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

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 8976

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Prof. Dr. Riccardo Spaccini

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Department of Agricultural Sciences, University of Napoli Federico II, Portici, Italy
Interests: biomasse recycling; structural activity relationship; molecular characterization
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Dear Colleagues,

This Special Issue of Molecules is dedicated to recent advances in bioorganic chemistry research areas and comprises a diverse selection of exclusive papers from the Editorial Board Members (EBMs) of the Bioorganic Chemistry Section. It aims to highlight recent interesting investigations conducted in the laboratories of our section’s EBMs and display our section as an attractive open-access publishing platform for bioorganic chemistry research data.

Prof. Dr. Riccardo Spaccini
Guest Editor

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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.

Published Papers (5 papers)

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Research

11 pages, 2710 KiB

Open AccessArticle

Molecular Mechanisms of Aggregation of Canine SOD1 E40K Amyloidogenic Mutant Protein

by Kento Wakayama, Shintaro Kimura, Yui Kobatake, Hiroaki Kamishina, Naohito Nishii, Satoshi Takashima, Ryo Honda and Yuji O. Kamatari

Molecules 2023, 28(1), 156; https://doi.org/10.3390/molecules28010156 - 24 Dec 2022

Viewed by 1479

Abstract

Canine degenerative myelopathy (DM) is a human amyotrophic lateral sclerosis (ALS)-like neurodegenerative disease. It is a unique, naturally occurring animal model of human ALS. Canine DM is associated with the aggregation of canine superoxide dismutase 1 (cSOD1), which is similar to human ALS. Almost 100% of cases in dogs are familial, and the E40K mutation in cSOD1 is a major causative mutation of DM. Therefore, it is important to understand the molecular mechanisms underlying cSOD1(E40K) aggregation. To address this, we first analyzed the structural model of wild type cSOD1. Interactions were evident between amino acid E40 and K91. Therefore, the mutation at residue E40 causes loss of the interaction and may destabilize the native structure of cSOD1. Differential scanning fluorimetry revealed that the E40K mutant was less stable than the wild type. Moreover, stability could be recovered by the E40K and K91E double mutation. Acceleration of amyloid fibril formation in vitro and aggregate formation in cells of cSOD1(E40K) was also suppressed by the introduction of this double mutation in thioflavin T fluorescence assay results and in transfectant cells, respectively. These results clearly show the importance of the interaction between amino acid residues E40 and K91 in cSOD1 for the stability of the native structure and aggregation. Full article

(This article belongs to the Special Issue Exclusive Papers of the Editorial Board Members (EBMs) of the Bioorganic Chemistry Section of Molecules (2022))

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15 pages, 6128 KiB

Open AccessArticle

Hydrogels from the Assembly of SAA/Elastin-Inspired Peptides Reveal Non-Canonical Nanotopologies

by Alessandra Scelsi, Brigida Bochicchio, Andrew M. Smith, Antonio Laezza, Alberto Saiani and Antonietta Pepe

Molecules 2022, 27(22), 7901; https://doi.org/10.3390/molecules27227901 - 15 Nov 2022

Viewed by 881

Abstract

Peptide-based hydrogels are of great interest in the biomedical field according to their biocompatibility, simple structure and tunable properties via sequence modification. In recent years, multicomponent assembly of peptides have expanded the possibilities to produce more versatile hydrogels, by blending gelating peptides with different type of peptides to add new features. In the present study, the assembly of gelating P5 peptide SFFSF blended with P21 peptide, SFFSFGVPGVGVPGVGSFFSF, an elastin-inspired peptides or, alternatively, with FF dipeptide, was investigated by oscillatory rheology and different microscopy techniques in order to shed light on the nanotopologies formed by the self-assembled peptide mixtures. Our data show that, depending on the added peptides, cooperative or disruptive assembly can be observed giving rise to distinct nanotopologies to which correspond different mechanical properties that could be exploited to fabricate materials with desired properties. Full article

(This article belongs to the Special Issue Exclusive Papers of the Editorial Board Members (EBMs) of the Bioorganic Chemistry Section of Molecules (2022))

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15 pages, 1648 KiB

Open AccessFeature PaperArticle

Production and Digestibility Studies of β-Galactosyl Xylitol Derivatives Using Heterogeneous Catalysts of LacA β-Galactosidase from Lactobacillus Plantarum WCFS1

by Eduardo Rosado, Paloma Delgado-Fernández, Blanca de las Rivas, Rosario Muñoz, Francisco Javier Moreno, Nieves Corzo and Cesar Mateo

Molecules 2022, 27(4), 1235; https://doi.org/10.3390/molecules27041235 - 12 Feb 2022

Cited by 1 | Viewed by 1752

Abstract

The synthesis of β-galactosyl xylitol derivatives using immobilized LacA β-galactosidase from Lactobacillus plantarum WCFS1 is presented. These compounds have the potential to replace traditional sugars by their properties as sweetener and taking the advantages of a low digestibility. The enzyme was immobilized on different supports, obtaining immobilized preparations with different activity and stability. The immobilization on agarose-IDA-Zn-CHO in the presence of galactose allowed for the conserving of 78% of the offered activity. This preparation was 3.8 times more stable than soluble. Since the enzyme has polyhistidine tags, this support allowed the immobilization, purification and stabilization in one step. The immobilized preparation was used in synthesis obtaining two main products and a total of around 68 g/L of β-galactosyl xylitol derivatives and improving the synthesis/hydrolysis ratio by around 30% compared to that of the soluble enzyme. The catalyst was recycled 10 times, preserving an activity higher than 50%. The in vitro intestinal digestibility of the main β-galactosyl xylitol derivatives was lower than that of lactose, being around 6 and 15% for the galacto-xylitol derivatives compared to 55% of lactose after 120 min of digestion. The optimal amount immobilized constitutes a very useful tool to synthetize β-galactosyl xylitol derivatives since it can be used as a catalyst with high yield and being recycled for at least 10 more cycles. Full article

(This article belongs to the Special Issue Exclusive Papers of the Editorial Board Members (EBMs) of the Bioorganic Chemistry Section of Molecules (2022))

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12 pages, 2060 KiB

Open AccessArticle

Recognition of Dimethylarginine Analogues by Tandem Tudor Domain Protein Spindlin1

by Miriam R. B. Porzberg, Laust Moesgaard, Catrine Johansson, Udo Oppermann, Jacob Kongsted and Jasmin Mecinović

Molecules 2022, 27(3), 983; https://doi.org/10.3390/molecules27030983 - 01 Feb 2022

Cited by 2 | Viewed by 1952

Abstract

Epigenetic readout of the combinatorial posttranslational modification comprised of trimethyllysine and asymmetric dimethylarginine (H3K4me3R8me2a) takes place via biomolecular recognition of tandem Tudor-domain-containing protein Spindlin1. Through comparative thermodynamic data and molecular dynamics simulations, we sought to explore the binding scope of asymmetric dimethylarginine mimics by Spindlin1. Herein, we provide evidence that the biomolecular recognition of H3K4me2R8me2a is not significantly affected when R8me2a is replaced by dimethylarginine analogues, implying that the binding of K4me3 provides the major binding contribution. High-energy water molecules inside both aromatic cages of the ligand binding sites contribute to the reader–histone association upon displacement by histone peptide, with the K4me3 hydration site being lower in free energy due to a flip of Trp151. Full article

(This article belongs to the Special Issue Exclusive Papers of the Editorial Board Members (EBMs) of the Bioorganic Chemistry Section of Molecules (2022))

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15 pages, 3926 KiB

Open AccessFeature PaperArticle

A Chromo-Fluorogenic Naphthoquinolinedione-Based Probe for Dual Detection of Cu²⁺ and Its Use for Various Water Samples

by Ashwani Kumar, Subodh Kumar and Pil Seok Chae

Molecules 2022, 27(3), 785; https://doi.org/10.3390/molecules27030785 - 25 Jan 2022

Cited by 7 | Viewed by 2450

Abstract

The presence of an abnormal amount of Cu²⁺ in the human body causes various health issues. In the current study, we synthesized a new naphthoquinolinedione-based probe (probe 1) to monitor Cu²⁺ in different water systems, such as tap water, lakes, and drain water. Two triazole units were introduced into the probe via a click reaction to increase the binding affinity to a metal ion. In day-light, probe 1 dissolved in a mixed solvent system (HEPES: EtOH = 1:4) showed a vivid color change from light greenish-yellow to pink in the presence of only Cu²⁺ among various metal ions. In addition, the green luminescence and fluorescence emission of the probe were effectively bleached out immediately after Cu²⁺ addition. The limit of detection (LOD) of the probe was 0.5 µM when a ratio-metric method was used for metal ion detection. The fluorescence titration data of the probe with Cu²⁺ showed a calculated LOD of 41.5 pM. Hence, probe 1 possesses the following dual response toward Cu²⁺ detection: color change and fluorescence quenching. Probe 1 was also useful for detecting Cu²⁺ spiked in tap/lake water as well as the cytoplasm of live HeLa cells. The current system was investigated using ultraviolet-visible and fluorescence spectroscopy as well as density functional theory calculations (DFT). Full article

(This article belongs to the Special Issue Exclusive Papers of the Editorial Board Members (EBMs) of the Bioorganic Chemistry Section of Molecules (2022))

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