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Biomolecules
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Molecular Profiling and Identification of Molecular Signatures Associated with Natural...
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Molecular Profiling and Identification of Molecular Signatures Associated with Natural Products

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Natural and Bio-derived Molecules".

Deadline for manuscript submissions: 31 May 2025 | Viewed by 9430

Special Issue Editor

Prof. Dr. Juei-Tang Cheng

E-Mail Website
Guest Editor
Department of Medical Research, Chi-Mei Medical Center, Tainan City 71004, Taiwan
Interests: metabolic disorders; insulin resistance; hepatokines; natural products; animal models
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Natural products (NP) are a good resource for health problems around the world, and they have been widely investigated for use on humans and animals. Because NPs have been applied for a long time, they have been linked with functional disorders and the progression of diseases; many scientists have contributed to NP research. Their fruitful results have been beneficial to health and basic research. However, numerous areas have not been studied, particularly their molecular mechanisms. Therefore, this Special Issue aims to present a collection of articles focused on the in vivo and in vitro molecular mechanisms and effects of NPs. Recently, important molecules and/or signaling events in NPs have been discovered. The repurposing of NP is a popular topic. It is important to assess the significance of these molecules in the mechanisms of NPs. You are most welcome to share NP findings that have been obtained in your lab using reliable animal models and/or the established cell models. Moreover, considering the health merits of modern therapies, this Special Issue will cover a wide variety of areas, including the repurposing of well-known molecules, with the aim of developing useful agents and/or biomolecules from NPs for clinical therapy. Reviews, mini-reviews, commentaries, and original research articles, among others, are welcome, and we look forward to receiving contributions from all over the world.

Prof. Dr. Juei-Tang Cheng
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. Biomolecules 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 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

  • natural product
  • molecular mechanisms
  • repurposed molecules
  • disease model
  • human health

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Published Papers (6 papers)

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Research

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17 pages, 3880 KiB  
Article
The Antifungal Potential of Ozonated Extra-Virgin Olive Oil Against Candida albicans: Mechanisms and Efficacy
by Simone Augello, Valentina Cameli, Arianna Montanari, Stefano Tacconi, Daniela Uccelletti, Luciana Dini and Emily Schifano
Biomolecules 2024, 14(11), 1472; https://doi.org/10.3390/biom14111472 - 19 Nov 2024
Cited by 1 | Viewed by 2027
Abstract
The growing emergence of resistance mechanisms and side effects associated with antifungal agents highlight the need for alternative therapies. This study aims to investigate the antifungal potential of ozonated extra-virgin olive oil (EOO) against Candida albicans, with the goal of developing eco-friendly [...] Read more.
The growing emergence of resistance mechanisms and side effects associated with antifungal agents highlight the need for alternative therapies. This study aims to investigate the antifungal potential of ozonated extra-virgin olive oil (EOO) against Candida albicans, with the goal of developing eco-friendly and highly effective treatments based on natural products. Antifungal activity was evaluated via cell viability and biofilm formation assays using Crystal Violet and Sytox green staining. The results showed that EOO reduced C. albicans viability in a dose-dependent manner, achieving over 90% cell death at a 3% (v/v) concentration. Transmission Electron Microscopy (TEM) revealed cell wall structural damage, and ROS levels increased by approximately 60% compared to untreated controls within 10 min of treatment. Additionally, the expression of autophagy-related genes atg-7 and atg-13was upregulated by 2- and 3.5-fold, respectively, after 15 min, suggesting a stress-induced cell death response. EOO also significantly inhibited hyphal formation and biofilm development, thus reducing C. albicans pathogenicity while preserving cell biocompatibility. EOO antifungal activity was also observed in the case of Candida glabrata. In conclusion, ozonated olive oil demonstrates potent antifungal activity against C. albicans by reducing cell viability, inhibiting hyphal and biofilm formation, and triggering oxidative stress and autophagy pathways. These findings position EOO as a promising alternative therapy for fungal infections. Full article
(This article belongs to the Special Issue Molecular Profiling and Identification of Molecular Signatures Associated with Natural Products)
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18 pages, 3047 KiB  
Article
Morphological Characterization, Polyphenolic Profile, and Bioactive Properties of Limoncella, an Ancient Mediterranean Variety of Sweet Citrus
by Lucia Potenza, Roberta Saltarelli, Francesco Palma, Laura Di Patria, Giosuè Annibalini, Sabrina Burattini, Pietro Gobbi, Laura Valentini, Giovanni Caprioli, Agnese Santanatoglia, Sauro Vittori and Elena Barbieri
Biomolecules 2024, 14(10), 1275; https://doi.org/10.3390/biom14101275 - 10 Oct 2024
Viewed by 929
Abstract
Limoncella of Mattinata, a rare and ancient Mediterranean citrus fruit, was investigated by sequence analysis of the ribosomal internal transcribed spacer regions, which assigns it as a variety of Citrus medica L. Morphological, chemical, and biomolecular approaches, including light and electron microscopy, HPLC-ESI-MS/MS, [...] Read more.
Limoncella of Mattinata, a rare and ancient Mediterranean citrus fruit, was investigated by sequence analysis of the ribosomal internal transcribed spacer regions, which assigns it as a variety of Citrus medica L. Morphological, chemical, and biomolecular approaches, including light and electron microscopy, HPLC-ESI-MS/MS, and antioxidant and anti-inflammatory assays, were used to characterize the flavedo and albedo parts, usually rich in bioactive compounds. The morphological findings showed albedo and flavedo cellular structures as “reservoirs” of nutritional components. Both albedo and flavedo hydroalcoholic extracts were rich in polyphenols, but they were different in compounds and quantity. The flavedo is rich in p-coumaric acid and rutin, whereas the albedo contains high levels of hesperidin and quercitrin. Antioxidant, anti-inflammatory, and genoprotective effects for albedo and flavedo were found. The results confirmed the health properties of flavedo and highlighted that albedo is also a rich source of antioxidants. Moreover, this study valorizes Limoncella of Mattinata’s nutritional properties, cueing its crops’ repopulation. Full article
(This article belongs to the Special Issue Molecular Profiling and Identification of Molecular Signatures Associated with Natural Products)
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12 pages, 2498 KiB  
Article
Identification of Sinapic Acid Derivatives from Petit Vert Leaves and Their Effects on Glucose Uptake in C2C12 Murine Myoblasts
by Shizuo Yamada, Tsutomu Warashina, Osamu Shirota, Yoshihisa Kato and Toshiyuki Fukuda
Biomolecules 2024, 14(10), 1246; https://doi.org/10.3390/biom14101246 - 1 Oct 2024
Cited by 1 | Viewed by 1190
Abstract
Petit vert (scientific name: Brassica oleracea var. gemmifera DC. × Brassica oleracea var. acephala DC.) is a new variety of vegetable created by crossbreeding kale and brussel sprouts (Brassica oleracea species). The present study aimed to identify biologically active compounds in extracts of [...] Read more.
Petit vert (scientific name: Brassica oleracea var. gemmifera DC. × Brassica oleracea var. acephala DC.) is a new variety of vegetable created by crossbreeding kale and brussel sprouts (Brassica oleracea species). The present study aimed to identify biologically active compounds in extracts of the outer leaves of Petit vert by purification and to examine their biological activities. The dried and powdered outer leaves of Petit vert were extracted, fractionated, and purified to isolate active compounds. Mass spectrometry (MS) was used to identify the compounds, and nuclear magnetic resonance (NMR) spectroscopy was performed to elucidate their structures. The compounds isolated from Petit vert leaves were glycosides that contained kaempferol, quercetin (flavonol), or sinapic acid (phenylpropanoid). Glucose uptake in cultured C2C12 murine myoblasts in the absence of insulin was significantly increased by these compounds, kaempferol, sinapic acid, and ferulic acid, while uptake in the presence of insulin was also significantly increased by compounds 3 and 4, kaempferol, and sinapic acid. The effect was not necessarily concentration-dependent, and some agents decreased the glucose uptake at higher concentrations. The present study reports for the first time the isolation of five compounds containing sinapic acid from the outer leaves of Petit vert and their stimulation of glucose uptake in cultured C2C12 murine myoblasts. The results obtained herein suggest the potential of these compounds to effectively attenuate hyperglycemia and maintain muscle strength by promoting glucose metabolism in muscle cells. Full article
(This article belongs to the Special Issue Molecular Profiling and Identification of Molecular Signatures Associated with Natural Products)
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19 pages, 2491 KiB  
Article
Assessment of Antimicrobial and Cytotoxic Activities of Liposomes Loaded with Curcumin and Lippia origanoides Essential Oil
by Juan Pablo Bedoya-Agudelo, Jhon Esteban López-Carvajal, Edwin Stiven Quiguanás-Guarín, Nestor Cardona, Leonardo Padilla-Sanabria and Jhon Carlos Castaño-Osorio
Biomolecules 2024, 14(7), 851; https://doi.org/10.3390/biom14070851 - 15 Jul 2024
Cited by 6 | Viewed by 1781
Abstract
(1) Introduction: Curcumin and Lippia origanoides essential oils have a broad spectrum of biological activities; however, their physicochemical instability, low solubility, and high volatility limit their therapeutic use. Encapsulation in liposomes has been reported as a feasible approach to increase the physicochemical stability [...] Read more.
(1) Introduction: Curcumin and Lippia origanoides essential oils have a broad spectrum of biological activities; however, their physicochemical instability, low solubility, and high volatility limit their therapeutic use. Encapsulation in liposomes has been reported as a feasible approach to increase the physicochemical stability of active substances, protect them from interactions with the environment, modulate their release, reduce their volatility, improve their bioactivity, and reduce their toxicity. To date, there are no reports on the co-encapsulation of curcumin and Lippia origanoides essential oils in liposomes. Therefore, the objective of this work is to prepare and physiochemical characterize liposomes loaded with the mixture of these compounds and to evaluate different in vitro biological activities. (2) Methods: Liposomes were produced using the thin-layer method and physiochemical characteristics were calculated. The antimicrobial and cytotoxic activities of both encapsulated and non-encapsulated compounds were evaluated. (3) Results: Empty and loaded nanometric-sized liposomes were obtained that are monodisperse and have a negative zeta potential. They inhibited the growth of Staphylococcus aureus and did not exhibit cytotoxic activity against mammalian cells. (4) Conclusions: Encapsulation in liposomes was demonstrated to be a promising strategy for natural compounds possessing antimicrobial activity. Full article
(This article belongs to the Special Issue Molecular Profiling and Identification of Molecular Signatures Associated with Natural Products)
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17 pages, 12688 KiB  
Article
The AP2/ERF Transcription Factor PgERF120 Regulates Ginsenoside Biosynthesis in Ginseng
by Yang Jiang, Qi Zhang, Zixia Zeng, Yi Wang, Mingzhu Zhao, Kangyu Wang and Meiping Zhang
Biomolecules 2024, 14(3), 345; https://doi.org/10.3390/biom14030345 - 13 Mar 2024
Cited by 2 | Viewed by 2059
Abstract
Ginseng (Panax ginseng C.A. Meyer) is a perennial herb belonging to the family Araliaceae and has been used for thousands of years in East Asia as an essential traditional medicine with a wide range of pharmacological activities of its main active ingredient, [...] Read more.
Ginseng (Panax ginseng C.A. Meyer) is a perennial herb belonging to the family Araliaceae and has been used for thousands of years in East Asia as an essential traditional medicine with a wide range of pharmacological activities of its main active ingredient, ginsenosides. The AP2/ERF gene family, widely present in plants, is a class of transcription factors capable of responding to ethylene regulation that has an influential role in regulating the synthesis of major active ingredients in medicinal plants and in response to biotic and abiotic stresses, which have not been reported in Panax ginseng. In this study, the AP2/ERF gene was localized on the ginseng chromosome, and an AP2/ERF gene duplication event was also discovered in Panax ginseng. The expression of seven ERF genes and three key enzyme genes related to saponin synthesis was measured by fluorescence quantitative PCR using ethylene treatment of ginseng hairy roots, and it was observed that ethylene promoted the expression of genes related to the synthesis of ginsenosides, among which the PgERF120 gene was the most sensitive to ethylene. We analyzed the sequence features and expression patterns of the PgERF120 gene and found that the expression of the PgERF120 gene was specific in time and space. The PgERF120 gene was subsequently cloned, and plant overexpression and RNA interference vectors were constructed. Ginseng adventitious roots were transformed using the Agrobacterium tumefaciens-mediated method to obtain transgenic ginseng hairy roots, and the gene expression, ginsenoside content and malondialdehyde content in overexpression-positive hairy roots were also analyzed. This study preliminarily verified that the PgERF120 gene can be involved in the regulation of ginsenoside synthesis, which provides a theoretical basis for the study of functional genes in ginseng and a genetic resource for the subsequent use of synthetic biology methods to improve the yield of ginsenosides. Full article
(This article belongs to the Special Issue Molecular Profiling and Identification of Molecular Signatures Associated with Natural Products)
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Review

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20 pages, 1188 KiB  
Review
Antioxidant Properties of Biosurfactants: Multifunctional Biomolecules with Added Value in Formulation Chemistry
by Matilde Tancredi, Carlo Carandente Coscia, Irene Russo Krauss and Gerardino D’Errico
Biomolecules 2025, 15(2), 308; https://doi.org/10.3390/biom15020308 - 19 Feb 2025
Viewed by 559
Abstract
Biosurfactants, amphiphilic metabolites produced by bacteria and yeasts, fulfill a variety of functions in microbial life. They exhibit a well-recognized multifunctionality, spanning from the reduction in surface tension to specific biological activities, including antimicrobial, antiviral, anti-inflammatory, and anticancer effects. These compounds have the [...] Read more.
Biosurfactants, amphiphilic metabolites produced by bacteria and yeasts, fulfill a variety of functions in microbial life. They exhibit a well-recognized multifunctionality, spanning from the reduction in surface tension to specific biological activities, including antimicrobial, antiviral, anti-inflammatory, and anticancer effects. These compounds have the potential to serve as environmentally friendly alternatives to synthetic surfactants in industrial formulations, where they could act as emulsifiers and wetting agents. The exploitation of their full potentiality could be a significant added value. Biosurfactants are often cited as effective antioxidants. However, experimental evidence for their antioxidant activity/capacity is sparse. To shed light on the subject, in this review we collect and critically examine all the available literature data for each of the major classes of microbial biosurfactants: rhamnolipids, mannosylerythritol lipids, sophorolipids, and lipopeptides. Despite the variability arising from the diverse composition and polydispersity of the samples analyzed, along with the variety of testing methodologies, the findings consistently indicate a moderate-to-strong antioxidant capacity. Several hypotheses are advanced about the molecular mechanisms behind this action; however, further studies are needed to gain a molecular understanding. This knowledge would fully define the biological roles of biosurfactants and is a prerequisite for the development of innovative formulations based on the valorization of their antioxidant properties. Full article
(This article belongs to the Special Issue Molecular Profiling and Identification of Molecular Signatures Associated with Natural Products)
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