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Bioorthogonal Chemistry
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Bioorthogonal Chemistry

A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: closed (30 November 2013) | Viewed by 49780

Special Issue Editor

Dr. Floris Van Delft

E-Mail Website
Guest Editor
Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
Interests: bioconjugation; copper-free click chemistry; glycopeptides; nucleotide conjugates; oligosaccharide synthesis; small molecule synthesis; catalysis; chemical biology

Special Issue Information

Dear Colleagues.

The recent strategy to apply chemical reactions to address fundamental biological questions has led to the emergence of entirely new conjugation reactions that are fast and irreversible, yet so mild and selective that they can be performed even in or on living cells or in whole organisms. These so-called bioorthogonal reactions, for example the strain-promoted cycloaddition of cyclooctyne with azide or tetrazine, or trans-cyclooctene with tetrazine, open novel avenues, not only in chemical biology research, but also in many other life sciences applications, including the site-specific modification of proteins, in vitro diagnostics, biomaterials, regenerative medicine, imaging and potentially even image-guided surgery. Research papers and reviews dealing with the presented fields are welcome for the preparation of this Special Issue of Molecules.

Dr. Floris van Delft
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


Keywords

  • bioorthogonal reactions
  • copper-free click
  • strain-promoted cycloaddition
  • in vivo chemistry
  • biomaterial science
  • peptidoglycans
  • glycoproteins
  • nucleotide conjugates
  • site-specific conjugation
  • immobilization

Published Papers (4 papers)

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Research

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1983 KiB  
Article
Pharmacophore Generation from a Drug-like Core Molecule Surrounded by a Library Peptide via the 10BASEd-T on Bacteriophage T7
by Yuuki Tokunaga, Yuuki Azetsu, Keisuke Fukunaga, Takaaki Hatanaka, Yuji Ito and Masumi Taki
Molecules 2014, 19(2), 2481-2496; https://doi.org/10.3390/molecules19022481 - 21 Feb 2014
Cited by 5 | Viewed by 11617
Abstract
We have achieved site-specific conjugation of several haloacetamide derivatives into designated cysteines on bacteriophage T7-displayed peptides, which are fused to T7 capsid protein gp10. This easiest gp10 based-thioetherification (10BASEd-T) undergoes almost quantitatively like a click reaction without side reaction or loss [...] Read more.
We have achieved site-specific conjugation of several haloacetamide derivatives into designated cysteines on bacteriophage T7-displayed peptides, which are fused to T7 capsid protein gp10. This easiest gp10 based-thioetherification (10BASEd-T) undergoes almost quantitatively like a click reaction without side reaction or loss of phage infectivity. The post-translational modification yield, as well as the site-specificity, is quantitatively analyzed by a fluorescent densitometric analysis after gel electrophoresis. The detailed structure of the modified peptide on phage is identified with tandem mass spectrometry. Construction of such a peptide-fused phage library possessing non-natural core structures will be useful for future drug discovery. For this aim, we propose a novel concept of pharmacophore generation from a drug-like molecule (i.e., salicylic acid) conjugated with surrounding randomized peptides. By using the hybrid library, streptavidin-specific binders are isolated through four rounds of biopanning. Full article
(This article belongs to the Special Issue Bioorthogonal Chemistry)
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735 KiB  
Article
Coupling Bioorthogonal Chemistries with Artificial Metabolism: Intracellular Biosynthesis of Azidohomoalanine and Its Incorporation into Recombinant Proteins
by Ying Ma, Hernán Biava, Roberto Contestabile, Nediljko Budisa and Martino Luigi Di Salvo
Molecules 2014, 19(1), 1004-1022; https://doi.org/10.3390/molecules19011004 - 15 Jan 2014
Cited by 44 | Viewed by 13339
Abstract
In this paper, we present a novel, “single experiment” methodology based on genetic engineering of metabolic pathways for direct intracellular production of non-canonical amino acids from simple precursors, coupled with expanded genetic code. In particular, we engineered the intracellular biosynthesis of L-azidohomoalanine from [...] Read more.
In this paper, we present a novel, “single experiment” methodology based on genetic engineering of metabolic pathways for direct intracellular production of non-canonical amino acids from simple precursors, coupled with expanded genetic code. In particular, we engineered the intracellular biosynthesis of L-azidohomoalanine from O-acetyl-L-homoserine and NaN3, and achieved its direct incorporation into recombinant target proteins by AUG codon reassignment in a methionine-auxotroph E. coli strain. In our system, the host’s methionine biosynthetic pathway was first diverted towards the production of the desired non-canonical amino acid by exploiting the broad reaction specificity of recombinant pyridoxal phosphate-dependent O-acetylhomoserine sulfhydrylase from Corynebacterium glutamicum. Then, the expression of the target protein barstar, accompanied with efficient L-azidohomoalanine incorporation in place of L-methionine, was accomplished. This work stands as proof-of-principle and paves the way for additional work towards intracellular production and site-specific incorporation of biotechnologically relevant non-canonical amino acids directly from common fermentable sources. Full article
(This article belongs to the Special Issue Bioorthogonal Chemistry)
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Review

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390 KiB  
Review
Applications of Copper-Catalyzed Click Chemistry in Activity-Based Protein Profiling
by Julianne Martell and Eranthie Weerapana
Molecules 2014, 19(2), 1378-1393; https://doi.org/10.3390/molecules19021378 - 27 Jan 2014
Cited by 66 | Viewed by 17103
Abstract
Activity-based protein profiling (ABPP) is a chemical proteomic technique that enables the interrogation of protein activity directly within complex proteomes. Given the dominant role of posttranslational modifications in regulating protein function in vivo, ABPP provides a direct readout of activity that is [...] Read more.
Activity-based protein profiling (ABPP) is a chemical proteomic technique that enables the interrogation of protein activity directly within complex proteomes. Given the dominant role of posttranslational modifications in regulating protein function in vivo, ABPP provides a direct readout of activity that is not attained through traditional proteomic methods. ABPP relies on the design of covalent binding probes that either target a specific enzyme or a class of enzymes with related function. These covalent warheads are coupled to either fluorophores or biotin groups for visualization and enrichment of these active proteins. The advent of bioorthogonal chemistries, in particular, the copper (I)-catalyzed azide-alkyne cycloaddition (CuAAC), has benefitted the field of ABPP by achieving the following: (1) replacing bulky reporter groups with smaller alkyne or azide groups to promote cell permeability; (2) adding modularity to the system such that a single probe can be diversified with a variety of reporter groups without the need to develop new synthetic routes; and (3) enabling the conjugation of complex linkers to facilitate quantitative proteomic analyses. Here, we summarize recent examples of CuAAC in ABPP that serve to illustrate the contribution of bioorthogonal chemistry to advancing discoveries in this field. Full article
(This article belongs to the Special Issue Bioorthogonal Chemistry)
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612 KiB  
Review
Ring Expansion of Vinylaziridines through the Strain-Release Pericyclic Reaction: Recent Developments and Applications
by Yu Mi Heo and Seung-Mann Paek
Molecules 2013, 18(8), 9650-9662; https://doi.org/10.3390/molecules18089650 - 12 Aug 2013
Cited by 20 | Viewed by 6788
Abstract
Recent syntheses of azetidines, pyrrolidines, piperidines and azepines through cycloaddition or sigmatropic rearrangements of vinylaziridines are described. Applications to natural product synthesis and mechanistic investigations are also summarized. Full article
(This article belongs to the Special Issue Bioorthogonal Chemistry)
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