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Peptides and Peptide Technologies: A Themed Issue in Honor of Professor Morten Meldal on the Occasion of His Citation Laureates

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Organic Chemistry".

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 38980

Special Issue Editor

Prof. Dr. Mark Bradley

E-Mail Website
Guest Editor
EaStChem School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, UK
Interests: stem cells and 3D scaffolds; bioactive scaffolds; polymer microarrays; combinatorial chemistry; optical imaging; peptides; in vivo chemistry

Special Issue Information

Dear Colleagues,

Prof. Morten has made enormous contributions to the world of solid-phase chemistry – encompassing both peptide and organic chemistries and technologies as well as providing the first example of copper-catalyzed azide/alkyne cycloaddition chemistry. These have led to key advances and developments across the areas of combinatorial chemistry and chemical biology respectively. This issue celebrates the pioneering efforts of Morten and his enormous contributions to the peptide arena.

Prof. Dr. Mark Bradley
Guest Editor

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Keywords

  • Peptides
  • Resins
  • Encoding
  • Combinatorial
  • Solid-phase synthesis
  • Proteases

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Published Papers (7 papers)

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Research

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11 pages, 2888 KiB  
Article
Serinol-Based Versatile Disulfide-Reducing Reagent
by Babita Kushwaha, Sinenhlanhla N. Mthembu, Anamika Sharma, Fernando Albericio and Beatriz G. de la Torre
Molecules 2023, 28(14), 5489; https://doi.org/10.3390/molecules28145489 - 18 Jul 2023
Cited by 2 | Viewed by 2534
Abstract
Here, we report the synthesis of disulfide-reducing agents 2-(dibenzylamino) propane-1,3-dithiol (DPDT) and 2-(dibenzylamino)-2-methylpropane-1,3-dithiol (DMPDT) from serinol and methyl serinol, respectively. DPDT was found to show greater stability than DMPDT. Hence, the effectiveness of DPDT as a reducing agent was evaluated in both liquid [...] Read more.
Here, we report the synthesis of disulfide-reducing agents 2-(dibenzylamino) propane-1,3-dithiol (DPDT) and 2-(dibenzylamino)-2-methylpropane-1,3-dithiol (DMPDT) from serinol and methyl serinol, respectively. DPDT was found to show greater stability than DMPDT. Hence, the effectiveness of DPDT as a reducing agent was evaluated in both liquid and solid phases. The reducing capacity of this agent was comparable to that of DTT. Full article
(This article belongs to the Special Issue Peptides and Peptide Technologies: A Themed Issue in Honor of Professor Morten Meldal on the Occasion of His Citation Laureates)
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13 pages, 655 KiB  
Article
Propagation Capacity of Phage Display Peptide Libraries Is Affected by the Length and Conformation of Displayed Peptide
by Danna Kamstrup Sell, Anders Wilgaard Sinkjaer, Babak Bakhshinejad and Andreas Kjaer
Molecules 2023, 28(14), 5318; https://doi.org/10.3390/molecules28145318 - 10 Jul 2023
Cited by 2 | Viewed by 2257
Abstract
The larger size and diversity of phage display peptide libraries enhance the probability of finding clinically valuable ligands. A simple way of increasing the throughput of selection is to mix multiple peptide libraries with different characteristics of displayed peptides and use it as [...] Read more.
The larger size and diversity of phage display peptide libraries enhance the probability of finding clinically valuable ligands. A simple way of increasing the throughput of selection is to mix multiple peptide libraries with different characteristics of displayed peptides and use it as biopanning input. In phage display, the peptide is genetically coupled with a biological entity (the phage), and the representation of peptides in the selection system is dependent on the propagation capacity of phages. Little is known about how the characteristics of displayed peptides affect the propagation capacity of the pooled library. In this work, next-generation sequencing (NGS) was used to investigate the amplification capacity of three widely used commercial phage display peptide libraries (Ph.D.™-7, Ph.D.™-12, and Ph.D.™-C7C from New England Biolabs). The three libraries were pooled and subjected to competitive propagation, and the proportion of each library in the pool was quantitated at two time points during propagation. The results of the inter-library competitive propagation assay led to the conclusion that the propagation capacity of phage libraries on a population level is decreased with increasing length and cyclic conformation of displayed peptides. Moreover, the enrichment factor (EF) analysis of the phage population revealed a higher propagation capacity of the Ph.D.TM-7 library. Our findings provide evidence for the contribution of the length and structural conformation of displayed peptides to the unequal propagation rates of phage display libraries and suggest that it is important to take peptide characteristics into account once pooling multiple combinatorial libraries for phage display selection through biopanning. Full article
(This article belongs to the Special Issue Peptides and Peptide Technologies: A Themed Issue in Honor of Professor Morten Meldal on the Occasion of His Citation Laureates)
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15 pages, 2659 KiB  
Article
Bottom-Up Design Approach for OBOC Peptide Libraries
by Daniela Kalafatovic, Goran Mauša, Dina Rešetar Maslov and Ernest Giralt
Molecules 2020, 25(15), 3316; https://doi.org/10.3390/molecules25153316 - 22 Jul 2020
Cited by 7 | Viewed by 4912
Abstract
One-bead-one-compound peptide libraries, developed following the top-down experimental approach, have attracted great interest in the identification of potential ligands or active peptides. By exploiting a reverse experimental design approach based on the bottom-up strategy, we aimed to develop simplified, maximally diverse peptide libraries [...] Read more.
One-bead-one-compound peptide libraries, developed following the top-down experimental approach, have attracted great interest in the identification of potential ligands or active peptides. By exploiting a reverse experimental design approach based on the bottom-up strategy, we aimed to develop simplified, maximally diverse peptide libraries that resulted in the successful characterization of mixture components. We show that libraries of 32 and 48 components can be successfully detected in a single run using chromatography coupled to mass spectrometry (UPLC-MS). The proposed libraries were further theoretically evaluated in terms of their composition and physico-chemical properties. By combining the knowledge obtained on single libraries we can cover larger sequence spaces and provide a controlled exploration of the peptide chemical space both theoretically and experimentally. Designing libraries by using the bottom-up approach opens up the possibility of rationally fine-tuning the library complexity based on the available analytical methods. Full article
(This article belongs to the Special Issue Peptides and Peptide Technologies: A Themed Issue in Honor of Professor Morten Meldal on the Occasion of His Citation Laureates)
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10 pages, 3287 KiB  
Article
Self-Assembling Behavior of pH-Responsive Peptide A6K without End-Capping
by Peng Zhang, Fenghuan Wang, Yuxuan Wang, Shuangyang Li and Sai Wen
Molecules 2020, 25(9), 2017; https://doi.org/10.3390/molecules25092017 - 26 Apr 2020
Cited by 9 | Viewed by 4194
Abstract
A short self-assembly peptide A6K (H2N−AAAAAAK−OH) with unmodified N− and C−terminus was designed, and the charge distribution model of this short peptide at different pH was established by computer simulation. The pH of the solution was adjusted according to [...] Read more.
A short self-assembly peptide A6K (H2N−AAAAAAK−OH) with unmodified N− and C−terminus was designed, and the charge distribution model of this short peptide at different pH was established by computer simulation. The pH of the solution was adjusted according to the model and the corresponding self-assembled structure was observed using a transmission electron microscope (TEM). As the pH changes, the peptide will assemble into blocks or nanoribbons, which indicates that the A6K peptide is a pH-responsive peptide. Circular dichroism (CD) and molecular dynamics (MD) simulation showed that the block structure was formed by random coils, while the increase in β-turn content contributes to the formation of intact nanoribbons. A reasonable explanation of the self-assembling structure was made according to the electrostatic distribution model and the effect of electrostatic interaction on self-assembly was investigated. This study laid the foundation for further design of nanomaterials based on pH-responsive peptides. Full article
(This article belongs to the Special Issue Peptides and Peptide Technologies: A Themed Issue in Honor of Professor Morten Meldal on the Occasion of His Citation Laureates)
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Review

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26 pages, 1599 KiB  
Review
Critical Review of Existing MHC I Immunopeptidome Isolation Methods
by Alexandr Kuznetsov, Alice Voronina, Vadim Govorun and Georgij Arapidi
Molecules 2020, 25(22), 5409; https://doi.org/10.3390/molecules25225409 - 19 Nov 2020
Cited by 23 | Viewed by 12979
Abstract
Major histocompatibility complex class I (MHC I) plays a crucial role in the development of adaptive immune response in vertebrates. MHC molecules are cell surface protein complexes loaded with short peptides and recognized by the T-cell receptors (TCR). Peptides associated with MHC are [...] Read more.
Major histocompatibility complex class I (MHC I) plays a crucial role in the development of adaptive immune response in vertebrates. MHC molecules are cell surface protein complexes loaded with short peptides and recognized by the T-cell receptors (TCR). Peptides associated with MHC are named immunopeptidome. The MHC I immunopeptidome is produced by the proteasome degradation of intracellular proteins. The knowledge of the immunopeptidome repertoire facilitates the creation of personalized antitumor or antiviral vaccines. A huge number of publications on the immunopeptidome diversity of different human and mouse biological samples—plasma, peripheral blood mononuclear cells (PBMCs), and solid tissues, including tumors—appeared in the scientific journals in the last decade. Significant immunopeptidome identification efficiency was achieved by advances in technology: the immunoprecipitation of MHC and mass spectrometry-based approaches. Researchers optimized common strategies to isolate MHC-associated peptides for individual tasks. They published many protocols with differences in the amount and type of biological sample, amount of antibodies, type and amount of insoluble support, methods of post-fractionation and purification, and approaches to LC-MS/MS identification of immunopeptidome. These parameters have a large impact on the final repertoire of isolated immunopeptidome. In this review, we summarize and compare immunopeptidome isolation techniques with an emphasis on the results obtained. Full article
(This article belongs to the Special Issue Peptides and Peptide Technologies: A Themed Issue in Honor of Professor Morten Meldal on the Occasion of His Citation Laureates)
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26 pages, 2758 KiB  
Review
1,4-Disubstituted 1,2,3-Triazoles as Amide Bond Surrogates for the Stabilisation of Linear Peptides with Biological Activity
by Lisa-Maria Rečnik, Wolfgang Kandioller and Thomas L. Mindt
Molecules 2020, 25(16), 3576; https://doi.org/10.3390/molecules25163576 - 6 Aug 2020
Cited by 45 | Viewed by 8238
Abstract
Peptides represent an important class of biologically active molecules with high potential for the development of diagnostic and therapeutic agents due to their structural diversity, favourable pharmacokinetic properties, and synthetic availability. However, the widespread use of peptides and conjugates thereof in clinical applications [...] Read more.
Peptides represent an important class of biologically active molecules with high potential for the development of diagnostic and therapeutic agents due to their structural diversity, favourable pharmacokinetic properties, and synthetic availability. However, the widespread use of peptides and conjugates thereof in clinical applications can be hampered by their low stability in vivo due to rapid degradation by endogenous proteases. A promising approach to circumvent this potential limitation includes the substitution of metabolically labile amide bonds in the peptide backbone by stable isosteric amide bond mimetics. In this review, we focus on the incorporation of 1,4-disubstituted 1,2,3-triazoles as amide bond surrogates in linear peptides with the aim to increase their stability without impacting their biological function(s). We highlight the properties of this heterocycle as a trans-amide bond surrogate and summarise approaches for the synthesis of triazole-containing peptidomimetics via the Cu(I)-catalysed azide-alkyne cycloaddition (CuAAC). The impacts of the incorporation of triazoles in the backbone of diverse peptides on their biological properties such as, e.g., blood serum stability and affinity as well as selectivity towards their respective molecular target(s) are discussed. Full article
(This article belongs to the Special Issue Peptides and Peptide Technologies: A Themed Issue in Honor of Professor Morten Meldal on the Occasion of His Citation Laureates)
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Other

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48 pages, 9470 KiB  
Perspective
Reflections on a Copenhagen–Minneapolis Axis in Bioorganic Chemistry
by George Barany and Paul R. Hansen
Molecules 2024, 29(6), 1317; https://doi.org/10.3390/molecules29061317 - 15 Mar 2024
Viewed by 2410
Abstract
The international peptide community rejoiced when one of its most distinguished members, Morten Meldal of Denmark, shared the 2022 Nobel Prize in Chemistry. In fact, the regiospecific solid-phase “copper(I)-catalyzed 1,3-dipolar cycloaddition of terminal alkynes to azides” (CuACC) reaction—that formed the specific basis for [...] Read more.
The international peptide community rejoiced when one of its most distinguished members, Morten Meldal of Denmark, shared the 2022 Nobel Prize in Chemistry. In fact, the regiospecific solid-phase “copper(I)-catalyzed 1,3-dipolar cycloaddition of terminal alkynes to azides” (CuACC) reaction—that formed the specific basis for Meldal’s recognition—was reported first at the 17th American Peptide Symposium held in San Diego in June 2001. The present perspective outlines intertwining conceptual and experimental threads pursued concurrently in Copenhagen and Minneapolis, sometimes by the same individuals, that provided context for Meldal’s breakthrough discovery. Major topics covered include orthogonality in chemistry; the dithiasuccinoyl (Dts) protecting group for amino groups in α-amino acids, carbohydrates, and monomers for peptide nucleic acids (PNA); and poly(ethylene glycol) (PEG)-based solid supports such as PEG–PS, PEGA, and CLEAR [and variations inspired by them] for solid-phase peptide synthesis (SPPS), solid-phase organic synthesis (SPOS), and combinatorial chemistry that can support biological assays in aqueous media. Full article
(This article belongs to the Special Issue Peptides and Peptide Technologies: A Themed Issue in Honor of Professor Morten Meldal on the Occasion of His Citation Laureates)
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