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Special Issue "Biomolecules Modification"

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

Deadline for manuscript submissions: closed (10 April 2016)

Special Issue Editors

Guest Editor
Prof. Dr. Jose M. Palomo

Departament of Biocatalysis, Institute of Catalysis (ICP-CSIC), Marie Curie 2, Cantoblanco, Campus UAM, 28049 Madrid, Spain
Website | E-Mail
Interests: biotransformations; catalysis; carbohydrate chemistry; medicinal chemistry
Guest Editor
Prof. Dr. Chris Frost

Department of Chemistry, University of Bath, Claverton Down, Bath, UK
Website | E-Mail
Interests: catalysis; protein modification; oligonucleotides; biosensors; signal amplification

Special Issue Information

Dear Colleagues,

Biomolecules are essential components involved in all biological processes in living organisms. In particular, peptides and proteins are essential for many different biological processes. Posttranslational modifications of proteins represent essential steps in their final biological activity. In this way, chemical biology approaches have been developed in the last few years in order to create new modified artificial or semisynthetic proteins very useful to study and know the behavior of different biological processes in different diseases, such as Alzheimer, cancer, Parkinson, etc. Furthermore, the capacity of some proteins to act, catalyzing several natural or unnatural processes have been altered and improved by different modification strategies. New oligonucleotides or oligosaccharides represent a class of new pharmaceuticals, such as drugs or vaccines for different diseases, such as Hepatitis, HIV, malaria, etc. Nevertheless, to access novel modified biomolecules, specially developing new strategies and methodologies to create them is still needed.

This Special Issue will be focused on innovative and novel research in the modification of biomolecules by different biological or chemical strategies and their application in organic, bioorganic, or medicinal chemistry.

Prof. Jose M. Palomo
Prof. Chris Frost
Guest Editors

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 papers will be 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 monthly 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 1800 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

  • protein chemistry
  • enzymes
  • biotransformations
  • peptides
  • molecular biology
  • nucleosides
  • oligosaccharides
  • medicinal chemistry
  • chemical biology

Published Papers (7 papers)

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Research

Open AccessArticle Design of Heterogeneous Hoveyda–Grubbs Second-Generation Catalyst–Lipase Conjugates
Molecules 2016, 21(12), 1680; doi:10.3390/molecules21121680
Received: 4 October 2016 / Revised: 25 November 2016 / Accepted: 30 November 2016 / Published: 6 December 2016
Cited by 1 | PDF Full-text (5709 KB) | HTML Full-text | XML Full-text
Abstract
Heterogeneous catalysts have been synthesized by the conjugation of Hoveyda–Grubbs second-generation catalyst with a lipase. The catalytic properties of the organometallic compound in solution were firstly optimized, evaluating the activity of Ru in the ring-closing metathesis of diethyldiallymalonate at 25 °C at different
[...] Read more.
Heterogeneous catalysts have been synthesized by the conjugation of Hoveyda–Grubbs second-generation catalyst with a lipase. The catalytic properties of the organometallic compound in solution were firstly optimized, evaluating the activity of Ru in the ring-closing metathesis of diethyldiallymalonate at 25 °C at different solvents and in the presence of different additives. The best result was found using tetrahydrofuran as a solvent. Some additives such as phenylboronic acid or polyetheneglycol slightly improved the activity of the Ru catalyst whereas others, such as pyridine or dipeptides affected it negatively. The organometallic compound immobilized on functionalized-surface materials activated with boronic acid or epoxy groups (around 50–60 µg per mg support) and showed 50% conversion at 24 h in the ring-closing metathesis. Cross-linked enzyme aggregates (CLEA’s) of the Hoveyda–Grubbs second-generation catalyst with Candida antarctica lipase (CAL-B) were prepared, although low Ru catalyst was found to be translated in low conversion. Therefore, a sol–gel preparation of the Hoveyda–Grubbs second-generation and CAL-B was performed. This catalyst exhibited good activity in the metathesis of diethyldiallymalonate in toluene and in aqueous media. Finally, a new sustainable approach was used by the conjugation lipase–Grubbs in solid phase in aqueous media. Two strategies were used: one using lipase previously covalently immobilized on an epoxy-Sepharose support (hydrophilic matrix) and then conjugated with grubbs; and in the second, the free lipase was incubated with organometallic in aqueous solution and then immobilized on epoxy-Sepharose. The different catalysts showed excellent conversion values in the ring-closing metathesis of diethyldiallymalonate in aqueous media at 25 °C. Full article
(This article belongs to the Special Issue Biomolecules Modification)
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Open AccessArticle Spectroscopic and Kinetic Characterization of Peroxidase-Like π-Cation Radical Pinch-Porphyrin-Iron(III) Reaction Intermediate Models of Peroxidase Enzymes
Molecules 2016, 21(7), 804; doi:10.3390/molecules21070804
Received: 29 April 2016 / Revised: 1 June 2016 / Accepted: 13 June 2016 / Published: 27 June 2016
PDF Full-text (3662 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The spectroscopic and kinetic characterization of two intermediates from the H2O2 oxidation of three dimethyl ester [(proto), (meso), (deuteroporphyrinato) (picdien)]Fe(III) complexes ([FePPPic], [FeMPPic] and [FeDPPic], respectively) pinch-porphyrin peroxidase enzyme models, with s = 5/2 and 3/2 Fe(III) quantum mixed spin
[...] Read more.
The spectroscopic and kinetic characterization of two intermediates from the H2O2 oxidation of three dimethyl ester [(proto), (meso), (deuteroporphyrinato) (picdien)]Fe(III) complexes ([FePPPic], [FeMPPic] and [FeDPPic], respectively) pinch-porphyrin peroxidase enzyme models, with s = 5/2 and 3/2 Fe(III) quantum mixed spin (qms) ground states is described herein. The kinetic study by UV/Vis at λmax = 465 nm showed two different types of kinetics during the oxidation process in the guaiacol test for peroxidases (13 + guaiacol + H2O2 → oxidation guaiacol products). The first intermediate was observed during the first 24 s of the reaction. When the reaction conditions were changed to higher concentration of pinch-porphyrins and hydrogen peroxide only one type of kinetics was observed. Next, the reaction was performed only between pinch-porphyrins-Fe(III) and H2O2, resulting in only two types of kinetics that were developed during the first 0–4 s. After this time a self-oxidation process was observed. Our hypotheses state that the formation of the π-cation radicals, reaction intermediates of the pinch-porphyrin-Fe(III) family with the ligand picdien [N,N’-bis-pyridin-2-ylmethyl-propane-1,3-diamine], occurred with unique kinetics that are different from the overall process and was involved in the oxidation pathway. UV-Vis, 1H-NMR and ESR spectra confirmed the formation of such intermediates. The results in this paper highlight the link between different spectroscopic techniques that positively depict the kinetic traits of artificial compounds with enzyme-like activity. Full article
(This article belongs to the Special Issue Biomolecules Modification)
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Open AccessArticle High Affinity Immobilization of Proteins Using the CrAsH/TC Tag
Molecules 2016, 21(6), 750; doi:10.3390/molecules21060750
Received: 5 May 2016 / Revised: 2 June 2016 / Accepted: 3 June 2016 / Published: 8 June 2016
PDF Full-text (1495 KB) | HTML Full-text | XML Full-text
Abstract
Protein microarrays represent important tools for biomedical analysis. We have recently described the use of the biarsenical-tetracysteine (TC) tag for the preparation of protein microarrays. The unique feature of this tag enables the site-specific immobilization of TC-containing proteins on biarsenical-modified surfaces, resulting in
[...] Read more.
Protein microarrays represent important tools for biomedical analysis. We have recently described the use of the biarsenical-tetracysteine (TC) tag for the preparation of protein microarrays. The unique feature of this tag enables the site-specific immobilization of TC-containing proteins on biarsenical-modified surfaces, resulting in a fluorescence enhancement that allows the direct quantification of the immobilized proteins. Moreover, the reversibility of the binding upon incubation with large quantities of thiols permits the detachment of the proteins from the surface, thereby enabling recovery of the substrate to extend the life time of the slide. Herein, we describe our recent results that further extend the applicability of the CrAsH/TC tag to the fabrication of biochips. With this aim, the immobilization of proteins on surfaces has been investigated using two different spacers and two TC tags, the minimal TC sequence (CCPGCC) and an optimized motif (FLNCCPGCCMEP). While the minimal peptide motif enables a rapid recycling of the slide, the optimized TC sequence reveals an increased affinity due to its greater resistance to displacement by thiols. Moreover, the developed methodology was applied to the immobilization of proteins via on-chip ligation of recombinant protein thioesters. Full article
(This article belongs to the Special Issue Biomolecules Modification)
Open AccessArticle Low-Molecular Weight Polyethylenimine Modified with Pluronic 123 and RGD- or Chimeric RGD-NLS Peptide: Characteristics and Transfection Efficacy of Their Complexes with Plasmid DNA
Molecules 2016, 21(5), 655; doi:10.3390/molecules21050655
Received: 22 February 2016 / Revised: 12 May 2016 / Accepted: 13 May 2016 / Published: 18 May 2016
Cited by 4 | PDF Full-text (2301 KB) | HTML Full-text | XML Full-text
Abstract
To solve the problem of transfection efficiency vs. cytotoxicity and tumor-targeting ability when polyethylenimine (PEI) was used as a nonviral gene delivery vector, new degradable PEI polymers were synthesized via cross-linking low-molecular-weight PEI with Pluronic P123 and then further coupled with a targeting
[...] Read more.
To solve the problem of transfection efficiency vs. cytotoxicity and tumor-targeting ability when polyethylenimine (PEI) was used as a nonviral gene delivery vector, new degradable PEI polymers were synthesized via cross-linking low-molecular-weight PEI with Pluronic P123 and then further coupled with a targeting peptide R4 (RGD) and a bifunctional R11 (RGD-NLS), which were termed as P123-PEI-R4 and P123-PEI-R11, respectively. Agarose gel electrophoresis showed that both P123-PEI-R4 and P123-PEI-R11 efficaciously condense plasmid DNA at a polymer-to-pDNA w/w ratio of 3.0 and 0.4, respectively. The polyplexes were stable in the presence of serum and could protect plasmid DNA against DNaseI. They had uniform spherical nanoparticles with appropriate sizes around 100–280 nm and zeta-potentials about +40 mV. Furthermore, in vitro experiments showed that these polyplexes had lower cytotoxicity at any concentration compared with PEI 25 kDa, thus giving promise to high transfection efficiency as compared with another P123-PEI derivate conjugated with trifunctional peptide RGD-TAT-NLS (P123-PEI-R18). More importantly, compared with the other polymers, P123-PEI-R11 showed the highest transfection efficiency with relatively lower cytotoxicity at any concentration, indicating that the new synthetic polymer P123-PEI-R11 could be used as a safe and efficient gene deliver vector. Full article
(This article belongs to the Special Issue Biomolecules Modification)
Open AccessArticle Regioselective Palmitoylation of 9-(2,3-Dihydroxy- propyl)adenine Catalyzed by a Glycopolymer-enzyme Conjugate
Molecules 2016, 21(5), 648; doi:10.3390/molecules21050648
Received: 28 March 2016 / Revised: 4 May 2016 / Accepted: 10 May 2016 / Published: 16 May 2016
PDF Full-text (1942 KB) | HTML Full-text | XML Full-text
Abstract
The enzymatic regioselective monopalmitoylation of racemic 9-(2,3-dihydroxypropyl)- adenine (DHPA), an approved antiviral agent, has been performed by an immobilized form of Candida antarctica B lipase (CAL-B) using a 4:1 DMF/hexane mixture as the reaction medium. To improve the chemical yield of the desired
[...] Read more.
The enzymatic regioselective monopalmitoylation of racemic 9-(2,3-dihydroxypropyl)- adenine (DHPA), an approved antiviral agent, has been performed by an immobilized form of Candida antarctica B lipase (CAL-B) using a 4:1 DMF/hexane mixture as the reaction medium. To improve the chemical yield of the desired monopalmitoylation reaction, solid-phase chemical modifications of the lipase were evaluated. The reaction yield was successfully increased obtaining 100% product after a second treatment of the product solution with fresh immobilised chemically glycosylated-CAL-B. Full article
(This article belongs to the Special Issue Biomolecules Modification)
Open AccessArticle A Computational Study of the Mechanism of Succinimide Formation in the Asn–His Sequence: Intramolecular Catalysis by the His Side Chain
Molecules 2016, 21(3), 327; doi:10.3390/molecules21030327
Received: 30 January 2016 / Revised: 3 March 2016 / Accepted: 4 March 2016 / Published: 9 March 2016
Cited by 1 | PDF Full-text (1127 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The rates of deamidation reactions of asparagine (Asn) residues which occur spontaneously and nonenzymatically in peptides and proteins via the succinimide intermediate are known to be strongly dependent on the nature of the following residue on the carboxyl side (Xxx). The formation of
[...] Read more.
The rates of deamidation reactions of asparagine (Asn) residues which occur spontaneously and nonenzymatically in peptides and proteins via the succinimide intermediate are known to be strongly dependent on the nature of the following residue on the carboxyl side (Xxx). The formation of the succinimide intermediate is by far the fastest when Xxx is glycine (Gly), the smallest amino acid residue, while extremely slow when Xxx is bulky such as isoleucine (Ile) and valine (Val). In this respect, it is very interesting to note that the succinimide formation is definitely accelerated when Xxx is histidine (His) despite its large size. In this paper, we computationally show that, in an Asn–His sequence, the His side-chain imidazole group (in the neutral Nε-protonated form) can specifically catalyze the formation of the tetrahedral intermediate in the succinimide formation by mediating a proton transfer. The calculations were performed for Ace−Asn−His−Nme (Ace = acetyl, Nme = methylamino) as a model compound by the density functional theory with the B3LYP functional and the 6-31+G(d,p) basis set. We also show that the tetrahedral intermediate, once protonated at the NH2 group, easily releases an ammonia molecule to give the succinimide species. Full article
(This article belongs to the Special Issue Biomolecules Modification)
Open AccessArticle Incorporation of Amino Acids with Long-Chain Terminal Olefins into Proteins
Molecules 2016, 21(3), 287; doi:10.3390/molecules21030287
Received: 16 January 2016 / Revised: 23 February 2016 / Accepted: 25 February 2016 / Published: 29 February 2016
Cited by 3 | PDF Full-text (1535 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The increasing need for site-specific protein decorations that mimic natural posttranslational modifications requires access to a variety of noncanonical amino acids with moieties enabling bioorthogonal conjugation chemistry. Here we present the incorporation of long-chain olefinic amino acids into model proteins with rational variants
[...] Read more.
The increasing need for site-specific protein decorations that mimic natural posttranslational modifications requires access to a variety of noncanonical amino acids with moieties enabling bioorthogonal conjugation chemistry. Here we present the incorporation of long-chain olefinic amino acids into model proteins with rational variants of pyrrolysyl-tRNA synthetase (PylRS). Nε-heptenoyl lysine was incorporated for the first time using the known promiscuous variant PylRS(Y306A/Y384F), and Nε-pentenoyl lysine was incorporated in significant yields with the novel variant PylRS(C348A/Y384F). This is the only example of rational modification at position C348 to enlarge the enzyme’s binding pocket. Furthermore, we demonstrate the feasibility of our chosen amino acids in the thiol-ene conjugation reaction with a thiolated polysaccharide. Full article
(This article belongs to the Special Issue Biomolecules Modification)
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