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25th Anniversary of Molecules—Hot Topics in Bioorganic Chemistry

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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 2020) | Viewed by 38330

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Special Issue Editors

Prof. Dr. Mark von Itzstein

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Guest Editor

Institute for Glycomics, Gold Coast Campus, Griffith University, Gold Coast, QLD 4222, Australia
Interests: drug discovery; glycobiology; chemoenzymatic transformations; chemical virology; infectious diseases; cancer
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Harri Lönnberg

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Guest Editor

Department of Chemistry, University of Turku, 20014 Turku, Finland
Interests: kinetic studies on chemical models of ribonucleases and ribozymes; synthesis and application of oligonucleotide conjugates; pro-drug strategies for phosphoester drugs; novel approaches for medium scale synthesis of oligonucleotides
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In 2020, we are celebrating the 25th anniversary of our journal Molecules. To date, the journal has published more than 20,000 papers, and the journal website attracts 115,000 monthly visits and more than 395,000 monthly page views. We would like to express our sincerest thanks to our readers, innumerable authors, anonymous peer reviewers, editors, and all the people working in some way for the journal who have made substantial contributions for years. Without your support, we would never have made it.

To mark this important milestone, a Special Issue entitled “25th Anniversary of Molecules—Hot Topics in Bioorganic Chemistry” is being launched. This Special Issue will collect communications, research articles, and high-quality review papers in the bioorganic research fields. We kindly encourage all research groups working in various bioorganic chemistry areas to make contributions to this Special Issue.

Prof. Mark von Itzstein
Prof. Harri Lönnberg
Guest Editors

Manuscript Submission Information

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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.

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Published Papers (7 papers)

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Research

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23 pages, 9544 KiB

Open AccessArticle

Phosphorylation of Phylogenetically Conserved Amino Acid Residues Confines HBx within Different Cell Compartments of Human Hepatocarcinoma Cells

by Cristian Prieto, Juan Montecinos, Gustavo Jiménez, Constanza Riquelme, Daniel Garrido, Sergio Hernández, Alejandra Loyola and Rodrigo A. Villanueva

Molecules 2021, 26(5), 1254; https://doi.org/10.3390/molecules26051254 - 26 Feb 2021

Cited by 6 | Viewed by 3317

Abstract

Hepatitis B virus (HBV) is a circular, and partially double-stranded DNA virus. Upon infection, the viral genome is translocated into the cell nucleus, generating the covalently closed circular DNA (cccDNA) intermediate, and forming a mini chromosome. HBV HBx is a small protein displaying multiple roles in HBV-infected cells, and in different subcellular locations. In the nucleus, the HBx protein is required to initiate and maintain viral transcription from the viral mini chromosome. In contrast, HBx also functions in the cytoplasm, where it is able to alter multiple cellular functions such as mitochondria metabolism, apoptosis and signal transduction pathways. It has been reported that in cultured cells, at low expression levels, the HBx protein is localized in the nucleus, whereas at high expression levels, it accumulates in the cytoplasm. This dynamic subcellular distribution of HBx might be essential to exert its multiple roles during viral infection. However, the mechanism that regulates different subcellular localizations of the HBx protein is unknown. We have previously taken a bioinformatics approach to investigate whether HBx might be regulated via post-translational modification, and we have proposed that the multiple nucleocytoplasmic functions of HBx might be regulated by an evolutionarily conserved mechanism via phosphorylation. In the current study, phylogenetically conserved amino acids of HBx with a high potential of phosphorylation were targeted for site-directed mutagenesis. Two conserved serine (Ser25 and Ser41), and one conserved threonine (Thr81) amino acids were replaced by either alanine or aspartic acid residues to simulate an unphosphorylated or phosphorylated state, respectively. Human hepatoma cells were transfected with increasing amounts of the HBx DNA constructs, and the cells were analyzed by fluorescence microscopy. Together, our results show that the nucleocytoplasmic distribution of the HBx protein could be regulated by phosphorylation since some of the modified proteins were mainly confined to distinct subcellular compartments. Remarkably, both HBx Ser41A, and HBx Thr81D proteins were predominantly localized within the nuclear compartment throughout the different expression levels of HBx mutants. Full article

(This article belongs to the Special Issue 25th Anniversary of Molecules—Hot Topics in Bioorganic Chemistry)

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14 pages, 1467 KiB

Open AccessArticle

Optimization of the Microwave Assisted Glycosylamines Synthesis Based on a Statistical Design of Experiments Approach

by Jo Sing Julia Tang, Kristin Schade, Lucas Tepper, Sany Chea, Gregor Ziegler and Ruben R. Rosencrantz

Molecules 2020, 25(21), 5121; https://doi.org/10.3390/molecules25215121 - 4 Nov 2020

Cited by 7 | Viewed by 2527

Abstract

Glycans carry a vast range of functions in nature. Utilizing their properties and functions in form of polymers, coatings or glycan derivatives for various applications makes the synthesis of modified glycans crucial. Since amines are easy to modify for subsequent reactions, we investigated regioselective amination conditions of different saccharides. Amination reactions were performed according to Kochetkov and Likhoshertov and accelerated by microwave irradiation. We optimized the synthesis of glycosylamines for N-acetyl-d-galactosamine, d-lactose, d-glucuronic acid and l-(−)-fucose using the design of experiments (DoE) approach. DoE enables efficient optimization with limited number of experimental data. A DoE software generated a set of experiments where reaction temperature, concentration of carbohydrate, nature of aminating agent and solvent were investigated. We found that the synthesis of glycosylamines significantly depends on the nature of the carbohydrate and on the reaction temperature. There is strong indication that high temperatures are favored for the amination reaction. Full article

(This article belongs to the Special Issue 25th Anniversary of Molecules—Hot Topics in Bioorganic Chemistry)

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12 pages, 1844 KiB

Open AccessArticle

LncMirNet: Predicting LncRNA–miRNA Interaction Based on Deep Learning of Ribonucleic Acid Sequences

by Sen Yang, Yan Wang, Yu Lin, Dan Shao, Kai He and Lan Huang

Molecules 2020, 25(19), 4372; https://doi.org/10.3390/molecules25194372 - 23 Sep 2020

Cited by 49 | Viewed by 7620

Abstract

Long non-coding RNA (LncRNA) and microRNA (miRNA) are both non-coding RNAs that play significant regulatory roles in many life processes. There is cumulating evidence showing that the interaction patterns between lncRNAs and miRNAs are highly related to cancer development, gene regulation, cellular metabolic process, etc. Contemporaneously, with the rapid development of RNA sequence technology, numerous novel lncRNAs and miRNAs have been found, which might help to explore novel regulated patterns. However, the increasing unknown interactions between lncRNAs and miRNAs may hinder finding the novel regulated pattern, and wet experiments to identify the potential interaction are costly and time-consuming. Furthermore, few computational tools are available for predicting lncRNA–miRNA interaction based on a sequential level. In this paper, we propose a hybrid sequence feature-based model, LncMirNet (lncRNA–miRNA interactions network), to predict lncRNA–miRNA interactions via deep convolutional neural networks (CNN). First, four categories of sequence-based features are introduced to encode lncRNA/miRNA sequences including k-mer (k = 1, 2, 3, 4), composition transition distribution (CTD), doc2vec, and graph embedding features. Then, to fit the CNN learning pattern, a histogram-dd method is incorporated to fuse multiple types of features into a matrix. Finally, LncMirNet attained excellent performance in comparison with six other state-of-the-art methods on a real dataset collected from lncRNASNP2 via five-fold cross validation. LncMirNet increased accuracy and area under curve (AUC) by more than 3%, respectively, over that of the other tools, and improved the Matthews correlation coefficient (MCC) by more than 6%. These results show that LncMirNet can obtain high confidence in predicting potential interactions between lncRNAs and miRNAs. Full article

(This article belongs to the Special Issue 25th Anniversary of Molecules—Hot Topics in Bioorganic Chemistry)

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21 pages, 3644 KiB

Open AccessReview

Recent Advances in the Chemical Biology of N-Glycans

by Asuka Shirakawa, Yoshiyuki Manabe and Koichi Fukase

Molecules 2021, 26(4), 1040; https://doi.org/10.3390/molecules26041040 - 16 Feb 2021

Cited by 16 | Viewed by 5784

Abstract

Asparagine-linked N-glycans on proteins have diverse structures, and their functions vary according to their structures. In recent years, it has become possible to obtain high quantities of N-glycans via isolation and chemical/enzymatic/chemoenzymatic synthesis. This has allowed for progress in the elucidation of N-glycan functions at the molecular level. Interaction analyses with lectins by glycan arrays or nuclear magnetic resonance (NMR) using various N-glycans have revealed the molecular basis for the recognition of complex structures of N-glycans. Preparation of proteins modified with homogeneous N-glycans revealed the influence of N-glycan modifications on protein functions. Furthermore, N-glycans have potential applications in drug development. This review discusses recent advances in the chemical biology of N-glycans. Full article

(This article belongs to the Special Issue 25th Anniversary of Molecules—Hot Topics in Bioorganic Chemistry)

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46 pages, 4618 KiB

Open AccessReview

Benefits and Detriments of Gadolinium from Medical Advances to Health and Ecological Risks

by Colin Unruh, Nicolas Van Bavel, Max Anikovskiy and Elmar J. Prenner

Molecules 2020, 25(23), 5762; https://doi.org/10.3390/molecules25235762 - 7 Dec 2020

Cited by 27 | Viewed by 7086

Abstract

Gadolinium (Gd)-containing chelates have been established as diagnostics tools. However, extensive use in magnetic resonance imaging has led to increased Gd levels in industrialized parts of the world, adding to natural occurrence and causing environmental and health concerns. A vast amount of data shows that metal may accumulate in the human body and its deposition has been detected in organs such as brain and liver. Moreover, the disease nephrogenic systemic fibrosis has been linked to increased Gd³⁺ levels. Investigation of Gd³⁺ effects at the cellular and molecular levels mostly revolves around calcium-dependent proteins, since Gd³⁺ competes with calcium due to their similar size; other reports focus on interaction of Gd³⁺ with nucleic acids and carbohydrates. However, little is known about Gd³⁺ effects on membranes; yet some results suggest that Gd³⁺ interacts strongly with biologically-relevant lipids (e.g., brain membrane constituents) and causes serious structural changes including enhanced membrane rigidity and propensity for lipid fusion and aggregation at much lower concentrations than other ions, both toxic and essential. This review surveys the impact of the anthropogenic use of Gd emphasizing health risks and discussing debilitating effects of Gd³⁺ on cell membrane organization that may lead to deleterious health consequences. Full article

(This article belongs to the Special Issue 25th Anniversary of Molecules—Hot Topics in Bioorganic Chemistry)

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23 pages, 3744 KiB

Open AccessReview

Vibrational Spectroscopy for Identification of Metabolites in Biologic Samples

by Kevin V. Hackshaw, Joseph S. Miller, Didem P. Aykas and Luis Rodriguez-Saona

Molecules 2020, 25(20), 4725; https://doi.org/10.3390/molecules25204725 - 15 Oct 2020

Cited by 43 | Viewed by 6341

Abstract

Vibrational spectroscopy (mid-infrared (IR) and Raman) and its fingerprinting capabilities offer rapid, high-throughput, and non-destructive analysis of a wide range of sample types producing a characteristic chemical “fingerprint” with a unique signature profile. Nuclear magnetic resonance (NMR) spectroscopy and an array of mass spectrometry (MS) techniques provide selectivity and specificity for screening metabolites, but demand costly instrumentation, complex sample pretreatment, are labor-intensive, require well-trained technicians to operate the instrumentation, and are less amenable for implementation in clinics. The potential for vibration spectroscopy techniques to be brought to the bedside gives hope for huge cost savings and potential revolutionary advances in diagnostics in the clinic. We discuss the utilization of current vibrational spectroscopy methodologies on biologic samples as an avenue towards rapid cost saving diagnostics. Full article

(This article belongs to the Special Issue 25th Anniversary of Molecules—Hot Topics in Bioorganic Chemistry)

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50 pages, 3495 KiB

Open AccessReview

Participation of MicroRNAs in the Treatment of Cancer with Phytochemicals

by Seung Wan Son, Han Yeoung Lee, Sokviseth Moeng, Hyo Jeong Kuh, Soo Young Choi and Jong Kook Park

Molecules 2020, 25(20), 4701; https://doi.org/10.3390/molecules25204701 - 14 Oct 2020

Cited by 12 | Viewed by 4225

Abstract

Cancer is a global health concern and one of the main causes of disease-related death. Even with considerable progress in investigations on cancer therapy, effective anti-cancer agents and regimens have thus far been insufficient. There has been compelling evidence that natural phytochemicals and their derivatives have potent anti-cancer activities. Plant-based anti-cancer agents, such as etoposide, irinotecan, paclitaxel, and vincristine, are currently being applied in medical treatments for patients with cancer. Further, the efficacy of plenty of phytochemicals has been evaluated to discover a promising candidate for cancer therapy. For developing more effective cancer therapy, it is required to apprehend the molecular mechanism deployed by natural compounds. MicroRNAs (miRNAs) have been realized to play a pivotal role in regulating cellular signaling pathways, affecting the efficacy of therapeutic agents in cancer. This review presents a feature of phytochemicals with anti-cancer activity, focusing mainly on the relationship between phytochemicals and miRNAs, with insights into the role of miRNAs as the mediators and the regulators of anti-cancer effects of phytochemicals. Full article

(This article belongs to the Special Issue 25th Anniversary of Molecules—Hot Topics in Bioorganic Chemistry)

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