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Feature Papers in the Natural and Bio-Derived Molecules Section
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Feature Papers in the Natural and Bio-Derived Molecules Section

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 December 2025 | Viewed by 22131

Special Issue Editor

Prof. Dr. Hang Fai (Henry) Kwok

E-Mail Website
Guest Editor
1. Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
2. Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR 999078, China
Interests: novel therapeutic antibodies development; venom-based peptide & natural biomolecule prototype drugs development; cancer biomarkers & immunotherapy markers discovery for prognostic and therapeutic validation
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Special Issue Information

Dear Colleagues,

This Special Issue, titled "Feature Papers in the Natural and Bio-Derived Molecules Section", serves as a platform for gathering top-quality research articles, review articles and communications related to the field of natural product research. The primary focus of this Special Issue is to highlight recent advancements in the chemistry and biochemistry of naturally occurring compounds, the biology of their source organisms, as well as the chemical and biological properties of synthetic derivatives and structurally related compounds. We invite submissions discussing novel and highly significant secondary metabolites of microorganisms, including antibiotics and mycotoxins, physiologically active compounds from plants or animal sources, and biochemical studies encompassing biosynthesis, microbiological transformations, isolation, structure elucidation, chemical synthesis, and pharmacology of compounds derived from natural sources. Additionally, we welcome papers centred on the design and synthesis of novel structures inspired by natural compounds, aiming to investigate and modulate their biological activities for potential therapeutic strategies. The Special Issue will feature a selection of exclusive papers contributed by the Editorial Board Members (EBMs) of Biomolecules, as well as invited papers from esteemed experts in the field. We extend a warm invitation to senior experts in the field to make valuable contributions to this Special Issue. It is important to note that all invited papers will be published online free of charge upon acceptance. Our ultimate goal is to establish our section as an appealing open-access publishing platform for research on natural and bio-derived molecules.

Prof. Dr. Hang Fai (Henry) Kwok
Guest Editor

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Published Papers (7 papers)

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Research

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20 pages, 4065 KiB  
Article
Development of a Combined 2D-MGD TLC/HPTLC Method for the Separation of Terpinen-4-ol and α-Terpineol from Tea Tree, Melaleuca alternifolia, Essential Oil
by Aimé Vázquez and Nurhayat Tabanca
Biomolecules 2025, 15(1), 147; https://doi.org/10.3390/biom15010147 - 18 Jan 2025
Viewed by 1120
Abstract
Tea tree oil (TTO), acquired from Melaleuca alternifolia (Maiden & Betche) Cheel, Myrtaceae, is a widely utilized essential oil (EO) due to its bioactive properties. The identification and quantification of TTO ingredients is generally performed by GC-MS, which provides the most accurate results. [...] Read more.
Tea tree oil (TTO), acquired from Melaleuca alternifolia (Maiden & Betche) Cheel, Myrtaceae, is a widely utilized essential oil (EO) due to its bioactive properties. The identification and quantification of TTO ingredients is generally performed by GC-MS, which provides the most accurate results. However, in some instances, the cost and time of analysis may pose a challenge. Thin-layer chromatography (TLC) and high-performance thin-layer chromatography (HPTLC) offer a simpler, faster, cost-effective alternative capable of simultaneously analyzing and quantifying multiple samples. In addition, for more complex oils, two-dimensional (2D) or multigradient development (MGD) TLC provide better separation. Nevertheless, further development is sometimes necessary for the isolation of comigrating components. This study showcases a combined 2D-MGD TLC/HPTLC method for the successful separation of TTO components of interest. While human error, limited separation, and the partial evaporation of volatile components may still present a challenge during the process, considerable recovery of mono- and sesquiterpenes was achieved. This protocol also resulted in the successful isolation of target oxygenated monoterpenes (OMs) producing highly pure terpinen-4-ol (100%) and α-terpineol (≥94%), confirmed by GC-MS. The accurate enantiomeric distribution of these major OMs was verified by GC-FID through the use of a chiral cyclodextrin-based stationary phase. The observed positive enantiomer range (area percent) as well as (+)/(−) ratio for each terpinen-4-ol and α-terpineol were within acceptable ISO criteria. Full article
(This article belongs to the Special Issue Feature Papers in the Natural and Bio-Derived Molecules Section)
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16 pages, 13158 KiB  
Article
Intact Transition Epitope Mapping—Force Interferences by Variable Extensions (ITEM-FIVE)
by Cornelia Koy, Claudia Röwer, Hans-Jürgen Thiesen, Andrei Neamtu and Michael O. Glocker
Biomolecules 2024, 14(4), 454; https://doi.org/10.3390/biom14040454 - 8 Apr 2024
Cited by 1 | Viewed by 1413
Abstract
Investigations on binding strength differences of non-covalent protein complex components were performed by mass spectrometry. T4 fibritin foldon (T4Ff) is a well-studied miniprotein, which together with its biotinylated version served as model system to represent a compactly folded protein to which an Intrinsically [...] Read more.
Investigations on binding strength differences of non-covalent protein complex components were performed by mass spectrometry. T4 fibritin foldon (T4Ff) is a well-studied miniprotein, which together with its biotinylated version served as model system to represent a compactly folded protein to which an Intrinsically Disordered Region (IDR) was attached. The apparent enthalpies of the gas phase dissociation reactions of the homo-trimeric foldon F-F-F and of the homo-trimeric triply biotinylated foldon bF-bF-bF have been determined to be rather similar (3.32 kJ/mol and 3.85 kJ/mol) but quite distinct from those of the singly and doubly biotinylated hetero-trimers F-F-bF and F-bF-bF (1.86 kJ/mol and 1.08 kJ/mol). Molecular dynamics simulations suggest that the ground states of the (biotinylated) T4Ff trimers are highly symmetric and well comparable to each other, indicating that the energy levels of all four (biotinylated) T4Ff trimer ground states are nearly indistinguishable. The experimentally determined differences and/or similarities in enthalpies of the complex dissociation reactions are explained by entropic spring effects, which are noticeable in the T4Ff hetero-trimers but not in the T4Ff homo-trimers. A lowering of the transition state energy levels of the T4Ff hetero-trimers seems likely because the biotin moieties, mimicking intrinsically disordered regions (IDRs), induced asymmetries in the transition states of the biotinylated T4Ff hetero-trimers. This transition state energy level lowering effect is absent in the T4Ff homo-trimer, as well as in the triply biotinylated T4Ff homo-trimer. In the latter, the IDR-associated entropic spring effects on complex stability cancel each other out. ITEM-FIVE enabled semi-quantitative determination of energy differences of complex dissociation reactions, whose differences were modulated by IDRs attached to compactly folded proteins. Full article
(This article belongs to the Special Issue Feature Papers in the Natural and Bio-Derived Molecules Section)
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17 pages, 3659 KiB  
Article
Bis-Indole Derivatives as Dual Nuclear Receptor 4A1 (NR4A1) and NR4A2 Ligands
by Srijana Upadhyay, Amanuel Esayas Hailemariam, Fuada Mariyam, Zahin Hafiz, Gregory Martin, Jainish Kothari, Evan Farkas, Gargi Sivaram, Logan Bell, Ronald Tjalkens and Stephen Safe
Biomolecules 2024, 14(3), 284; https://doi.org/10.3390/biom14030284 - 27 Feb 2024
Cited by 3 | Viewed by 2966
Abstract
Bis-indole derived compounds such as 1,1-bis(3′-indolyl)-1-(3,5-disubstitutedphenyl) methane (DIM-3,5) and the corresponding 4-hydroxyl analogs (DIM8-3,5) are NR4A1 ligands that act as inverse NR4A1 agonists and are potent inhibitors of tumor growth. The high potency of several DIM-3,5 analogs (IC50 < 1 mg/kg/day), coupled [...] Read more.
Bis-indole derived compounds such as 1,1-bis(3′-indolyl)-1-(3,5-disubstitutedphenyl) methane (DIM-3,5) and the corresponding 4-hydroxyl analogs (DIM8-3,5) are NR4A1 ligands that act as inverse NR4A1 agonists and are potent inhibitors of tumor growth. The high potency of several DIM-3,5 analogs (IC50 < 1 mg/kg/day), coupled with the >60% similarity of the ligand-binding domains (LBDs) of NR4A1 and NR4A2 and the pro-oncogenic activities of both receptors lead us to hypothesize that these compounds may act as dual NR4A1 and NR4A2 ligands. Using a fluorescence binding assay, it was shown that 22 synthetic DIM8-3,5 and DIM-3,5 analogs bound the LBD of NR4A1 and NR4A2 with most KD values in the low µM range. Moreover, the DIM-3,5 and DIM8-3,5 analogs also decreased NR4A1- and NR4A2-dependent transactivation in U87G glioblastoma cells transfected with GAL4-NR4A1 or GAL4-NR4A2 chimeras and a UAS-luciferase reporter gene construct. The DIM-3,5 and DIM8-3,5 analogs were cytotoxic to U87 glioblastoma and RKO colon cancer cells and the DIM-3,5 compounds were more cytotoxic than the DIM8-3,5 compounds. These studies show that both DIM-3,5 and DIM8-3,5 compounds previously identified as NR4A1 ligands bind both NR4A1 and NR4A2 and are dual NR4A1/2 ligands. Full article
(This article belongs to the Special Issue Feature Papers in the Natural and Bio-Derived Molecules Section)
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16 pages, 9984 KiB  
Article
Neutrophils in HNSCC Can Be Associated with Both a Worse or Favorable Prognosis
by Hendrik Brunkhorst, Sören Schnellhardt, Maike Büttner-Herold, Christoph Daniel, Rainer Fietkau and Luitpold V. Distel
Biomolecules 2024, 14(2), 205; https://doi.org/10.3390/biom14020205 - 9 Feb 2024
Cited by 3 | Viewed by 1890
Abstract
The prognostic significance of tumor-infiltrating neutrophils in head and neck squamous cell carcinoma (HNSCC) is poorly understood. It is unclear how the presence of neutrophils affects prognosis due to their polarization into cytotoxic N1 or immunosuppressive N2. Therefore, we determined the number of [...] Read more.
The prognostic significance of tumor-infiltrating neutrophils in head and neck squamous cell carcinoma (HNSCC) is poorly understood. It is unclear how the presence of neutrophils affects prognosis due to their polarization into cytotoxic N1 or immunosuppressive N2. Therefore, we determined the number of CD66b+ neutrophil granulocytes separately in the stromal and epithelial compartments in cancer tissues from 397 patients with HNSCC. Tumor samples from six historical patient groups were processed into tissue microarrays and stained immunohistochemically. In total, 21.9% were HPV positive (p16+). Neutrophil counts were much lower in the stromal compartment (372 ± 812) than in the epithelial cancer compartment (1040 ± 1477) (p < 0.001), with large differences between groups. In three groups with high neutrophil infiltration, high rates were associated with a favorable prognosis, whereas in two groups, high rates were a negative prognostic factor. In p16- oropharyngeal and hypopharyngeal cancer high infiltration was associated with a favorable prognosis. Cancers with an exclusion of neutrophils in the epithelial compartment were associated with improved prognosis. In oropharyngeal and hypopharyngeal HPV-negative cancer high neutrophil infiltration rates were clearly associated with prolonged survival. Neutrophil granulocytes in HNSCC may contribute to a favorable or unfavorable prognosis. Full article
(This article belongs to the Special Issue Feature Papers in the Natural and Bio-Derived Molecules Section)
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Review

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23 pages, 1096 KiB  
Review
Exploring the Cardiovascular Benefits of Extra Virgin Olive Oil: Insights into Mechanisms and Therapeutic Potential
by Esposito Milena and Mandalà Maurizio
Biomolecules 2025, 15(2), 284; https://doi.org/10.3390/biom15020284 - 14 Feb 2025
Cited by 1 | Viewed by 3168
Abstract
Cardiovascular diseases (CVDs) are the leading cause of mortality worldwide, driven by complex interactions among genetic, environmental, and lifestyle factors, with diet playing a pivotal role. Extra Virgin Olive Oil (EVOO), a cornerstone of the Mediterranean diet (MedDiet), is a plant-based fat that [...] Read more.
Cardiovascular diseases (CVDs) are the leading cause of mortality worldwide, driven by complex interactions among genetic, environmental, and lifestyle factors, with diet playing a pivotal role. Extra Virgin Olive Oil (EVOO), a cornerstone of the Mediterranean diet (MedDiet), is a plant-based fat that has garnered attention for its robust cardiovascular benefits, which are attributed to its unique composition of monounsaturated fatty acids (MUFAs), particularly oleic acid (OA); and bioactive polyphenols, such as Hydroxytyrosol (HT) and oleocanthal. These compounds collectively exert antioxidant, anti-inflammatory, vasodilatory, and lipid-modulating effects. Numerous clinical and preclinical studies have demonstrated that EVOO’s properties reduce major modifiable cardiovascular risk factors, including hypertension, dyslipidemia, obesity, and type 2 diabetes. EVOO also promotes endothelial function by increasing nitric oxide (NO) bioavailability, thus favoring vasodilation, lowering blood pressure (BP), and supporting vascular integrity. Furthermore, it modulates biomarkers of cardiovascular health, such as C-reactive protein, low-density lipoprotein (LDL) cholesterol, and NT-proBNP, aligning with improved hemostatic balance and reduced arterial vulnerability. Emerging evidence highlights its interaction with gut microbiota, further augmenting its cardioprotective effects. This review synthesizes current evidence, elucidating EVOO’s multifaceted mechanisms of action and therapeutic potential. Future directions emphasize the need for advanced extraction techniques, nutraceutical formulations, and personalized dietary recommendations to maximize its health benefits. EVOO represents a valuable addition to dietary strategies aimed at reducing the global burden of cardiovascular diseases. Full article
(This article belongs to the Special Issue Feature Papers in the Natural and Bio-Derived Molecules Section)
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56 pages, 5111 KiB  
Review
The Role of Quercetin, a Flavonoid in the Management of Pathogenesis Through Regulation of Oxidative Stress, Inflammation, and Biological Activities
by Hajed Obaid A. Alharbi, Mohammad Alshebremi, Ali Yousif Babiker and Arshad Husain Rahmani
Biomolecules 2025, 15(1), 151; https://doi.org/10.3390/biom15010151 - 20 Jan 2025
Cited by 11 | Viewed by 5473
Abstract
Quercetin, a flavonoid found in vegetables and fruits, has been extensively studied for its health benefits and disease management. Its role in the prevention of various pathogenesis has been well-documented, primarily through its ability to inhibit oxidative stress, inflammation, and enhance the endogenous [...] Read more.
Quercetin, a flavonoid found in vegetables and fruits, has been extensively studied for its health benefits and disease management. Its role in the prevention of various pathogenesis has been well-documented, primarily through its ability to inhibit oxidative stress, inflammation, and enhance the endogenous antioxidant defense mechanisms. Electronic databases such as Google Scholar, Scopus, PubMed, Medline, and Web of Science were searched for information regarding quercetin and its role in various pathogeneses. The included literature comprised experimental studies, randomized controlled trials, and epidemiological studies related to quercetin, while editorials, case analyses, theses, and letters were excluded. It has been reported to have a wide range of health benefits including hepatoprotective, antidiabetic, anti-obesity, neuroprotective, cardioprotective, wound healing, antimicrobial, and immunomodulatory effects, achieved through the modulation of various biological activities. Additionally, numerous in vitro and in vivo studies have shown that quercetin’s efficacies in cancer management involve inhibiting cell signaling pathways, such as inflammation, cell cycle, and angiogenesis, activating cell signaling pathways including tumor suppressor genes, and inducing apoptosis. This review aims to provide a comprehensive understanding of the health benefits of quercetin in various pathogeneses. Additionally, this review outlines the sources of quercetin, nanoformulations, and its applications in health management, along with key findings from important clinical trial studies. Limited clinical data regarding quercetin’s safety and mechanism of action are available. It is important to conduct more clinical trials to gain a deeper understanding of the disease-preventive potential, mechanisms of action, safety, and optimal therapeutic dosages. Furthermore, more research based on nanoformulations should be performed to minimize/overcome the hindrance associated with bioavailability, rapid degradation, and toxicity. Full article
(This article belongs to the Special Issue Feature Papers in the Natural and Bio-Derived Molecules Section)
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28 pages, 1998 KiB  
Review
Third-Generation Tetracyclines: Current Knowledge and Therapeutic Potential
by Dimitris Kounatidis, Maria Dalamaga, Eugenia Grivakou, Irene Karampela, Petros Koufopoulos, Vasileios Dalopoulos, Nikolaos Adamidis, Eleni Mylona, Aikaterini Kaziani and Natalia G. Vallianou
Biomolecules 2024, 14(7), 783; https://doi.org/10.3390/biom14070783 - 30 Jun 2024
Cited by 12 | Viewed by 5029
Abstract
Tetracyclines constitute a unique class of antibiotic agents, widely prescribed for both community and hospital infections due to their broad spectrum of activity. Acting by disrupting protein synthesis through tight binding to the 30S ribosomal subunit, their interference is typically reversible, rendering them [...] Read more.
Tetracyclines constitute a unique class of antibiotic agents, widely prescribed for both community and hospital infections due to their broad spectrum of activity. Acting by disrupting protein synthesis through tight binding to the 30S ribosomal subunit, their interference is typically reversible, rendering them bacteriostatic in action. Resistance to tetracyclines has primarily been associated with changes in pump efflux or ribosomal protection mechanisms. To address this challenge, tetracycline molecules have been chemically modified, resulting in the development of third-generation tetracyclines. These novel tetracyclines offer significant advantages in treating infections, whether used alone or in combination therapies, especially in hospital settings. Beyond their conventional antimicrobial properties, research has highlighted their potential non-antibiotic properties, including their impact on immunomodulation and malignancy. This review will focus on third-generation tetracyclines, namely tigecycline, eravacycline, and omadacycline. We will delve into their mechanisms of action and resistance, while also evaluating their pros and cons over time. Additionally, we will explore their therapeutic potential, analyzing their primary indications of prescription, potential future uses, and non-antibiotic features. This review aims to provide valuable insights into the clinical applications of third-generation tetracyclines, thereby enhancing understanding and guiding optimal clinical use. Full article
(This article belongs to the Special Issue Feature Papers in the Natural and Bio-Derived Molecules Section)
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