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Biomolecules, Volume 13, Issue 7 (July 2023) – 144 articles

Cover Story (view full-size image): In this article, we provide a comprehensive analysis of heme-binding motifs (HBMs) in mammalian proteins, which can help in deciphering the recognition mechanisms for the initial association of heme to target proteins and the constitution of the resulting complexes. The pivotal role of Cys-Pro dipeptide motifs is highlighted together with a comparative insight into the sequences and structural anomalies observed in all types of HBMs. A general consensus sequence depending on the coordination site Cys, His, or Tyr, which can be used to predict HBMs more accurately using machine learning algorithms, can be established. To further fortify the studies involving structural pattern recognition, the availability and quality of protein 3D structures is paramount, despite the usefulness of AlphaFold. View this paper
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23 pages, 4939 KiB  
Article
Glaucoma-Associated CDR1 Peptide Promotes RGC Survival in Retinal Explants through Molecular Interaction with Acidic Leucine Rich Nuclear Phosphoprotein 32A (ANP32A)
Biomolecules 2023, 13(7), 1161; https://doi.org/10.3390/biom13071161 - 22 Jul 2023
Viewed by 1645
Abstract
Glaucoma is a complex, multifactorial optic neuropathy mainly characterized by the progressive loss of retinal ganglion cells (RGCs) and their axons, resulting in a decline of visual function. The pathogenic molecular mechanism of glaucoma is still not well understood, and therapeutic strategies specifically [...] Read more.
Glaucoma is a complex, multifactorial optic neuropathy mainly characterized by the progressive loss of retinal ganglion cells (RGCs) and their axons, resulting in a decline of visual function. The pathogenic molecular mechanism of glaucoma is still not well understood, and therapeutic strategies specifically addressing the neurodegenerative component of this ocular disease are urgently needed. Novel immunotherapeutics might overcome this problem by targeting specific molecular structures in the retina and providing direct neuroprotection via different modes of action. Within the scope of this research, the present study showed for the first time beneficial effects of the synthetic CDR1 peptide SCTGTSSDVGGYNYVSWYQ on the viability of RGCs ex vivo in a concentration-dependent manner compared to untreated control explants (CTRL, 50 µg/mL: p < 0.05 and 100 µg/mL: p < 0.001). Thereby, this specific peptide was identified first as a potential biomarker candidate in the serum of glaucoma patients and was significantly lower expressed in systemic IgG molecules compared to healthy control subjects. Furthermore, MS-based co-immunoprecipitation experiments confirmed the specific interaction of synthetic CDR1 with retinal acidic leucine-rich nuclear phosphoprotein 32A (ANP32A; p < 0.001 and log2 fold change > 3), which is a highly expressed protein in neurological tissues with multifactorial biological functions. In silico binding prediction analysis revealed the N-terminal leucine-rich repeat (LRR) domain of ANP32A as a significant binding site for synthetic CDR1, which was previously reported as an important docking site for protein-protein interactions (PPI). In accordance with these findings, quantitative proteomic analysis of the retinae ± CDR1 treatment resulted in the identification of 25 protein markers, which were significantly differentially distributed between both experimental groups (CTRL and CDR1, p < 0.05). Particularly, acetyl-CoA biosynthesis I-related enzymes (e.g., DLAT and PDHA1), as well as cytoskeleton-regulating proteins (e.g., MSN), were highly expressed by synthetic CDR1 treatment in the retina; on the contrary, direct ANP32A-interacting proteins (e.g., NME1 and PPP2R4), as well as neurodegenerative-related markers (e.g., CEND1), were identified with significant lower abundancy in the CDR1-treated retinae compared to CTRL. Furthermore, retinal protein phosphorylation and histone acetylation were also affected by synthetic CDR1, which are both partially controlled by ANP32A. In conclusion, the synthetic CDR1 peptide provides a great translational potential for the treatment of glaucoma in the future by eliciting its neuroprotective mechanism via specific interaction with ANP32A’s N terminal LRR domain. Full article
(This article belongs to the Special Issue Functional Peptides and Their Interactions)
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17 pages, 2016 KiB  
Article
Differential Participation of Plant Ribosomal Proteins from the Small Ribosomal Subunit in Protein Translation under Stress
Biomolecules 2023, 13(7), 1160; https://doi.org/10.3390/biom13071160 - 21 Jul 2023
Cited by 2 | Viewed by 1341
Abstract
Upon exposure to biotic and abiotic stress, plants have developed strategies to adapt to the challenges imposed by these unfavorable conditions. The energetically demanding translation process is one of the main elements regulated to reduce energy consumption and to selectively synthesize proteins involved [...] Read more.
Upon exposure to biotic and abiotic stress, plants have developed strategies to adapt to the challenges imposed by these unfavorable conditions. The energetically demanding translation process is one of the main elements regulated to reduce energy consumption and to selectively synthesize proteins involved in the establishment of an adequate response. Emerging data have shown that ribosomes remodel to adapt to stresses. In Arabidopsis thaliana, ribosomes consist of approximately eighty-one distinct ribosomal proteins (RPs), each of which is encoded by two to seven genes. Recent research has revealed that a mutation in a given single RP in plants can not only affect the functions of the RP itself but can also influence the properties of the ribosome, which could bring about changes in the translation to varying degrees. However, a pending question is whether some RPs enable ribosomes to preferentially translate specific mRNAs. To reveal the role of ribosomal proteins from the small subunit (RPS) in a specific translation, we developed a novel approach to visualize the effect of RPS silencing on the translation of a reporter mRNA (GFP) combined to the 5’UTR of different housekeeping and defense genes. The silencing of genes encoding for NbRPSaA, NbRPS5A, and NbRPS24A in Nicotiana benthamiana decreased the translation of defense genes. The NbRACK1A-silenced plant showed compromised translations of specific antioxidant enzymes. However, the translations of all tested genes were affected in NbRPS27D-silenced plants. These findings suggest that some RPS may be potentially involved in the control of protein translation. Full article
(This article belongs to the Special Issue Ribosomal Proteins in Ribosome Assembly)
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19 pages, 790 KiB  
Review
Recognition of Arboviruses by the Mosquito Immune System
Biomolecules 2023, 13(7), 1159; https://doi.org/10.3390/biom13071159 - 21 Jul 2023
Cited by 1 | Viewed by 1460
Abstract
Arthropod-borne viruses (arboviruses) pose a significant threat to both human and animal health worldwide. These viruses are transmitted through the bites of mosquitoes, ticks, sandflies, or biting midges to humans or animals. In humans, arbovirus infection often results in mild flu-like symptoms, but [...] Read more.
Arthropod-borne viruses (arboviruses) pose a significant threat to both human and animal health worldwide. These viruses are transmitted through the bites of mosquitoes, ticks, sandflies, or biting midges to humans or animals. In humans, arbovirus infection often results in mild flu-like symptoms, but severe disease and death also occur. There are few vaccines available, so control efforts focus on the mosquito population and virus transmission control. One area of research that may enable the development of new strategies to control arbovirus transmission is the field of vector immunology. Arthropod vectors, such as mosquitoes, have coevolved with arboviruses, resulting in a balance of virus replication and vector immune responses. If this balance were disrupted, virus transmission would likely be reduced, either through reduced replication, or even through enhanced replication, resulting in mosquito mortality. The first step in mounting any immune response is to recognize the presence of an invading pathogen. Recent research advances have been made to tease apart the mechanisms of arbovirus detection by mosquitoes. Here, we summarize what is known about arbovirus recognition by the mosquito immune system, try to generate a comprehensive picture, and highlight where there are still gaps in our current understanding. Full article
(This article belongs to the Special Issue New Insight into Vector Borne Diseases)
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21 pages, 2034 KiB  
Review
Nanoparticle-Mediated Delivery of Flavonoids: Impact on Proinflammatory Cytokine Production: A Systematic Review
Biomolecules 2023, 13(7), 1158; https://doi.org/10.3390/biom13071158 - 21 Jul 2023
Cited by 2 | Viewed by 1069
Abstract
Flavonoids are a diverse group of plant-derived compounds that have been shown to have various health benefits, including anti-inflammatory effects. However, their use in the treatment of inflammatory diseases has been limited due to their low bioavailability. The nanoparticle-mediated delivery of flavonoids has [...] Read more.
Flavonoids are a diverse group of plant-derived compounds that have been shown to have various health benefits, including anti-inflammatory effects. However, their use in the treatment of inflammatory diseases has been limited due to their low bioavailability. The nanoparticle-mediated delivery of flavonoids has been proposed as a potential solution to this issue, as it allows the sustained release of the flavonoids over time. There are several different nanoparticle systems that have been developed for flavonoid delivery, including polymeric nanoparticles, liposomes, and inorganic nanoparticles. This systematic review aims to evaluate the impact of nanoparticle-mediated delivery of flavonoids on pro-inflammatory cytokine production in various diseases. We analyzed the performance of flavonoid-encapsulated nanoparticles in regulating cytokine production in different in vitro and in vivo studies. To this end, we followed the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) to conduct a comprehensive search of the literature and to assess the quality of the included studies. The results showed that flavonoid-encapsulated nanoparticles significantly downregulated pro-inflammatory cytokines, such as TNF-α, IL-1β, IL-6, and IL-18. In some cases, this effect was significantly greater than that observed with non-encapsulated flavonoids These findings suggest that nanoparticle-mediated delivery of flavonoids may have potential as a therapeutic approach for the treatment of inflammatory diseases. Full article
(This article belongs to the Special Issue Advanced Nanotechnology for Health and Diseases)
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15 pages, 1852 KiB  
Article
Chemical Composition of the Essential Oils of Three Popular Sideritis Species Cultivated in Greece Using GC-MS Analysis
Biomolecules 2023, 13(7), 1157; https://doi.org/10.3390/biom13071157 - 20 Jul 2023
Cited by 3 | Viewed by 1463
Abstract
(1) Background: The essential oils (EOs) of Sideritis L. have attracted great interest due to their pharmacological activities and potential applications in the cosmetic and perfume industries. The aim of this work was to study the EO chemical composition of three of the [...] Read more.
(1) Background: The essential oils (EOs) of Sideritis L. have attracted great interest due to their pharmacological activities and potential applications in the cosmetic and perfume industries. The aim of this work was to study the EO chemical composition of three of the most popular, in Greece, mountain tea species: namely, these include Sideritis scardica, Sideritis raeseri, and Sideritis syriaca. (2) Methods: The EOs were obtained from the aerial parts of three Sideritis species that were cultivated in various regions of Greece by hydrodistillation, and the chemical composition was studied by gas chromatography–mass spectrometry (GC-MS) analysis. (3) Results: The EOs of the Sideritis species—S. scardica (SSC1, SSC2, SSC3), S. raeseri (SR1, SR2, SR3), and S. syriaca (SS1, SS2, SS3)—were analyzed by GC-MS, and they showed both qualitatively and quantitatively high variation in their chemical composition. (4) Conclusions: The EOs of S. scardica and S. raeseri from three different regions of Greece, and the S. syriaca from three different localities of Crete Island in Southern Greece, showed high chemical variability. Although 165 different components were found to be present in the nine samples through GC-MS analysis, only 7 (1-octen-3-ol, linalool, trans-pinocarveol, p-mentha-1,5-dien-8-ol, α-terpineol, myrtenol, and verbenone) were common components in the nine EOs, which were identified to be highly variable in different percentages among the samples. Even the EOs of SS1 and SS2, which were cultivated nearby, showed different GC profiles. The composition variation observed might be attributed to differentiations in the soil and climatic conditions. Full article
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14 pages, 1532 KiB  
Article
Purification and Immobilization of Superoxide Dismutase Obtained from Saccharomyces cerevisiae TBRC657 on Bacterial Cellulose and Its Protective Effect against Oxidative Damage in Fibroblasts
Biomolecules 2023, 13(7), 1156; https://doi.org/10.3390/biom13071156 - 20 Jul 2023
Cited by 2 | Viewed by 1078
Abstract
Superoxide dismutase (SOD) is an essential enzyme that eliminates harmful reactive oxygen species (ROS) generating inside living cells. Due to its efficacities, SOD is widely applied in many applications. In this study, the purification of SOD produced from Saccharomyces cerevisiae TBRC657 was conducted [...] Read more.
Superoxide dismutase (SOD) is an essential enzyme that eliminates harmful reactive oxygen species (ROS) generating inside living cells. Due to its efficacities, SOD is widely applied in many applications. In this study, the purification of SOD produced from Saccharomyces cerevisiae TBRC657 was conducted to obtain the purified SOD that exhibited specific activity of 513.74 U/mg with a purification factor of 10.36-fold. The inhibitory test revealed that the purified SOD was classified as Mn-SOD with an estimated molecular weight of 25 kDa on SDS-PAGE. After investigating the biochemical characterization, the purified SOD exhibited optimal activity under conditions of pH 7.0 and 35 °C, which are suitable for various applications. The stability test showed that the purified SOD rapidly decreased in activity under high temperatures. To overcome this, SOD was successfully immobilized on bacterial cellulose (BC), resulting in enhanced stability under those conditions. The immobilized SOD was investigated for its ability to eliminate ROS in fibroblasts. The results indicated that the immobilized SOD released and retained its function to regulate the ROS level inside the cells. Thus, the immobilized SOD on BC could be a promising candidate for application in many industries that require antioxidant functionality under operating conditions. Full article
(This article belongs to the Section Enzymology)
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17 pages, 3567 KiB  
Article
Goldilocks Dilemma: LPS Works Both as the Initial Target and a Barrier for the Antimicrobial Action of Cationic AMPs on E. coli
Biomolecules 2023, 13(7), 1155; https://doi.org/10.3390/biom13071155 - 20 Jul 2023
Cited by 3 | Viewed by 1415
Abstract
Antimicrobial peptides (AMPs) are generally membrane-active compounds that physically disrupt bacterial membranes. Despite extensive research, the precise mode of action of AMPs is still a topic of great debate. This work demonstrates that the initial interaction between the Gram-negative E. coli and AMPs [...] Read more.
Antimicrobial peptides (AMPs) are generally membrane-active compounds that physically disrupt bacterial membranes. Despite extensive research, the precise mode of action of AMPs is still a topic of great debate. This work demonstrates that the initial interaction between the Gram-negative E. coli and AMPs is driven by lipopolysaccharides (LPS) that act as kinetic barriers for the binding of AMPs to the bacterial membrane. A combination of SPR and NMR experiments provide evidence suggesting that cationic AMPs first bind to the negatively charged LPS before reaching a binding place in the lipid bilayer. In the event that the initial LPS-binding is too strong (corresponding to a low dissociation rate), the cationic AMPs cannot effectively get from the LPS to the membrane, and their antimicrobial potency will thus be diminished. On the other hand, the AMPs must also be able to effectively interact with the membrane to exert its activity. The ability of the studied cyclic hexapeptides to bind LPS and to translocate into a lipid membrane is related to the nature of the cationic charge (arginine vs. lysine) and to the distribution of hydrophobicity along the molecule (alternating vs. clumped tryptophan). Full article
(This article belongs to the Special Issue Mechanisms and Kinetics of Interactions of Biomolecules at Interfaces)
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19 pages, 6248 KiB  
Article
Adenosine/β-Cyclodextrin-Based Metal–Organic Frameworks as a Potential Material for Cancer Therapy
Biomolecules 2023, 13(7), 1154; https://doi.org/10.3390/biom13071154 - 20 Jul 2023
Cited by 2 | Viewed by 1224
Abstract
Recently, researchers have employed metal–organic frameworks (MOFs) for loading pharmaceutically important substances. MOFs are a novel class of porous class of materials formed by the self-assembly of organic ligands and metal ions, creating a network structure. The current investigation effectively achieves the loading [...] Read more.
Recently, researchers have employed metal–organic frameworks (MOFs) for loading pharmaceutically important substances. MOFs are a novel class of porous class of materials formed by the self-assembly of organic ligands and metal ions, creating a network structure. The current investigation effectively achieves the loading of adenosine (ADN) into a metal–organic framework based on cyclodextrin (CD) using a solvent diffusion method. The composite material, referred to as ADN:β-CD-K MOFs, is created by loading ADN into beta-cyclodextrin (β-CD) with the addition of K+ salts. This study delves into the detailed examination of the interaction between ADN and β-CD in the form of MOFs. The focus is primarily on investigating the hydrogen bonding interaction and energy parameters through the aid of semi-empirical quantum mechanical computations. The analysis of peaks that are associated with the ADN-loaded ICs (inclusion complexes) within the MOFs indicates that ADN becomes incorporated into a partially amorphous state. Observations from SEM images reveal well-defined crystalline structures within the MOFs. Interestingly, when ADN is absent from the MOFs, smaller and irregularly shaped crystals are formed. This could potentially be attributed to the MOF manufacturing process. Furthermore, this study explores the additional cross-linking of β-CD with K through the coupling of -OH on the β-CD-K MOFs. The findings corroborate the results obtained from FT-IR analysis, suggesting that β-CD plays a crucial role as a seed in the creation of β-CD-K MOFs. Furthermore, the cytotoxicity of the MOFs is assessed in vitro using MDA-MB-231 cells (human breast cancer cells). Full article
(This article belongs to the Special Issue Molecular Targets for Breast Cancer Therapy)
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14 pages, 6660 KiB  
Article
Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features
Biomolecules 2023, 13(7), 1153; https://doi.org/10.3390/biom13071153 - 20 Jul 2023
Cited by 1 | Viewed by 1385
Abstract
Random Forest (RF) is a widely used machine learning method with good performance on classification and regression tasks. It works well under low sample size situations, which benefits applications in the field of biology. For example, gene expression data often involve much larger [...] Read more.
Random Forest (RF) is a widely used machine learning method with good performance on classification and regression tasks. It works well under low sample size situations, which benefits applications in the field of biology. For example, gene expression data often involve much larger numbers of features (p) compared to the size of samples (n). Though the predictive accuracy using RF is often high, there are some problems when selecting important genes using RF. The important genes selected by RF are usually scattered on the gene network, which conflicts with the biological assumption of functional consistency between effective features. To improve feature selection by incorporating external topological information between genes, we propose the Graph Random Forest (GRF) for identifying highly connected important features by involving the known biological network when constructing the forest. The algorithm can identify effective features that form highly connected sub-graphs and achieve equivalent classification accuracy to RF. To evaluate the capability of our proposed method, we conducted simulation experiments and applied the method to two real datasets—non-small cell lung cancer RNA-seq data from The Cancer Genome Atlas, and human embryonic stem cell RNA-seq dataset (GSE93593). The resulting high classification accuracy, connectivity of selected sub-graphs, and interpretable feature selection results suggest the method is a helpful addition to graph-based classification models and feature selection procedures. Full article
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6 pages, 571 KiB  
Editorial
Electrospun Biomolecule-Based Drug Delivery Systems
Biomolecules 2023, 13(7), 1152; https://doi.org/10.3390/biom13071152 - 20 Jul 2023
Cited by 19 | Viewed by 1240
Abstract
Drug delivery, mainly a professional term in pharmaceutics, is a field of interdisciplinary intersection and integration [...] Full article
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12 pages, 1615 KiB  
Review
The History and Science of the Major Birch Pollen Allergen Bet v 1
Biomolecules 2023, 13(7), 1151; https://doi.org/10.3390/biom13071151 - 19 Jul 2023
Cited by 3 | Viewed by 1351
Abstract
The term allergy was coined in 1906 by the Austrian scientist and pediatrician Clemens Freiherr von Pirquet. In 1976, Dietrich Kraft became the head of the Allergy and Immunology Research Group at the Department of General and Experimental Pathology of the University of [...] Read more.
The term allergy was coined in 1906 by the Austrian scientist and pediatrician Clemens Freiherr von Pirquet. In 1976, Dietrich Kraft became the head of the Allergy and Immunology Research Group at the Department of General and Experimental Pathology of the University of Vienna. In 1983, Kraft proposed to replace natural extracts used in allergy diagnostic tests and vaccines with recombinant allergen molecules and persuaded Michael Breitenbach to contribute his expertise in molecular cloning as one of the mentors of this project. Thus, the foundation for the Vienna School of Molecular Allergology was laid. With the recruitment of Heimo Breiteneder as a young molecular biology researcher, the work began in earnest, resulting in the publication of the cloning of the first plant allergen Bet v 1 in 1989. Bet v 1 has become the subject of a very large number of basic scientific as well as clinical studies. Bet v 1 is also the founding member of the large Bet v 1-like superfamily of proteins with members—based on the ancient conserved Bet v 1 fold—being present in all three domains of life, i.e., archaea, bacteria and eukaryotes. This suggests that the Bet v 1 fold most likely already existed in the last universal common ancestor. The biological function of this protein was probably related to lipid binding. However, during evolution, a functional diversity within the Bet v 1-like superfamily was established. The superfamily comprises 25 families, one of which is the Bet v 1 family, which in turn is composed of 11 subfamilies. One of these, the PR-10-like subfamily of proteins, contains almost all of the Bet v 1 homologous allergens from pollen and plant foods. Structural and functional comparisons of Bet v 1 and its non-allergenic homologs of the superfamily will pave the way for a deeper understanding of the allergic sensitization process. Full article
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13 pages, 2465 KiB  
Article
Assigning the Absolute Configuration of Inositol Poly- and Pyrophosphates by NMR Using a Single Chiral Solvating Agent
Biomolecules 2023, 13(7), 1150; https://doi.org/10.3390/biom13071150 - 19 Jul 2023
Viewed by 1006
Abstract
Inositol phosphates constitute a family of highly charged messenger molecules that play diverse roles in cellular processes. The various phosphorylation patterns they exhibit give rise to a vast array of different compounds. To fully comprehend the biological interconnections, the precise molecular identification of [...] Read more.
Inositol phosphates constitute a family of highly charged messenger molecules that play diverse roles in cellular processes. The various phosphorylation patterns they exhibit give rise to a vast array of different compounds. To fully comprehend the biological interconnections, the precise molecular identification of each compound is crucial. Since the myo-inositol scaffold possesses an internal mirror plane, enantiomeric pairs can be formed. Most commonly employed methods for analyzing InsPs have been geared towards resolving regioisomers, but they have not been capable of resolving enantiomers. In this study, we present a general approach for enantiomer assignment using NMR measurements. To achieve this goal, we used 31P-NMR in the presence of L-arginine amide as a chiral solvating agent, which enables the differentiation of enantiomers. Using chemically synthesized standard compounds allows for an unambiguous assignment of the enantiomers. This method was applied to highly phosphorylated inositol pyrophosphates, as well as to lowly phosphorylated inositol phosphates and bisphosphonate analogs. Our method will facilitate the assignment of biologically relevant isomers when isolating naturally occurring compounds from biological specimens. Full article
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13 pages, 1202 KiB  
Review
Notes from the Underground: Heme Homeostasis in C. elegans
Biomolecules 2023, 13(7), 1149; https://doi.org/10.3390/biom13071149 - 19 Jul 2023
Cited by 1 | Viewed by 1200
Abstract
Heme is an iron-containing tetrapyrrole that plays a critical role in various biological processes, including oxygen transport, electron transport, signal transduction, and catalysis. However, free heme is hydrophobic and potentially toxic to cells. Organisms have evolved specific pathways to safely transport this essential [...] Read more.
Heme is an iron-containing tetrapyrrole that plays a critical role in various biological processes, including oxygen transport, electron transport, signal transduction, and catalysis. However, free heme is hydrophobic and potentially toxic to cells. Organisms have evolved specific pathways to safely transport this essential but toxic macrocycle within and between cells. The bacterivorous soil-dwelling nematode Caenorhabditis elegans is a powerful animal model for studying heme-trafficking pathways, as it lacks the ability to synthesize heme but instead relies on specialized trafficking pathways to acquire, distribute, and utilize heme. Over the past 15 years, studies on this microscopic animal have led to the identification of a number of heme-trafficking proteins, with corresponding functional homologs in vertebrates. In this review, we provide a comprehensive overview of the heme-trafficking proteins identified in C. elegans and their corresponding homologs in related organisms. Full article
(This article belongs to the Special Issue Unraveling Mysteries of Heme Metabolism)
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18 pages, 12595 KiB  
Article
Validation of an Ultraviolet Light Response Gene Signature for Predicting Prognosis in Patients with Uveal Melanoma
Biomolecules 2023, 13(7), 1148; https://doi.org/10.3390/biom13071148 - 19 Jul 2023
Viewed by 1857
Abstract
Uveal melanoma (UVM) is a highly aggressive ocular cancer with limited therapeutic options and poor prognosis particularly for patients with liver metastasis. As such, the identification of new prognostic biomarkers is critical for developing effective treatment strategies. In this study, we aimed to [...] Read more.
Uveal melanoma (UVM) is a highly aggressive ocular cancer with limited therapeutic options and poor prognosis particularly for patients with liver metastasis. As such, the identification of new prognostic biomarkers is critical for developing effective treatment strategies. In this study, we aimed to investigate the potential of an ultraviolet light response gene signature to predict the prognosis of UVM patients. Our approach involved the development of a prognostic model based on genes associated with the cellular response to UV light. By employing this model, we generated risk scores to stratify patients into high- and low-risk groups. Furthermore, we conducted differential expression analysis between these two groups and explored the estimation of immune infiltration. To validate our findings, we applied our methodology to an independent UVM cohort. Through our study, we introduced a novel survival prediction tool and shed light on the underlying cellular processes within UVM tumors, emphasizing the involvement of immune subsets in tumor progression. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Graphs)
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26 pages, 5092 KiB  
Article
Yeast Models of Amyotrophic Lateral Sclerosis Type 8 Mimic Phenotypes Seen in Mammalian Cells Expressing Mutant VAPBP56S
Biomolecules 2023, 13(7), 1147; https://doi.org/10.3390/biom13071147 - 19 Jul 2023
Viewed by 1310
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disease that results in the loss of motor neurons and can occur sporadically or due to genetic mutations. Among the 30 genes linked to familial ALS, a P56S mutation in VAPB, an ER-resident protein [...] Read more.
Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disease that results in the loss of motor neurons and can occur sporadically or due to genetic mutations. Among the 30 genes linked to familial ALS, a P56S mutation in VAPB, an ER-resident protein that functions at membrane contact sites, causes ALS type 8. Mammalian cells expressing VAPBP56S have distinctive phenotypes, including ER collapse, protein and/or membrane-containing inclusions, and sensitivity to ER stress. VAPB is conserved through evolution and has two homologs in budding yeast, SCS2 and SCS22. Previously, a humanized version of SCS2 bearing disease-linked mutations was described, and it caused Scs2-containing inclusions when overexpressed in yeast. Here, we describe a yeast model for ALS8 in which the two SCS genes are deleted and replaced with a single chromosomal copy of either wild-type or mutant yeast SCS2 or human VAPB expressed from the SCS2 promoter. These cells display ER collapse, the formation of inclusion-like structures, and sensitivity to tunicamycin, an ER stress-inducing drug. Based on the phenotypic similarity to mammalian cells expressing VAPBP56S, we propose that these models can be used to study the molecular basis of cell death or dysfunction in ALS8. Moreover, other conserved ALS-linked genes may create opportunities for the generation of yeast models of disease. Full article
(This article belongs to the Special Issue Yeast as a Model Organism to Study Human Disease)
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19 pages, 3511 KiB  
Article
Marker-Assisted Selection for Early Maturing E Loci in Soybean Yielded Prospective Breeding Lines for High Latitudes of Northern Kazakhstan
Biomolecules 2023, 13(7), 1146; https://doi.org/10.3390/biom13071146 - 18 Jul 2023
Viewed by 1312
Abstract
The photoperiodic sensitivity of soybean (Glycine max L.) is one of the limiting factors affecting plant growth and yield. At higher latitudes, early flowering and maturity with neutral reaction to photoperiods are required for adaptation of soybean plants to long-day conditions. Currently, [...] Read more.
The photoperiodic sensitivity of soybean (Glycine max L.) is one of the limiting factors affecting plant growth and yield. At higher latitudes, early flowering and maturity with neutral reaction to photoperiods are required for adaptation of soybean plants to long-day conditions. Currently, the production and distribution of new varieties of soybeans adapted to widespread agricultural regions in northern Kazakhstan is in strong demand. Eleven soybean hybrid populations were obtained from crosses between 17 parents with four maturity groups, MG 000, 00, 0, and I. Marker-assisted selection (MAS) was assessed for suitable SSR markers and successfully applied for genes E1, E3, E4, and E7, targeting homozygous genotypes with recessive alleles. The identified and selected genotypes were propagated and tested in the conditions of 53° N latitude in the Kostanay region of northern Kazakhstan. Finally, 20 early maturing F4 breeding lines were identified and developed with genotypes e1 e3 E4 e7, e1 E3 E4 e7, and e1 E3 e4 e7, all completing their growth period within 92–102 days. These breeding lines were developed by MAS and should provide very prospective superior varieties of soybean for northern Kazakhstan through a strategy that may be very helpful to other countries with high latitudes. Full article
(This article belongs to the Special Issue Molecular-Genetic Basis of Plant Breeding 2.0)
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5 pages, 4772 KiB  
Correction
Correction: Hsiao et al. Claspin-Dependent and -Independent Chk1 Activation by a Panel of Biological Stresses. Biomolecules 2023, 13, 125
Biomolecules 2023, 13(7), 1145; https://doi.org/10.3390/biom13071145 - 18 Jul 2023
Viewed by 558
Abstract
In the original publication [...] Full article
(This article belongs to the Special Issue Metabolic Modifications in Genomic Stability Maintenance)
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29 pages, 2858 KiB  
Review
Essential Oils: Chemistry and Pharmacological Activities
Biomolecules 2023, 13(7), 1144; https://doi.org/10.3390/biom13071144 - 18 Jul 2023
Cited by 10 | Viewed by 6333
Abstract
In this review, we provide an overview of the current understanding of the main mechanisms of pharmacological action of essential oils and their components in various biological systems. A brief introduction on essential oil chemistry is presented to better understand the relationship of [...] Read more.
In this review, we provide an overview of the current understanding of the main mechanisms of pharmacological action of essential oils and their components in various biological systems. A brief introduction on essential oil chemistry is presented to better understand the relationship of chemical aspects with the bioactivity of these products. Next, the antioxidant, anti-inflammatory, antitumor, and antimicrobial activities are discussed. The mechanisms of action against various types of viruses are also addressed. The data show that the multiplicity of pharmacological properties of essential oils occurs due to the chemical diversity in their composition and their ability to interfere with biological processes at cellular and multicellular levels via interaction with various biological targets. Therefore, these natural products can be a promising source for the development of new drugs. Full article
(This article belongs to the Topic Natural Products and Drug Discovery)
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17 pages, 4107 KiB  
Article
Effect of Drought on the Future Sugar Content of Wine Grape Varieties till 2100: Possible Adaptation in the Hungarian Eger Wine Region
Biomolecules 2023, 13(7), 1143; https://doi.org/10.3390/biom13071143 - 18 Jul 2023
Cited by 1 | Viewed by 978
Abstract
The most significant risk for viticulture is that the sugar content of the grapes will increase in the future due to rising temperatures. As a result, it will be possible to produce wines with increasing alcohol content in the future. Excessively high alcohol [...] Read more.
The most significant risk for viticulture is that the sugar content of the grapes will increase in the future due to rising temperatures. As a result, it will be possible to produce wines with increasing alcohol content in the future. Excessively high alcohol content can significantly reduce the wines’ marketability and viticulture’s profitability. Our study seeks to answer how the expected drought in the Southern and Central regions of Europe will affect the future change in the sugar content of grapes. The degree of dryness was examined using the dryness index in the study. Finally, it was analyzed how the dryness index affects the past and future occurrence of maximum sugar content for six grape varieties. The probability of the occurrence of maximum sugar content for most vine grape varieties will decrease in the near future. However, in the distant future, there is a likelihood that the occurrence of maximum sugar content will increase again. If we can maintain the DI ≥ −10 condition with regulated deficit irrigation, the probability of the occurrence of maximum sugar content may decrease significantly in the near future. Ensuring moderate dryness is the only way to achieve the proper sugar content. Full article
(This article belongs to the Special Issue 2nd Edition: Biochemistry of Wine and Beer)
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15 pages, 1721 KiB  
Review
Primary Processes of Free Radical Formation in Pharmaceutical Formulations of Therapeutic Proteins
Biomolecules 2023, 13(7), 1142; https://doi.org/10.3390/biom13071142 - 17 Jul 2023
Cited by 2 | Viewed by 1429
Abstract
Oxidation represents a major pathway for the chemical degradation of pharmaceutical formulations. Few specific details are available on the mechanisms that trigger oxidation reactions in these formulations, specifically with respect to the formation of free radicals. Hence, these mechanisms must be formulated based [...] Read more.
Oxidation represents a major pathway for the chemical degradation of pharmaceutical formulations. Few specific details are available on the mechanisms that trigger oxidation reactions in these formulations, specifically with respect to the formation of free radicals. Hence, these mechanisms must be formulated based on information on impurities and stress factors resulting from manufacturing, transportation and storage. In more detail, this article focusses on autoxidation, metal-catalyzed oxidation, photo-degradation and radicals generated from cavitation as a result of mechanical stress. Emphasis is placed on probable rather than theoretically possible pathways. Full article
(This article belongs to the Special Issue Biomarkers of Oxidative and Radical Stress)
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3 pages, 169 KiB  
Editorial
HSP70: From Signaling Mechanisms to Therapeutics
Biomolecules 2023, 13(7), 1141; https://doi.org/10.3390/biom13071141 - 17 Jul 2023
Viewed by 867
Abstract
Heat-shock proteins (HSPs) are primary stress responders that are vital to maintaining homeostasis [...] Full article
(This article belongs to the Special Issue HSP70: From Signaling Mechanisms to Therapeutics)
30 pages, 2155 KiB  
Review
The Effects and Mechanisms of PBM Therapy in Accelerating Orthodontic Tooth Movement
Biomolecules 2023, 13(7), 1140; https://doi.org/10.3390/biom13071140 - 17 Jul 2023
Viewed by 1609
Abstract
Malocclusion is one of the three major diseases, the incidence of which could reach 56% of the imperiled oral and systemic health in the world today. Orthodontics is still the primary method to solve the problem. However, it is clear that many orthodontic [...] Read more.
Malocclusion is one of the three major diseases, the incidence of which could reach 56% of the imperiled oral and systemic health in the world today. Orthodontics is still the primary method to solve the problem. However, it is clear that many orthodontic complications are associated with courses of long-term therapy. Photobiomodulation (PBM) therapy could be used as a popular way to shorten the course of orthodontic treatment by nearly 26% to 40%. In this review, the efficacy in cells and animals, mechanisms, relevant cytokines and signaling, clinical trials and applications, and the future developments of PBM therapy in orthodontics were evaluated to demonstrate its validity. Simultaneously, based on orthodontic mechanisms and present findings, the mechanisms of acceleration of orthodontic tooth movement (OTM) caused by PBM therapy were explored in relation to four aspects, including blood vessels, inflammatory response, collagen and fibers, and mineralized tissues. Also, the cooperative effects and clinical translation of PBM therapy in orthodontics have been explored in a growing numbers of studies. Up to now, PBM therapy has been gaining popularity for its non-invasive nature, easy operation, and painless procedures. However, the validity and exact mechanism of PBM therapy as an adjuvant treatment in orthodontics have not been fully elucidated. Therefore, this review summarizes the efficacy of PBM therapy on the acceleration of OTM comprehensively from various aspects and was designed to provide an evidence-based platform for the research and development of light-related orthodontic tooth movement acceleration devices. Full article
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22 pages, 2500 KiB  
Review
The Role of S100A6 in Human Diseases: Molecular Mechanisms and Therapeutic Potential
Biomolecules 2023, 13(7), 1139; https://doi.org/10.3390/biom13071139 - 17 Jul 2023
Cited by 2 | Viewed by 1785
Abstract
S100A6, also known as calcyclin, is a low-molecular-weight Ca2+-binding protein from the S100 family that contains two EF-hands. S100A6 is expressed in a variety of mammalian cells and tissues. It is also expressed in lung, colorectal, pancreatic, and liver cancers, as [...] Read more.
S100A6, also known as calcyclin, is a low-molecular-weight Ca2+-binding protein from the S100 family that contains two EF-hands. S100A6 is expressed in a variety of mammalian cells and tissues. It is also expressed in lung, colorectal, pancreatic, and liver cancers, as well as other cancers such as melanoma. S100A6 has many molecular functions related to cell proliferation, the cell cycle, cell differentiation, and the cytoskeleton. It is not only involved in tumor invasion, proliferation, and migration, but also the pathogenesis of other non-neoplastic diseases. In this review, we focus on the molecular mechanisms and potential therapeutic targets of S100A6 in tumors, nervous system diseases, leukemia, endometriosis, cardiovascular disease, osteoarthritis, and other related diseases. Full article
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21 pages, 6597 KiB  
Article
Computational Analysis Reveals Unique Binding Patterns of Oxygenated and Deoxygenated Myoglobin to the Outer Mitochondrial Membrane
Biomolecules 2023, 13(7), 1138; https://doi.org/10.3390/biom13071138 - 17 Jul 2023
Viewed by 1104
Abstract
Myoglobin (Mb) interaction with the outer mitochondrial membrane (OMM) promotes oxygen (O2) release. However, comprehensive molecular details on specific contact regions of the OMM with oxygenated (oxy-) and deoxygenated (deoxy-)Mb are missing. We used molecular dynamics (MD) simulations to explore the [...] Read more.
Myoglobin (Mb) interaction with the outer mitochondrial membrane (OMM) promotes oxygen (O2) release. However, comprehensive molecular details on specific contact regions of the OMM with oxygenated (oxy-) and deoxygenated (deoxy-)Mb are missing. We used molecular dynamics (MD) simulations to explore the interaction of oxy- and deoxy-Mb with the membrane lipids of the OMM in two lipid compositions: (a) a typical whole membrane on average, and (b) specifically the cardiolipin-enriched cristae region (contact site). Unrestrained relaxations showed that on average, both the oxy- and deoxy-Mb established more stable contacts with the lipids typical of the cristae contact site, then with those of the average OMM. However, in steered detachment simulations, deoxy-Mb clung more tightly to the average OMM, and oxy-Mb strongly preferred the contact sites of the OMM. The MD simulation analysis further indicated that a non-specific binding, mediated by local electrostatic interactions, existed between charged or polar groups of Mb and the membrane, for stable interaction. To the best of our knowledge, this is the first computational study providing the molecular details of the direct Mb–mitochondria interaction that assisted in distinguishing the preferred localization of oxy- and deoxy-Mb on the OMM. Our findings support the existing experimental evidence on Mb–mitochondrial association and shed more insights on Mb-mediated O2 transport for cellular bioenergetics. Full article
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18 pages, 9631 KiB  
Article
Genome-Wide Acetylation Modification of H3K27ac in Bovine Rumen Cell Following Butyrate Exposure
Biomolecules 2023, 13(7), 1137; https://doi.org/10.3390/biom13071137 - 16 Jul 2023
Cited by 2 | Viewed by 1507
Abstract
Butyrate contributes epigenetically to the changes in cellular function and tissue development of the rumen in ruminant animals, which might be achieved by its genetic or epigenetic regulation of gene expression. To explore the role of butyrate on bovine rumen epithelial function and [...] Read more.
Butyrate contributes epigenetically to the changes in cellular function and tissue development of the rumen in ruminant animals, which might be achieved by its genetic or epigenetic regulation of gene expression. To explore the role of butyrate on bovine rumen epithelial function and development, this study characterized genome-wide H3K27ac modification changes and super-enhancer profiles in rumen epithelial primary cells (REPC) induced with butyrate by ChIP-seq, and analyzed its effects on gene expression and functional pathways by integrating RNA-seq data. The results showed that genome-wide acetylation modification was observed in the REPC with 94,675 and 48,688 peaks in the butyrate treatment and control group, respectively. A total of 9750 and 5020 genes with increased modification (H3K27ac-gain) and decreased modification (H3K27ac-loss) were detected in the treatment group. The super-enhancer associated genes in the butyrate-induction group were involved in the AMPK signaling pathway, MAPK signaling pathway, and ECM-receptor interaction. Finally, the up-regulated genes (PLCG1, CLEC3B, IGSF23, OTOP3, ADTRP) with H3K27ac gain modification by butyrate were involved in cholesterol metabolism, lysosome, cell adhesion molecules, and the PI3K-Akt signaling pathway. Butyrate treatment has the role of genome-wide H3K27ac acetylation on bovine REPC, and affects the changes in gene expression. The effect of butyrate on gene expression correlates with the acetylation of the H3K27ac level. Identifying genome-wide acetylation modifications and expressed genes of butyrate in bovine REPC cells will expand the understanding of the biological role of butyrate and its acetylation. Full article
(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Graphs)
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22 pages, 638 KiB  
Review
Regulation of Bone by Mechanical Loading, Sex Hormones, and Nerves: Integration of Such Regulatory Complexity and Implications for Bone Loss during Space Flight and Post-Menopausal Osteoporosis
Biomolecules 2023, 13(7), 1136; https://doi.org/10.3390/biom13071136 - 15 Jul 2023
Cited by 3 | Viewed by 1492
Abstract
During evolution, the development of bone was critical for many species to thrive and function in the boundary conditions of Earth. Furthermore, bone also became a storehouse for calcium that could be mobilized for reproductive purposes in mammals and other species. The critical [...] Read more.
During evolution, the development of bone was critical for many species to thrive and function in the boundary conditions of Earth. Furthermore, bone also became a storehouse for calcium that could be mobilized for reproductive purposes in mammals and other species. The critical nature of bone for both function and reproductive needs during evolution in the context of the boundary conditions of Earth has led to complex regulatory mechanisms that require integration for optimization of this tissue across the lifespan. Three important regulatory variables include mechanical loading, sex hormones, and innervation/neuroregulation. The importance of mechanical loading has been the target of much research as bone appears to subscribe to the “use it or lose it” paradigm. Furthermore, because of the importance of post-menopausal osteoporosis in the risk for fractures and loss of function, this aspect of bone regulation has also focused research on sex differences in bone regulation. The advent of space flight and exposure to microgravity has also led to renewed interest in this unique environment, which could not have been anticipated by evolution, to expose new insights into bone regulation. Finally, a body of evidence has also emerged indicating that the neuroregulation of bone is also central to maintaining function. However, there is still more that is needed to understand regarding how such variables are integrated across the lifespan to maintain function, particularly in a species that walks upright. This review will attempt to discuss these regulatory elements for bone integrity and propose how further study is needed to delineate the details to better understand how to improve treatments for those at risk for loss of bone integrity, such as in the post-menopausal state or during prolonged space flight. Full article
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17 pages, 1177 KiB  
Review
Epigenetic Reader Bromodomain-Containing Protein 4 in Aging-Related Vascular Pathologies and Diseases: Molecular Basis, Functional Relevance, and Clinical Potential
Biomolecules 2023, 13(7), 1135; https://doi.org/10.3390/biom13071135 - 15 Jul 2023
Viewed by 1464
Abstract
Aging is a key independent risk factor of various vascular diseases, for which the regulatory mechanisms remain largely unknown. Bromodomain-containing protein 4 (BRD4) is a member of the Bromodomain and Extra-Terminal domain (BET) family and is an epigenetic reader playing diverse roles in [...] Read more.
Aging is a key independent risk factor of various vascular diseases, for which the regulatory mechanisms remain largely unknown. Bromodomain-containing protein 4 (BRD4) is a member of the Bromodomain and Extra-Terminal domain (BET) family and is an epigenetic reader playing diverse roles in regulating transcriptional elongation, chromatin remodeling, DNA damage response, and alternative splicing in various cells and tissues. While BRD4 was initially recognized for its involvement in cancer progression, recent studies have revealed that the aberrant expression and impaired function of BRD4 were highly associated with aging-related vascular pathology, affecting multiple key biological processes in the vascular cells and tissues, providing new insights into the understanding of vascular pathophysiology and pathogenesis of vascular diseases. This review summarizes the recent advances in BRD4 biological function, and the progression of the studies related to BRD4 in aging-associated vascular pathologies and diseases, including atherosclerosis, aortic aneurism vascular neointima formation, pulmonary hypertension, and essential hypertension, providing updated information to advance our understanding of the epigenetic mechanisms in vascular diseases during aging and paving the way for future research and therapeutic approaches. Full article
(This article belongs to the Section Biological Factors)
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15 pages, 4966 KiB  
Article
Preclinical Characterization of a Stabilized Gastrin-Releasing Peptide Receptor Antagonist for Targeted Cancer Theranostics
Biomolecules 2023, 13(7), 1134; https://doi.org/10.3390/biom13071134 - 14 Jul 2023
Cited by 1 | Viewed by 1203
Abstract
Radiolabeled gastrin-releasing peptide receptor (GRPR) antagonists have shown great promise for the theranostics of prostate cancer; however, their suboptimal metabolic stability leaves room for improvements. It was recently shown that the replacement of Gly11 with Sar11 in the peptidic [D-Phe6 [...] Read more.
Radiolabeled gastrin-releasing peptide receptor (GRPR) antagonists have shown great promise for the theranostics of prostate cancer; however, their suboptimal metabolic stability leaves room for improvements. It was recently shown that the replacement of Gly11 with Sar11 in the peptidic [D-Phe6,Leu13-NHEt,des-Met14]BBN(6–14) chain stabilized the [99mTc]Tc-DB15 radiotracer against neprilysin (NEP). We herein present DOTAGA-PEG2-(Sar11)RM26 (AU-RM26-M1), after Gly11 to Sar11-replacement. The impact of this replacement on the metabolic stability and overall biological performance of [111In]In-AU-RM26-M1 was studied using a head-to-head comparison with the unmodified reference [111In]In-DOTAGA-PEG2-RM26. In vitro, the cell uptake of [111In]In-AU-RM26-M1 could be significantly reduced in the presence of a high-excess GRPR-blocker that demonstrated its specificity. The cell uptake of both radiolabeled GRPR antagonists increased with time and was superior for [111In]In-AU-RM26-M1. The dissociation constant reflected strong affinities for GRPR (500 pM for [111In]In-AU-RM26-M1). [111In]In-AU-RM26-M1 showed significantly higher stability in peripheral mice blood at 5 min pi (88 ± 8% intact) than unmodified [111In]In-DOTAGA-PEG2-RM26 (69 ± 2% intact; p < 0.0001). The administration of a NEP inhibitor had no significant impact on the Sar11-compound (91 ± 2% intact; p > 0.05). In vivo, [111In]In-AU-RM26-M1 showed high and GRPR-mediated uptake in the PC-3 tumors (7.0 ± 0.7%IA/g vs. 0.9 ± 0.6%IA/g in blocked mice) and pancreas (2.2 ± 0.6%IA/g vs. 0.3 ± 0.2%IA/g in blocked mice) at 1 h pi, with rapid clearance from healthy tissues. The tumor uptake of [111In]In-AU-RM26-M1 was higher than for [111In]In-DOTAGA-PEG2-RM26 (at 4 h pi, 5.7 ± 1.8%IA/g vs. 3 ± 1%IA/g), concordant with its higher stability. The implanted PC-3 tumors were visualized with high contrast in mice using [111In]In-AU-RM26-M1 SPECT/CT. The Gly11 to Sar11-substitution stabilized [111In]In-DOTAGA-PEG2-(Sar11)RM26 against NEP without negatively affecting other important biological features. These results support the further evaluation of AU-RM26-M1 for prostate cancer theranostics after labeling with clinically relevant radionuclides. Full article
(This article belongs to the Section Molecular Medicine)
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13 pages, 458 KiB  
Review
The Potential of Fasting-Mimicking Diet as a Preventive and Curative Strategy for Alzheimer’s Disease
Biomolecules 2023, 13(7), 1133; https://doi.org/10.3390/biom13071133 - 14 Jul 2023
Cited by 2 | Viewed by 3951
Abstract
This review examines the potential of fasting-mimicking diets (FMDs) in preventing and treating Alzheimer’s disease (AD). FMDs are low-calorie diets that mimic the physiological and metabolic effects of fasting, including the activation of cellular stress response pathways and autophagy. Recent studies have shown [...] Read more.
This review examines the potential of fasting-mimicking diets (FMDs) in preventing and treating Alzheimer’s disease (AD). FMDs are low-calorie diets that mimic the physiological and metabolic effects of fasting, including the activation of cellular stress response pathways and autophagy. Recent studies have shown that FMDs can reduce amyloid-beta accumulation, tau phosphorylation, and inflammation, as well as improve cognitive function in animal models of AD. Human studies have also reported improvements in AD biomarkers, cognitive functions, and subjective well-being measures following FMDs. However, the optimal duration and frequency of FMDs and their long-term safety and efficacy remain to be determined. Despite these uncertainties, FMDs hold promise as a non-pharmacological approach to AD prevention and treatment, and further research in this area is warranted. Full article
(This article belongs to the Special Issue From Biomarkers to Therapy to Puzzle Out Alzheimer’s Disease)
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23 pages, 14523 KiB  
Article
A Molecular Analysis of the Aminopeptidase P-Related Domain of PID-5 from Caenorhabditis elegans
Biomolecules 2023, 13(7), 1132; https://doi.org/10.3390/biom13071132 - 14 Jul 2023
Cited by 1 | Viewed by 1115
Abstract
A novel protein, PID-5, has been shown to be a requirement for germline immortality and has recently been implicated in RNA-induced epigenetic silencing in the Caenorhabditis elegans embryo. Importantly, it has been shown to contain both an eTudor and aminopeptidase P-related domain. However, [...] Read more.
A novel protein, PID-5, has been shown to be a requirement for germline immortality and has recently been implicated in RNA-induced epigenetic silencing in the Caenorhabditis elegans embryo. Importantly, it has been shown to contain both an eTudor and aminopeptidase P-related domain. However, the silencing mechanism has not yet been fully characterised. In this study, bioinformatic tools were used to compare pre-existing aminopeptidase P molecular structures to the AlphaFold2-predicted aminopeptidase P-related domain of PID-5 (PID-5 APP-RD). Structural homology, metal composition, inhibitor-bonding interactions, and the potential for dimerisation were critically assessed through computational techniques, including structural superimposition and protein-ligand docking. Results from this research suggest that the metallopeptidase-like domain shares high structural homology with known aminopeptidase P enzymes and possesses the canonical ‘pita-bread fold’. However, the absence of conserved metal-coordinating residues indicates that only a single Zn2+ may be bound at the active site. The PID-5 APP-RD may form transient interactions with a known aminopeptidase P inhibitor and may therefore recognise substrates in a comparable way to the known structures. However, loss of key catalytic residues suggests the domain will be inactive. Further evidence suggests that heterodimerisation with C. elegans aminopeptidase P is feasible and therefore PID-5 is predicted to regulate proteolytic cleavage in the silencing pathway. PID-5 may interact with PID-2 to bring aminopeptidase P activity to the Z-granule, where it could influence WAGO-4 activity to ensure the balanced production of 22G-RNA signals for transgenerational silencing. Targeted experiments into APPs implicated in malaria and cancer are required in order to build upon the biological and therapeutic significance of this research. Full article
(This article belongs to the Topic Metalloproteins and Metalloenzymes)
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