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The 30th Anniversary of Molecules—Recent Advances in Chemical Biology
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The 30th Anniversary of Molecules—Recent Advances in Chemical Biology

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

Deadline for manuscript submissions: 31 December 2025 | Viewed by 2210

Special Issue Editors

Prof. Dr. Akinori Kuzuya

E-Mail Website
Guest Editor
Organization for Research and Development of Innovative Science and Technology (ORDIST), Kansai University, Suita 564-8680, Osaka, Japan
Interests: nucleic acid chemistry; DNA nanotechnology; supramolecular chemistry; molecular machines; molecular robotics; molecular technology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Daisuke Miyoshi

E-Mail Website1 Website2
Guest Editor
Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
Interests: G-quadruplex; i-motif; molecular crowding; phase separation; thermodynamics; kinetics; aptamer; ligand
Special Issues, Collections and Topics in MDPI journals
Dr. Camila C. Portugal

E-Mail Website
Guest Editor
Institute of Research and Innovation in Health (i3S), Institute for Molecular and Cell Biology (IBMC), University of Porto, Porto, Portugal
Interests: neuroscience; microglia; oxidative stress; vitamin C; Alzheimer's disease
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In 2025, we will be celebrating the 30th anniversary of our journal Molecules. To date, the journal has published more than 50,000 papers. Molecules has carved out a notable space in the chemical literature, with an Impact Factor of 4.2 (2023) and a 5-Year Impact Factor of 4.6 (2023). Our sincerest thanks go to our readers, innumerable authors, anonymous peer reviewers, Editors, and all the people working for the journal in some capacity. Without your help, we would never have achieved this.

To mark this important milestone, a Special Issue entitled “The 30th Anniversary of Molecules—Recent Advances in Chemical Biology” is being launched. This Special Issue collects communications, full papers, and high-quality papers in the chemical biology fields. We kindly invite and encourage all research groups covering various areas of chemical biology to contribute to this Special Issue.

Prof. Dr. Akinori Kuzuya
Prof. Dr. Daisuke Miyoshi
Dr. Camila C. Portugal
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 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 chemistry
  • peptides
  • nucleic acids
  • proteins
  • analytical methods
  • chemical inhibitors
  • chemical probe
  • ubiquitination
  • structure-activity relationship

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (5 papers)

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Research

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20 pages, 2766 KiB  
Article
Liquid Chromatography-Tandem Mass Spectrometry Method Development and Validation for the Determination of a New Mitochondrial Antioxidant in Mouse Liver and Cerebellum, Employing Advanced Chemometrics
by Anthi Panara, Dimitra Biliraki, Markus Nussbaumer, Michaela D. Filiou, Nikolaos S. Thomaidis, Ioannis K. Kostakis and Evagelos Gikas
Molecules 2025, 30(9), 1900; https://doi.org/10.3390/molecules30091900 - 24 Apr 2025
Viewed by 206
Abstract
Anxiety and stress-related disorders affect all ages in all geographical areas. As high anxiety and chronic stress result in the modulation of mitochondrial pathways, intensive research is being carried out on pharmaceutical interventions that alleviate pertinent symptomatology. Therefore, innovative approaches being currently pursued [...] Read more.
Anxiety and stress-related disorders affect all ages in all geographical areas. As high anxiety and chronic stress result in the modulation of mitochondrial pathways, intensive research is being carried out on pharmaceutical interventions that alleviate pertinent symptomatology. Therefore, innovative approaches being currently pursued include substances that target mitochondria bearing an antioxidant moiety. In this study, a newly synthesized antioxidant consisting of triphenylphosphine (TPP), a six-carbon alkyl spacer, and hydroxytyrosol (HT) was administered orally to mice via drinking water. Cerebellum and liver samples were collected and analyzed using ultra-high-performance liquid chromatography-tandem triple quadrupole mass spectrometry (UHPLC-MS/MS) to assess the levels of TPP-HT in the respective tissues to evaluate in vivo administration efficacy. Sample preparation included extraction with appropriate solvents and a preconcentration step to achieve the required sensitivity. Both methods were validated in terms of selectivity, linearity, accuracy, and limits of detection and quantification. Additionally, a workflow for evaluating and statistically summarizing multiple fortified calibration curves was devised. TPP-HT penetrates the blood–brain barrier (BBB), with a level of 11.5 ng g−1 quantified in the cerebellum, whereas a level of 4.8 ng g−1 was detected in the liver, highlighting the plausibility of orally administering TPP-HT to achieve mitochondrial targeting. Full article
(This article belongs to the Special Issue The 30th Anniversary of Molecules—Recent Advances in Chemical Biology)
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28 pages, 4465 KiB  
Article
The Absence of a Very Long Chain Fatty Acid (VLCFA) in Lipid A Impairs Agrobacterium fabrum Plant Infection and Biofilm Formation and Increases Susceptibility to Environmental Stressors
by Iwona Komaniecka, Kamil Żebracki, Andrzej Mazur, Katarzyna Suśniak, Anna Sroka-Bartnicka, Anita Swatek and Adam Choma
Molecules 2025, 30(5), 1080; https://doi.org/10.3390/molecules30051080 - 26 Feb 2025
Viewed by 515
Abstract
The Agrobacterium fabrum C58 is a phytopathogen able to infect numerous species of cultivated and ornamental plants. During infection, bacteria genetically transform plant cells and induce the formation of tumours at the site of invasion. Bacterial cell wall components play a crucial role [...] Read more.
The Agrobacterium fabrum C58 is a phytopathogen able to infect numerous species of cultivated and ornamental plants. During infection, bacteria genetically transform plant cells and induce the formation of tumours at the site of invasion. Bacterial cell wall components play a crucial role in the infection process. Lipopolysaccharide is the main component of Gram-negative bacteria’s outer leaflet of outer membrane. Its lipophilic part, called lipid A, is built of di-glucosamine backbone substituted with a specific set of 3-hydroxyl fatty acids. A. fabrum incorporates a very long chain hydroxylated fatty acid (VLCFA), namely 27-hydroxyoctacosanoic acid (28:0-(27OH)), into its lipid A. A. fabrum C58 mutants deprived of this component due to mutation in the VLCFA’s genomic region, have been characterised. High-resolution mass spectrometry was used to establish acylation patterns in the mutant’s lipid A preparations. The physiological properties of mutants, as well as their motility, ability to biofilm formation and plant infectivity, were tested. The results obtained showed that the investigated mutants were more sensitive to environmental stress conditions, formed a weakened biofilm, exhibited impaired swimming motility and were less effective in infecting tomato seedlings compared to the wild strain. Full article
(This article belongs to the Special Issue The 30th Anniversary of Molecules—Recent Advances in Chemical Biology)
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Review

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52 pages, 1634 KiB  
Review
Early-Stage Pancreatic Cancer Diagnosis: Serum Biomarkers and the Potential for Aptamer-Based Biosensors
by Weisi He, Jingyu Cui, Xue-Yan Wang, Ryan H. P. Siu and Julian A. Tanner
Molecules 2025, 30(9), 2012; https://doi.org/10.3390/molecules30092012 - 30 Apr 2025
Viewed by 31
Abstract
Pancreatic cancer has a high mortality rate, and both the incidence and mortality are continuing to increase in many countries globally. The poor prognosis of pancreatic cancer is in part due to the challenges in early diagnosis. Improving early-stage pancreatic cancer diagnosis would [...] Read more.
Pancreatic cancer has a high mortality rate, and both the incidence and mortality are continuing to increase in many countries globally. The poor prognosis of pancreatic cancer is in part due to the challenges in early diagnosis. Improving early-stage pancreatic cancer diagnosis would improve survival outcomes. Aptamer-based biosensors provide an alternative technological approach for the analysis of serum biomarkers with several potential advantages. This review summarizes the major pancreatic cancer serum biomarkers, as well as discusses recent progress in biomarker exploration and aptasensor development. Here, we review both established and novel serum biomarkers identified recently, emphasizing their potential for early-stage pancreatic cancer diagnosis. We also propose strategies for further expanding multiplex biomarker panels beyond the established CA19-9 biomarker to enhance diagnostic performance. We discuss technological advancements in aptamer-based sensors for pancreatic cancer-related biomarkers over the last decade. Optical and electrochemical sensors are highlighted as two primary modalities in aptasensor design, each offering unique advantages. Finally, we propose steps towards clinical application using aptamer-based sensors with multiplexed biomarker detection for improved pancreatic cancer diagnostics. Full article
(This article belongs to the Special Issue The 30th Anniversary of Molecules—Recent Advances in Chemical Biology)
23 pages, 2234 KiB  
Review
Recent Progress and Potential of G4 Ligands in Cancer Immunotherapy
by Jiahui Lin, Zhu Gong, Yingyue Lu, Jiongheng Cai, Junjie Zhang, Jiaheng Tan, Zhishu Huang and Shuobin Chen
Molecules 2025, 30(8), 1805; https://doi.org/10.3390/molecules30081805 - 17 Apr 2025
Viewed by 329
Abstract
G-quadruplex (G4) structures are non-canonical nucleic acid conformations that play crucial roles in gene regulation, DNA replication, and telomere maintenance. Recent studies have highlighted G4 ligands as promising anticancer agents due to their ability to modulate oncogene expression and induce DNA damage. By [...] Read more.
G-quadruplex (G4) structures are non-canonical nucleic acid conformations that play crucial roles in gene regulation, DNA replication, and telomere maintenance. Recent studies have highlighted G4 ligands as promising anticancer agents due to their ability to modulate oncogene expression and induce DNA damage. By stabilizing G4 structures, these ligands affect tumor progression. Additionally, they have been implicated in tumor immunity modulation, particularly through the activation and immunogenic cell death induction of the cyclic GMP–AMP synthase (cGAS)–stimulator of interferon genes (STING) signaling pathway. Moreover, their disruption of telomere maintenance and regulation of key oncogenes, such as c-MYC and KRAS, position them as candidates for immune-based therapeutic interventions. Despite their therapeutic potential, challenges remain in optimizing their clinical applications, particularly in patient stratification and elucidating their immunomodulatory effects. This review provides a comprehensive overview of the mechanisms through which G4 ligands influence tumor progression and immune regulation, highlighting their potential role in future cancer immunotherapy strategies. Full article
(This article belongs to the Special Issue The 30th Anniversary of Molecules—Recent Advances in Chemical Biology)
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13 pages, 1772 KiB  
Review
Chemical Conversations
by Jana Michailidu, Olga Maťátková, Alena Čejková and Jan Masák
Molecules 2025, 30(3), 431; https://doi.org/10.3390/molecules30030431 - 21 Jan 2025
Viewed by 751
Abstract
Among living organisms, higher animals primarily use a combination of vocal and non-verbal cues for communication. In other species, however, chemical signaling holds a central role. The chemical and biological activity of the molecules produced by the organisms themselves and the existence of [...] Read more.
Among living organisms, higher animals primarily use a combination of vocal and non-verbal cues for communication. In other species, however, chemical signaling holds a central role. The chemical and biological activity of the molecules produced by the organisms themselves and the existence of receptors/targeting sites that allow recognition of such molecules leads to various forms of responses by the producer and recipient organisms and is a fundamental principle of such communication. Chemical language can be used to coordinate processes within one species or between species. Chemical signals are thus information for other organisms, potentially inducing modification of their behavior. Additionally, this conversation is influenced by the external environment in which organisms are found. This review presents examples of chemical communication among microorganisms, between microorganisms and plants, and between microorganisms and animals. The mechanisms and physiological importance of this communication are described. Chemical interactions can be both cooperative and antagonistic. Microbial chemical signals usually ensure the formation of the most advantageous population phenotype or the disadvantage of a competitive species in the environment. Between microorganisms and plants, we find symbiotic (e.g., in the root system) and parasitic relationships. Similarly, mutually beneficial relationships are established between microorganisms and animals (e.g., gastrointestinal tract), but microorganisms also invade and disrupt the immune and nervous systems of animals. Full article
(This article belongs to the Special Issue The 30th Anniversary of Molecules—Recent Advances in Chemical Biology)
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