides as thioester precursors for peptide cyclization and glycosylation. Chem Commun (Camb) 2021; 57:1006-1009. [PMID: 33399597 DOI: 10.1039/d0cc07404g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Head-to-sidechain macrocylic peptides, and neoglycopeptides, were readily prepared by site-specific amidation of aspartic and glutamic acid sidechain hydrazides. Hydrazides, serving as latent thioesters, were introduced through regioselective opening of the corresponding Nα-Fmoc protected anhydride precursors.
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Affiliation(s)
- Natalie G Barnes
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H0AJ, UK.
| | - Kudakwashe Nyandoro
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H0AJ, UK.
| | - Hanzhang Jin
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H0AJ, UK.
| | - Derek Macmillan
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H0AJ, UK.
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27
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Luo H, Tao C, Wang P, Li J, Huang K, Zhu X. Development of a prognostic index based on immunogenomic landscape analysis in glioma. IMMUNITY INFLAMMATION AND DISEASE 2021; 9:467-479. [PMID: 33503296 PMCID: PMC8127549 DOI: 10.1002/iid3.407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 12/21/2022]
Abstract
Background Glioma is the most common intracranial tumor. The inflammatory response actively participates in the malignancy of gliomas. There is still limited knowledge about the biological function of immune‐related genes (IRGs) and their potential involvement in the malignancy of gliomas. Methods We screened differentially expressed and survival‐associated IRGs, and explored their potential molecular characteristics. Then we developed a prognostic index derived from seven hub IRGs. A prognostic nomogram was built to indicate the prognostic value of the prognostic index and seven IRGs. We characterized the immune infiltration landscape to analyze tumor‐immune interactions. The real‐time quantitative polymerase chain reaction assay was performed to validate bioinformatics results. Results The differentially expressed IRGs are involved in cell chemotaxis, cytokine activity, and the chemokine‐mediated signaling pathway. The prognostic index derived from seven IRGs had clinical prognostic value in glioma, and positively correlated with the malignant clinicopathological characteristics. A nomogram further indicated that the prognostic index and seven hub IRGs had clinical prognostic value for gliomas. We revealed that the prognostic index could reflect the state of the glioma immune microenvironment. Conclusion This study demonstrates the importance of an IRG‐based prognostic index as a potential biomarker for predicting malignancy in gliomas.
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Affiliation(s)
- Haitao Luo
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Chuming Tao
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,East China Institute of Digital Medical Engineering, Shangrao, Jiangxi, China
| | - Peng Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jingying Li
- Department of Comprehensive Intensive Care Unit, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, China
| | - Xingen Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.,Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, China
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28
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Simien JM, Haglund E. Topological Twists in Nature. Trends Biochem Sci 2021; 46:461-471. [PMID: 33419636 DOI: 10.1016/j.tibs.2020.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 11/25/2022]
Abstract
The first entangled protein was observed about 30 years ago, resulting in an increased interest for uncovering the biological functions and biophysical properties of these complex topologies. Recently, the Pierced Lasso Topology (PLT) was discovered in which a covalent bond forms an intramolecular loop, leaving one or both termini free to pierce the loop. This topology is related to knots and other entanglements. PLTs exist in many well-researched systems where the PLTs have previously been unnoticed. PLTs represents 18% of all disulfide containing proteins across all kingdoms of life. In this review, we investigate the biological implications of this specific topology in which the PLT-forming disulfide may act as a molecular switch for protein function and consequently human health.
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Affiliation(s)
| | - Ellinor Haglund
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, USA.
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29
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Rowe SM, Spring DR. The role of chemical synthesis in developing RiPP antibiotics. Chem Soc Rev 2021; 50:4245-4258. [DOI: 10.1039/d0cs01386b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This tutorial review discusses the potential of ribosomally synthesised and post-translationally modified peptides (RiPPs) as antimicrobials and looks at the chemical synthesis of three classes of RiPP: lasso peptides, cyclotides, and lanthipeptides.
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Affiliation(s)
- Sam M. Rowe
- Department of Chemistry
- University of Cambridge
- Cambridge
- UK
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30
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Zhai C, Schreiber CL, Padilla-Coley S, Oliver AG, Smith BD. Fluorescent Self-Threaded Peptide Probes for Biological Imaging. Angew Chem Int Ed Engl 2020; 59:23740-23747. [PMID: 32930474 PMCID: PMC7736561 DOI: 10.1002/anie.202009599] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/08/2020] [Indexed: 12/19/2022]
Abstract
A general synthetic method creates a new class of covalently connected, self-threaded, fluorescent molecular probes with figure-eight topology, an encapsulated deep-red fluorophore, and two peripheral peptide loops. The globular molecular shape and rigidified peptide loops enhance imaging performance by promoting water solubility, eliminating probe self-aggregation, and increasing probe stability. Moreover, the peptide loops determine the affinity and selectivity for targets within complex biological samples such as cell culture, tissue histology slices, or living subjects. For example, a probe with cell-penetrating peptide loops targets the surface of cell plasma membranes, whereas, a probe with bone-targeting peptide loops selectively stains the skeleton within a living mouse. The unique combination of bright deep-red fluorescence, high stability, and predictable peptide-based targeting is ideal for photon intense fluorescence microscopy and biological imaging.
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Affiliation(s)
- Canjia Zhai
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Cynthia L. Schreiber
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Sasha Padilla-Coley
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Allen G. Oliver
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Bradley D. Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
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31
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Zhai C, Schreiber CL, Padilla‐Coley S, Oliver AG, Smith BD. Fluorescent Self‐Threaded Peptide Probes for Biological Imaging. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Canjia Zhai
- Department of Chemistry and Biochemistry University of Notre Dame 251 Nieuwland Science Hall Notre Dame IN 46556 USA
| | - Cynthia L. Schreiber
- Department of Chemistry and Biochemistry University of Notre Dame 251 Nieuwland Science Hall Notre Dame IN 46556 USA
| | - Sasha Padilla‐Coley
- Department of Chemistry and Biochemistry University of Notre Dame 251 Nieuwland Science Hall Notre Dame IN 46556 USA
| | - Allen G. Oliver
- Department of Chemistry and Biochemistry University of Notre Dame 251 Nieuwland Science Hall Notre Dame IN 46556 USA
| | - Bradley D. Smith
- Department of Chemistry and Biochemistry University of Notre Dame 251 Nieuwland Science Hall Notre Dame IN 46556 USA
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32
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Cheng C, Hua ZC. Lasso Peptides: Heterologous Production and Potential Medical Application. Front Bioeng Biotechnol 2020; 8:571165. [PMID: 33117783 PMCID: PMC7549694 DOI: 10.3389/fbioe.2020.571165] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
Lasso peptides are natural products found in bacteria. They belong to a specific family of ribosomally-synthesized and posttranslationally-modified peptides with an unusual lasso structure. Lasso peptides possess remarkable thermal and proteolytic stability and various biological activities, such as antimicrobial activity, enzyme inhibition, receptor blocking, anticancer properties and HIV antagonism. They have promising potential therapeutic effects on gastrointestinal diseases, tuberculosis, Alzheimer’s disease, cardiovascular disease, fungal infections and cancer. Lasso peptides with high stability have been shown to be good carriers for other bioactive peptides. These make them attractive candidates for pharmaceutical research. This review aimed to describe the strategies used for the heterologous production of lasso peptides. Also, it indicated their therapeutical potential and their capacity to use as an efficient scaffold for epitope grafting.
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Affiliation(s)
- Cheng Cheng
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,School of Biopharmacy, China Pharmaceutical University, Nanjing, China.,Changzhou High-Tech Research Institute of Nanjing University, Changzhou, China.,Jiangsu Target Pharma Laboratories Inc., Changzhou, China
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33
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Wilson ZE, Brimble MA. Molecules derived from the extremes of life: a decade later. Nat Prod Rep 2020; 38:24-82. [PMID: 32672280 DOI: 10.1039/d0np00021c] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: Early 2008 until the end of 2019Microorganisms which survive (extreme-tolerant) or even prefer (extremophilic) living at the limits of pH, temperature, salinity and pressure found on earth have proven to be a rich source of novel structures. In this update we summarise the wide variety of new molecules which have been isolated from extremophilic and extreme-tolerant microorganisms since our original 2009 review, highlighting the range of bioactivities these molecules have been reported to possess.
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Affiliation(s)
- Zoe E Wilson
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
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34
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Young MJ, Akien GR, Evans NH. An amide hydrogen bond templated [1]rotaxane displaying a peptide motif - demonstrating an expedient route to synthetic mimics of lasso peptides. Org Biomol Chem 2020; 18:5203-5209. [PMID: 32597913 DOI: 10.1039/d0ob01190h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The rapid synthesis of an amide hydrogen bond templated [1]rotaxane is reported - demonstrating a potential pathway to synthetic analogues of lasso peptides. The structures of the [1]rotaxane and its unthreaded isomer have been characterized by NMR spectroscopy and modelled using DFT calculations.
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Affiliation(s)
- Matthew J Young
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK.
| | - Geoffrey R Akien
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK.
| | - Nicholas H Evans
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK.
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35
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Waliczek M, Wierzbicka M, Arkuszewski M, Kijewska M, Jaremko Ł, Rajagopal P, Szczepski K, Sroczyńska A, Jaremko M, Stefanowicz P. Attempting to synthesize lasso peptides using high pressure. PLoS One 2020; 15:e0234901. [PMID: 32579565 PMCID: PMC7314030 DOI: 10.1371/journal.pone.0234901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/20/2020] [Indexed: 12/30/2022] Open
Abstract
Lasso peptides are unique in that the tail of the lasso peptide threads through its macrolactam ring. The unusual structure and biological activity of lasso peptides have generated increased interest from the scientific community in recent years. Because of this, many new types of lasso peptides have been discovered. These peptides can be synthesized by microorganisms efficiently, and yet, their chemical assembly is challenging. Herein, we investigated the possibility of high pressure inducing the cyclization of linear precursors of lasso peptides. Unlike other molecules like rotaxanes which mechanically interlock at high pressure, the threaded lasso peptides did not form, even at pressures the high pressure up to 14 000 kbar.
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Affiliation(s)
| | | | | | - Monika Kijewska
- Faculty of Chemistry, University of Wrocław, Wroclaw, Poland
| | - Łukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Priyadharshni Rajagopal
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kacper Szczepski
- Faculty of Chemistry, University of Wrocław, Wroclaw, Poland
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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36
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Acevedo-Jake A, Ball AT, Galli M, Kukwikila M, Denis M, Singleton DG, Tavassoli A, Goldup SM. AT-CuAAC Synthesis of Mechanically Interlocked Oligonucleotides. J Am Chem Soc 2020; 142:5985-5990. [PMID: 32155338 PMCID: PMC8016193 DOI: 10.1021/jacs.0c01670] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/22/2022]
Abstract
We present a simple strategy for the synthesis of main chain oligonucleotide rotaxanes with precise control over the position of the macrocycle. The novel DNA-based rotaxanes were analyzed to assess the effect of the mechanical bond on their properties.
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Affiliation(s)
- Amanda Acevedo-Jake
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Andrew T. Ball
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Marzia Galli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mikiembo Kukwikila
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mathieu Denis
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Daniel G. Singleton
- ATDBio
Ltd, School of Chemistry, University of
Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Ali Tavassoli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Stephen M. Goldup
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
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37
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Abstract
Burkholderia bacteria are an emerging source of natural products with applications in agriculture and medicine. The heterologous expression of biosynthetic gene clusters can streamline natural product discovery; however, production yields with the commonly used Escherichia coli host are usually low. Following the current paradigm that one host does not fit all, we aim to develop a Burkholderia host to ultimately tap into the biosynthetic potential of Burkholderia genomes, which can contain up to 27 biosynthetic gene clusters per genome. Because a close phylogenetic relationship is expected to improve the odds of success due to compatible gene expression and precursor supply, we tested Burkholderia sp. FERM BP-3421, a nonpathogenic isolate previously used to produce natural products at industrial scales. We show here that FERM BP-3421 can produce the model lasso peptide capistruin in yields that are at least 65 times and up to 580 times higher than the previously used E. coli host.
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Affiliation(s)
- Sylvia Kunakom
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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38
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Cortés-Albayay C, Jarmusch SA, Trusch F, Ebel R, Andrews BA, Jaspars M, Asenjo JA. Downsizing Class II Lasso Peptides: Genome Mining-Guided Isolation of Huascopeptin Containing the First Gly1-Asp7 Macrocycle. J Org Chem 2020; 85:1661-1667. [DOI: 10.1021/acs.joc.9b02231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Carlos Cortés-Albayay
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
| | - Scott A. Jarmusch
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Franziska Trusch
- Institute of Medical Sciences, University of Aberdeen, Foresterhill AB25 2ZD, Scotland, U.K
- Division of Plant Sciences, College of Life Science, University of Dundee (at JHI), Errol Road, Invergowrie, Dundee DD2 5DA, U.K
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Barbara A. Andrews
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, U.K
| | - Juan A. Asenjo
- Centre for Biotechnology and Bioengineering, CeBiB, Department of Chemical Engineering, Biotechnology and Materials, University of Chile, Beauchef 851, Santiago 8370450, Chile
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39
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Koehbach J, Craik DJ. The Vast Structural Diversity of Antimicrobial Peptides. Trends Pharmacol Sci 2019; 40:517-528. [DOI: 10.1016/j.tips.2019.04.012] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 01/08/2023]
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40
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Zhu S, Su Y, Shams S, Feng Y, Tong Y, Zheng G. Lassomycin and lariatin lasso peptides as suitable antibiotics for combating mycobacterial infections: current state of biosynthesis and perspectives for production. Appl Microbiol Biotechnol 2019; 103:3931-3940. [PMID: 30915503 DOI: 10.1007/s00253-019-09771-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 11/30/2022]
Abstract
Lasso peptides are ribosomally synthesized and post-translationally modified natural products with a characteristic slipknot-like structure, which confers these peptides remarkable stability and diverse pharmacologically relevant bioactivities. Among all the reported lasso peptides, lassomycin and lariatins are unique lasso peptides that exhibit noticeable anti-tuberculosis (TB) activity. Due to the unique threaded structure and the unusual bactericidal mechanism toward Mycobacterium tuberculosis, these peptides have drawn considerable interest, not only in the field of total synthesis but also in several other fields including biosynthesis, bioengineering, and structure-activity studies. During the past few years, significant progress has been made in understanding the biosynthetic mechanism of these intriguing compounds, which has provided a solid foundation for future work. This review highlights recent achievements in the discovery, structure elucidation, biological activity, and the unique anti-TB mechanism of lasso peptides. Moreover, the discovery of their biosynthetic pathway has laid the foundation for combinatorial biosynthesis of their analogs, which provides new perspectives for the production of novel anti-TB lasso peptides.
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Affiliation(s)
- Shaozhou Zhu
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| | - Yu Su
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Saira Shams
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yue Feng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Guojun Zheng
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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41
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Martin-Gómez H, Albericio F, Tulla-Puche J. A Lasso-Inspired Bicyclic Peptide: Synthesis, Structure and Properties. Chemistry 2018; 24:19250-19257. [PMID: 30255960 DOI: 10.1002/chem.201803899] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/25/2018] [Indexed: 11/05/2022]
Abstract
The chemical synthesis of a bicycle inspired by the natural lasso peptide sungsanpin using a combination of solid-phase and in-solution chemistries is described. The bicyclic-derived topoisomer was designed by introducing a covalent linkage between the ring and the loop, which allowed the tying of these two parts of the peptide, rendering the bicyclic structure. Several structural techniques, such as MS fragmentation, ion-mobility and NMR spectroscopic analysis were used to characterize the bicycle. Ion-mobility spectroscopy studies revealed that it showed lasso-like behavior. Its 3D structure was predicted on the basis of the NMR restraints. In addition, the high proteolytic and thermal stability of the bicycle potentially make it a suitable scaffold for epitope grafting.
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Affiliation(s)
- Helena Martin-Gómez
- Institute for Research in Biomedicine, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Fernando Albericio
- Department of Inorganic and Organic Chemistry, Organic Chemistry Section, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain.,CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 10, 08028, Barcelona, Spain.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Judit Tulla-Puche
- Department of Inorganic and Organic Chemistry, Organic Chemistry Section, University of Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain.,CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Baldiri Reixac 10, 08028, Barcelona, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028, Barcelona, Spain
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42
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Kodani S, Hemmi H, Miyake Y, Kaweewan I, Nakagawa H. Heterologous production of a new lasso peptide brevunsin in Sphingomonas subterranea. ACTA ACUST UNITED AC 2018; 45:983-992. [DOI: 10.1007/s10295-018-2077-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/30/2018] [Indexed: 11/29/2022]
Abstract
Abstract
A shuttle vector pHSG396Sp was constructed to perform gene expression using Sphingomonas subterranea as a host. A new lasso peptide biosynthetic gene cluster, derived from Brevundimonas diminuta, was amplified by PCR and integrated to afford a expression vector pHSG396Sp-12697L. The new lasso peptide brevunsin was successfully produced by S. subterranea, harboring the expression vector, with a high production yield (10.2 mg from 1 L culture). The chemical structure of brevunsin was established by NMR and MS/MS experiments. Based on the information obtained from the NOE experiment, the three-dimensional structure of brevunsin was determined, which indicated that brevunsin possessed a typical lasso structure. This expression vector system provides a new heterologous production method for unexplored lasso peptides that are encoded by bacterial genomes.
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Affiliation(s)
- Shinya Kodani
- College of Agriculture Academic Institute, Shizuoka University 836 Ohya, Suruga-ku 422-8529 Shizuoka Japan
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Integrated Science and Technology Shizuoka University 422-8529 Shizuoka Japan
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Science and Technology Shizuoka University 422-8529 Shizuoka Japan
| | - Hikaru Hemmi
- 0000 0001 2222 0432 grid.416835.d Food Research Institute, National Agriculture and Food Research Organization (NARO) 305-8642 Ibaraki Japan
| | - Yuto Miyake
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Integrated Science and Technology Shizuoka University 422-8529 Shizuoka Japan
| | - Issara Kaweewan
- 0000 0001 0656 4913 grid.263536.7 Graduate School of Science and Technology Shizuoka University 422-8529 Shizuoka Japan
| | - Hiroyuki Nakagawa
- 0000 0001 2222 0432 grid.416835.d Food Research Institute, National Agriculture and Food Research Organization (NARO) 305-8642 Ibaraki Japan
- 0000 0001 2222 0432 grid.416835.d Advanced Analysis Center National Agriculture and Food Research Organization (NARO) 305-8642 Ibaraki Japan
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Saura-Sanmartin A, Martinez-Cuezva A, Pastor A, Bautista D, Berna J. Light-driven exchange between extended and contracted lasso-like isomers of a bistable [1]rotaxane. Org Biomol Chem 2018; 16:6980-6987. [DOI: 10.1039/c8ob02234h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A photoactive hydrogen-bonded lasso having an amide-based [1]rotaxane structure has been constructed from acyclic precursors through a self-templating approach. The stability, structural integrity and switching are described.
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Affiliation(s)
- Adrian Saura-Sanmartin
- Departamento de Química Orgánica
- Facultad de Química
- Regional Campus of International Excellence “Campus Mare Nostrum”
- Universidad de Murcia
- Murcia
| | - Alberto Martinez-Cuezva
- Departamento de Química Orgánica
- Facultad de Química
- Regional Campus of International Excellence “Campus Mare Nostrum”
- Universidad de Murcia
- Murcia
| | - Aurelia Pastor
- Departamento de Química Orgánica
- Facultad de Química
- Regional Campus of International Excellence “Campus Mare Nostrum”
- Universidad de Murcia
- Murcia
| | | | - Jose Berna
- Departamento de Química Orgánica
- Facultad de Química
- Regional Campus of International Excellence “Campus Mare Nostrum”
- Universidad de Murcia
- Murcia
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