Biomolecules

17 pages, 297 KiB

Open AccessArticle

The Role of MECP2 and CCR5 Polymorphisms on the Development and Course of Systemic Lupus Erythematosus

by Ewa Rzeszotarska, Anna Sowinska, Barbara Stypinska, Ewa Walczuk, Anna Wajda, Anna Lutkowska, Anna Felis-Giemza, Marzena Olesinska, Mariusz Puszczewicz, Dominik Majewski, Pawel Piotr Jagodzinski, Michal Czerewaty, Damian Malinowski, Andrzej Pawlik, Malgorzata Jaronczyk and Agnieszka Paradowska-Gorycka

Biomolecules 2020, 10(3), 494; https://doi.org/10.3390/biom10030494 - 24 Mar 2020

Cited by 9 | Viewed by 3944

Abstract

Systemic lupus erythematosus (SLE) is a chronic and systemic autoimmune disease. SLE is described by production of autoantibodies and causes damage of many organs. T-cells play a crucial role in SLE pathogenesis. T-cells intensify inflammation through a number of processes, which leads to [...] Read more.

Systemic lupus erythematosus (SLE) is a chronic and systemic autoimmune disease. SLE is described by production of autoantibodies and causes damage of many organs. T-cells play a crucial role in SLE pathogenesis. T-cells intensify inflammation through a number of processes, which leads to autoimmunization. CCR5 and MECP2 genes are linked with T-cells and pathogenesis of SLE. Polymorphisms in these genes are related with the prognostic factors of risk of disease onset and disease severity. The aim of this study was to estimate the influence of polymorphisms in MECP2 and CCR5 genes on the development and course of systemic lupus erythematosus. We examined 137 SLE patients and 604 healthy controls. We studied polymorphisms for CCR5 gene: rs333 and for MECP2: rs2075596, rs1734787, rs17435, and rs2239464. We genotyped our MECP2 samples and we performed a restriction fragment length polymorphism (RFLP) analysis for CCR5 samples. We showed a risk factor for allele T in rs17435 and for allele A in rs2075596 in MECP2. We noticed that MECP2 rs2075596 G/A, rs1734787 C/A, rs17435 A/T, and rs2239464 G/A polymorphisms are more prevalent in SLE patients than in healthy controls. We believe that above-mentioned MECP2 polymorphisms can be considered as SLE susceptibility factor. Full article

20 pages, 6306 KiB

Open AccessArticle

The Vitamin D Receptor Regulates Glycerolipid and Phospholipid Metabolism in Human Hepatocytes

by Teresa Martínez-Sena, Polina Soluyanova, Carla Guzmán, José Manuel Valdivielso, José Vicente Castell and Ramiro Jover

Biomolecules 2020, 10(3), 493; https://doi.org/10.3390/biom10030493 - 24 Mar 2020

Cited by 33 | Viewed by 6267

Abstract

The vitamin D receptor (VDR) must be relevant to liver lipid metabolism because VDR deficient mice are protected from hepatosteatosis. Therefore, our objective was to define the role of VDR on the overall lipid metabolism in human hepatocytes. We developed an adenoviral vector [...] Read more.

The vitamin D receptor (VDR) must be relevant to liver lipid metabolism because VDR deficient mice are protected from hepatosteatosis. Therefore, our objective was to define the role of VDR on the overall lipid metabolism in human hepatocytes. We developed an adenoviral vector for human VDR and performed transcriptomic and metabolomic analyses of cultured human hepatocytes upon VDR activation by vitamin D (VitD). Twenty percent of the VDR responsive genes were related to lipid metabolism, including MOGAT1, LPGAT1, AGPAT2, and DGAT1 (glycerolipid metabolism); CDS1, PCTP, and MAT1A (phospholipid metabolism); and FATP2, SLC6A12, and AQP3 (uptake of fatty acids, betaine, and glycerol, respectively). They were rapidly induced (4–6 h) upon VDR activation by 10 nM VitD or 100 µM lithocholic acid (LCA). Most of these genes were also upregulated by VDR/VitD in mouse livers in vivo. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS) metabolomics demonstrated intracellular accumulation of triglycerides, with concomitant decreases in diglycerides and phosphatidates, at 8 and 24 h upon VDR activation. Significant alterations in phosphatidylcholines, increases in lyso-phosphatidylcholines and decreases in phosphatidylethanolamines and phosphatidylethanolamine plasmalogens were also observed. In conclusion, active VitD/VDR signaling in hepatocytes triggers an unanticipated coordinated gene response leading to triglyceride synthesis and to important perturbations in glycerolipids and phospholipids. Full article

(This article belongs to the Special Issue Lipid Metabolism in Health and Disease)

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12 pages, 2322 KiB

Open AccessArticle

Induction of p53-Dependent Apoptosis by Prostaglandin A₂

by Su-Been Lee, Sangsun Lee, Ji-Young Park, Sun-Young Lee and Ho-Shik Kim

Biomolecules 2020, 10(3), 492; https://doi.org/10.3390/biom10030492 - 24 Mar 2020

Cited by 32 | Viewed by 5683

Abstract

Prostaglandin (PG) A₂, one of cyclopentenone PGs, is known to induce activation of apoptosis in various cancer cells. Although PGA₂ has been reported to cause activation of apoptosis by altering the expression of apoptosis-related genes, the role of p53, one [...] Read more.

Prostaglandin (PG) A₂, one of cyclopentenone PGs, is known to induce activation of apoptosis in various cancer cells. Although PGA₂ has been reported to cause activation of apoptosis by altering the expression of apoptosis-related genes, the role of p53, one of the most critical pro-apoptotic genes, on PGA₂-induced apoptosis has not been clarified yet. To address this issue, we compared the apoptosis in HCT116 p53 null cells (HCT116 p53-/-) to that in HCT116 cells containing the wild type p53 gene. Cell death induced by PGA₂ was associated with phosphorylation of histone H2A variant H2AX (H2AX), activation of caspase-3 and cleavage of poly(ADP-ribose) polymerase 1 in HCT116 cells. Induction of apoptosis in PGA₂-treated cells was almost completely prevented by pretreatment with a pan-caspase inhibitor, z-VAD-Fmk, or an inhibitor of protein synthesis, cycloheximide. While PGA₂ induced apoptosis in HCT116 cells, phosphorylation of p53 and transcriptional induction of p53-target genes such as p21^WAF1, PUMA, BAX, NOXA, and DR5 occurred. Besides, pretreatment of pifithrin-α (PFT-α), a chemical inhibitor of p53’s transcriptional activity, interfered with the induction of apoptosis in PGA₂-treated HCT116 cells. Pretreatment of NU7441, a small molecule inhibitor of DNA-activated protein kinase (DNA-PK) suppressed PGA₂-induced phosphorylation of p53 and apoptosis as well. Moreover, among target genes of p53, knockdown of DR5 expression by RNA interference, suppressed PGA₂-induced apoptosis. In the meanwhile, in HCT116 p53-/- cells, PGA₂ induced apoptosis in delayed time points and with less potency. Delayed apoptosis by PGA₂ in HCT116 p53-/- cells was also associated with phosphorylation of H2AX but was not inhibited by either PFT-α or NU7441. Collectively, these results suggest the following. PGA₂ may induce p53-dependent apoptosis in which DNA-PK activates p53, and DR5, a transcriptional target of p53, plays a pivotal role in HCT116 cells. In contrast to apoptosis in HCT116 cells, PGA₂ may induce apoptosis in a fashion of less potency, which is independent of p53 and DNA-PK in HCT116 p53-/- cells Full article

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12 pages, 2005 KiB

Open AccessArticle

2-Oxoester Phospholipase A₂ Inhibitors with Enhanced Metabolic Stability

by Giorgos S. Koutoulogenis, Maroula G. Kokotou, Daiki Hayashi, Varnavas D. Mouchlis, Edward A. Dennis and George Kokotos

Biomolecules 2020, 10(3), 491; https://doi.org/10.3390/biom10030491 - 24 Mar 2020

Cited by 5 | Viewed by 3712

Abstract

2-Oxoesters constitute an important class of potent and selective inhibitors of human cytosolic phospholipase A₂ (GIVA cPLA₂) combining an aromatic scaffold or a long aliphatic chain with a short aliphatic chain containing a free carboxylic acid. Although highly potent 2-oxoester [...] Read more.

2-Oxoesters constitute an important class of potent and selective inhibitors of human cytosolic phospholipase A₂ (GIVA cPLA₂) combining an aromatic scaffold or a long aliphatic chain with a short aliphatic chain containing a free carboxylic acid. Although highly potent 2-oxoester inhibitors of GIVA cPLA₂ have been developed, their rapid degradation in human plasma limits their pharmaceutical utility. In an effort to address this problem, we designed and synthesized two new 2-oxoesters introducing a methyl group either on the α-carbon to the oxoester functionality or on the carbon carrying the ester oxygen. We studied the in vitro plasma stability of both derivatives and their in vitro inhibitory activity on GIVA cPLA₂. Both derivatives exhibited higher plasma stability in comparison with the unsubstituted compound and both derivatives inhibited GIVA cPLA₂, however to different degrees. The 2-oxoester containing a methyl group on the α-carbon atom to the oxoester functionality exhibits enhancement of the metabolic stability and retains considerable inhibitory potency. Full article

(This article belongs to the Special Issue Phospholipases: From Structure to Biological Function)

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21 pages, 3930 KiB

Open AccessArticle

Interactions Under Crowding Milieu: Chemical-Induced Denaturation of Myoglobin is Determined by the Extent of Heme Dissociation on Interaction with Crowders

by Khalida Nasreen, Zahoor Ahmad Parray, Shahzaib Ahamad, Faizan Ahmad, Anwar Ahmed, Salman Freeh Alamery, Tajamul Hussain, Md. Imtaiyaz Hassan and Asimul Islam

Biomolecules 2020, 10(3), 490; https://doi.org/10.3390/biom10030490 - 23 Mar 2020

Cited by 28 | Viewed by 5348

Abstract

Generally, in vivo function and structural changes are studied by probing proteins in a dilute solution under in vitro conditions, which is believed to be mimicking proteins in intracellular milieu. Earlier, thermal-induced denaturation of myoglobin, in the milieu of crowder molecule showed destabilization [...] Read more.

Generally, in vivo function and structural changes are studied by probing proteins in a dilute solution under in vitro conditions, which is believed to be mimicking proteins in intracellular milieu. Earlier, thermal-induced denaturation of myoglobin, in the milieu of crowder molecule showed destabilization of the metal protein. Destabilization of protein by thermal-induced denaturation involves a large extrapolation, so, the reliability is questionable. This led us to measure the effects of macromolecular crowding on its stability by chemical-induced denaturation of the protein using probes like circular dichroism and absorption spectroscopy in the presence of dextran 70 and ficoll 70 at various pHs (acidic: 6.0, almost neutral: 7.0 and basic: 8.0). Observations showed that the degree of destabilization of myoglobin was greater due to ficoll 70 as compared to that of dextran 70 so it can be understood that the nature of the crowder or the shape of the crowder has an important role towards the stability of proteins. Additionally, the degree of destabilization was observed as pH dependent, however the pH dependence is different for different crowders. Furthermore, isothermal titration calorimetry and molecular docking studies confirmed that both the crowders (ficoll and dextran) bind to heme moiety of myoglobin and a single binding site was observed for each. Full article

(This article belongs to the Special Issue Metal Binding Proteins 2020)

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18 pages, 2686 KiB

Open AccessArticle

Site-Specific Lipidomic Signatures of Sea Lettuce (Ulva spp., Chlorophyta) Hold the Potential to Trace Their Geographic Origin

by Elisabete da Costa, Fernando Ricardo, Tânia Melo, Renato Mamede, Maria H. Abreu, Pedro Domingues, M. Rosário Domingues and Ricardo Calado

Biomolecules 2020, 10(3), 489; https://doi.org/10.3390/biom10030489 - 23 Mar 2020

Cited by 18 | Viewed by 5540

Abstract

The wild harvest and aquaculture of Ulva spp. has deserved growing attention in Europe. However, the impact of geographical origin on the biochemical composition of different species and/or strains is yet to be described in detail. Hence, the present study aimed to detect [...] Read more.

The wild harvest and aquaculture of Ulva spp. has deserved growing attention in Europe. However, the impact of geographical origin on the biochemical composition of different species and/or strains is yet to be described in detail. Hence, the present study aimed to detect the variability of the lipidome of different species and/or strains of Ulva originating from different geographic locations. We hypothesized that lipidomic signatures can be used to trace the geographic origin post-harvesting of these valuable green seaweeds. Ulva spp. was sampled from eight distinct ecosystems along the Atlantic Iberian coast and Ulva rigida was sourced from an aquaculture farm operating a land-based integrated production site. Results showed significant differences in the lipidomic profile displayed by Ulva spp. originating from different locations, namely, due to different levels of polyunsaturated betaine lipids and galactolipids; saturated betaine lipids and sulfolipids; and some phospholipid species. Overall, a set of 25 site-specific molecular lipid species provide a unique lipidomic signature for authentication and geographic origin certification of Ulva species. Present findings highlight the potential of lipidome plasticity as a proxy to fight fraudulent practices, but also to ensure quality control and prospect biomass for target bioactive compounds. Full article

(This article belongs to the Special Issue Lipids of Marine Algae)

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11 pages, 2545 KiB

Open AccessArticle

BMP-SMAD1/5 Signaling Regulates Retinal Vascular Development

by Andreas Benn, Florian Alonso, Jo Mangelschots, Elisabeth Génot, Marleen Lox and An Zwijsen

Biomolecules 2020, 10(3), 488; https://doi.org/10.3390/biom10030488 - 23 Mar 2020

Cited by 31 | Viewed by 6012

Abstract

Vascular development is an orchestrated process of vessel formation from pre-existing vessels via sprouting and intussusceptive angiogenesis as well as vascular remodeling to generate the mature vasculature. Bone morphogenetic protein (BMP) signaling via intracellular SMAD1 and SMAD5 effectors regulates sprouting angiogenesis in the [...] Read more.

Vascular development is an orchestrated process of vessel formation from pre-existing vessels via sprouting and intussusceptive angiogenesis as well as vascular remodeling to generate the mature vasculature. Bone morphogenetic protein (BMP) signaling via intracellular SMAD1 and SMAD5 effectors regulates sprouting angiogenesis in the early mouse embryo, but its role in other processes of vascular development and in other vascular beds remains incompletely understood. Here, we investigate the function of SMAD1/5 during early postnatal retinal vascular development using inducible, endothelium-specific deletion of Smad1 and Smad5. We observe the formation of arterial-venous malformations in areas with high blood flow, and fewer and less functional tip cells at the angiogenic front. The vascular plexus region is remarkably hyperdense and this is associated with reduced vessel regression and aberrant vascular loop formation. Taken together, our results highlight important functions of SMAD1/5 during vessel formation and remodeling in the early postnatal retina. Full article

(This article belongs to the Special Issue TGF-Beta Signaling in Physiology and Pathology)

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38 pages, 4508 KiB

Open AccessReview

TGF-β Signaling

by Kalliopi Tzavlaki and Aristidis Moustakas

Biomolecules 2020, 10(3), 487; https://doi.org/10.3390/biom10030487 - 23 Mar 2020

Cited by 558 | Viewed by 29147

Abstract

Transforming growth factor-β (TGF-β) represents an evolutionarily conserved family of secreted polypeptide factors that regulate many aspects of physiological embryogenesis and adult tissue homeostasis. The TGF-β family members are also involved in pathophysiological mechanisms that underlie many diseases. Although the family comprises many [...] Read more.

Transforming growth factor-β (TGF-β) represents an evolutionarily conserved family of secreted polypeptide factors that regulate many aspects of physiological embryogenesis and adult tissue homeostasis. The TGF-β family members are also involved in pathophysiological mechanisms that underlie many diseases. Although the family comprises many factors, which exhibit cell type-specific and developmental stage-dependent biological actions, they all signal via conserved signaling pathways. The signaling mechanisms of the TGF-β family are controlled at the extracellular level, where ligand secretion, deposition to the extracellular matrix and activation prior to signaling play important roles. At the plasma membrane level, TGF-βs associate with receptor kinases that mediate phosphorylation-dependent signaling to downstream mediators, mainly the SMAD proteins, and mediate oligomerization-dependent signaling to ubiquitin ligases and intracellular protein kinases. The interplay between SMADs and other signaling proteins mediate regulatory signals that control expression of target genes, RNA processing at multiple levels, mRNA translation and nuclear or cytoplasmic protein regulation. This article emphasizes signaling mechanisms and the importance of biochemical control in executing biological functions by the prototype member of the family, TGF-β. Full article

(This article belongs to the Special Issue TGF-Beta Signaling in Physiology and Pathology)

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19 pages, 3081 KiB

Open AccessArticle

Camel Hemorphins Exhibit a More Potent Angiotensin-I Converting Enzyme Inhibitory Activity than Other Mammalian Hemorphins: An In Silico and In Vitro Study

by Amanat Ali, Seham Abdullah Rashed Alzeyoudi, Shamma Abdulla Almutawa, Alya Nasir Alnajjar, Yusra Al Dhaheri and Ranjit Vijayan

Biomolecules 2020, 10(3), 486; https://doi.org/10.3390/biom10030486 - 23 Mar 2020

Cited by 11 | Viewed by 4858

Abstract

Angiotensin-I converting enzyme (ACE) is a zinc metallopeptidase that has an important role in regulating the renin-angiotensin-aldosterone system (RAAS). It is also an important drug target for the management of cardiovascular diseases. Hemorphins are endogenous peptides that are produced by proteolytic cleavage of [...] Read more.

Angiotensin-I converting enzyme (ACE) is a zinc metallopeptidase that has an important role in regulating the renin-angiotensin-aldosterone system (RAAS). It is also an important drug target for the management of cardiovascular diseases. Hemorphins are endogenous peptides that are produced by proteolytic cleavage of beta hemoglobin. A number of studies have reported various therapeutic activities of hemorphins. Previous reports have shown antihypertensive action of hemorphins via the inhibition of ACE. The sequence of hemorphins is highly conserved among mammals, except in camels, which harbors a unique Q>R variation in the peptide. Here, we studied the ACE inhibitory activity of camel hemorphins (LVVYPWTRRF and YPWTRRF) and non-camel hemorphins (LVVYPWTQRF and YPWTQRF). Computational methods were used to determine the most likely binding pose and binding affinity of both camel and non-camel hemorphins within the active site of ACE. Molecular dynamics simulations showed that the peptides interacted with critical residues in the active site of ACE. Notably, camel hemorphins showed higher binding affinity and sustained interactions with all three subsites of the ACE active site. An in vitro ACE inhibition assay showed that the IC₅₀ of camel hemorphins were significantly lower than the IC₅₀ of non-camel hemorphins. Full article

(This article belongs to the Special Issue Peptides: Molecular and Biotechnological Aspects)

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17 pages, 1176 KiB

Open AccessReview

Notch3 in Development, Health and Disease

by Samira Hosseini-Alghaderi and Martin Baron

Biomolecules 2020, 10(3), 485; https://doi.org/10.3390/biom10030485 - 23 Mar 2020

Cited by 57 | Viewed by 11846

Abstract

Notch3 is one of four mammalian Notch proteins, which act as signalling receptors to control cell fate in many developmental and adult tissue contexts. Notch signalling continues to be important in the adult organism for tissue maintenance and renewal and mis-regulation of Notch [...] Read more.

Notch3 is one of four mammalian Notch proteins, which act as signalling receptors to control cell fate in many developmental and adult tissue contexts. Notch signalling continues to be important in the adult organism for tissue maintenance and renewal and mis-regulation of Notch is involved in many diseases. Genetic studies have shown that Notch3 gene knockouts are viable and have limited developmental defects, focussed mostly on defects in the arterial smooth muscle cell lineage. Additional studies have revealed overlapping roles for Notch3 with other Notch proteins, which widen the range of developmental functions. In the adult, Notch3, in collaboration with other Notch proteins, is involved in stem cell regulation in different tissues in stem cell regulation in different tissues, and it also controls the plasticity of the vascular smooth muscle phenotype involved in arterial vessel remodelling. Overexpression, gene amplification and mis-activation of Notch3 are associated with different cancers, in particular triple negative breast cancer and ovarian cancer. Mutations of Notch3 are associated with a dominantly inherited disease CADASIL (cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy), and there is further evidence linking Notch3 misregulation to hypertensive disease. Here we discuss the distinctive roles of Notch3 in development, health and disease, different views as to the underlying mechanisms of its activation and misregulation in different contexts and potential for therapeutic intervention. Full article

(This article belongs to the Special Issue Cell Type- and Context-Specific Roles and Regulation of Notch Signaling)

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13 pages, 5875 KiB

Open AccessArticle

Ginsenoside Compound K Induces Adult Hippocampal Proliferation and Survival of Newly Generated Cells in Young and Elderly Mice

by Jung-Mi Oh, Jae Hoon Jeong, Sun Young Park and Sungkun Chun

Biomolecules 2020, 10(3), 484; https://doi.org/10.3390/biom10030484 - 23 Mar 2020

Cited by 16 | Viewed by 4094

Abstract

Cognitive impairment can be associated with reduced adult hippocampal neurogenesis, and it may contribute to age-associated neurodegenerative diseases such as Alzheimer’s (AD). Compound K (CK) is produced from the protopanaxadiol (PPD)-type ginsenosides Rb1, Rb2, and Rc by intestinal microbial conversion. Although CK has [...] Read more.

Cognitive impairment can be associated with reduced adult hippocampal neurogenesis, and it may contribute to age-associated neurodegenerative diseases such as Alzheimer’s (AD). Compound K (CK) is produced from the protopanaxadiol (PPD)-type ginsenosides Rb1, Rb2, and Rc by intestinal microbial conversion. Although CK has been reported as an inducing effector for neuroprotection and improved cognition in hippocampus, its effect on adult neurogenesis has not been explored yet. Here, we investigated the effect of CK on hippocampal neurogenesis in both young (2 months) and elderly (24 months) mice. CK treatment increased the number of cells co-labeled with 5-ethynyl-2′-deoxyuridine (EdU) and proliferating cell nuclear antigen (PCNA); also, Ki67, specific markers for progenitor cells, was more expressed, thus enhancing the generation of new cells and progenitor cells in the dentate gyrus of both young and elderly mice. Moreover, CK treatment increased the number of cells co-labeled with EdU and NeuN, a specific marker for mature neuron in the dentate gyrus, suggesting that newly generated cells survived and differentiated into mature neurons at both ages. These findings demonstrate that CK increases adult hippocampal neurogenesis, which may be beneficial against neurodegenerative disorders such as AD. Full article

(This article belongs to the Special Issue Advances in Ginsenosides)

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14 pages, 1525 KiB

Open AccessFeature PaperArticle

Interactions between Avibactam and Ceftazidime-Hydrolyzing Class D β-Lactamases

by Jean-Marie Frère, Pierre Bogaerts, Te-Din Huang, Patrick Stefanic, Joël Moray, Fabrice Bouillenne and Alain Brans

Biomolecules 2020, 10(3), 483; https://doi.org/10.3390/biom10030483 - 23 Mar 2020

Cited by 9 | Viewed by 3101

Abstract

Class D β-lactamases exhibit very heterogeneous hydrolysis activity spectra against the various types of clinically useful β-lactams. Similarly, and according to the available data, their sensitivities to inactivation by avibactam can vary by a factor of more than 100. In this paper, we [...] Read more.

Class D β-lactamases exhibit very heterogeneous hydrolysis activity spectra against the various types of clinically useful β-lactams. Similarly, and according to the available data, their sensitivities to inactivation by avibactam can vary by a factor of more than 100. In this paper, we performed a detailed kinetic study of the interactions between two ceftazidime-hydrolyzing OXA enzymes and showed that they were significantly more susceptible to avibactam than several other class D enzymes that do not hydrolyze ceftazidime. From a clinical point of view, this result is rather interesting if one considers that avibactam is often administered in combination with ceftazidime. Full article

(This article belongs to the Special Issue Beta-Lactamases: Sequence, Structure, Function, and Inhibition)

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14 pages, 2450 KiB

Open AccessArticle

Exploring Successful Parameter Region for Coarse-Grained Simulation of Biomolecules by Bayesian Optimization and Active Learning

by Ryo Kanada, Atsushi Tokuhisa, Koji Tsuda, Yasushi Okuno and Kei Terayama

Biomolecules 2020, 10(3), 482; https://doi.org/10.3390/biom10030482 - 21 Mar 2020

Cited by 6 | Viewed by 4639

Abstract

Accompanied with an increase of revealed biomolecular structures owing to advancements in structural biology, the molecular dynamics (MD) approach, especially coarse-grained (CG) MD suitable for macromolecules, is becoming increasingly important for elucidating their dynamics and behavior. In fact, CG-MD simulation has succeeded in [...] Read more.

Accompanied with an increase of revealed biomolecular structures owing to advancements in structural biology, the molecular dynamics (MD) approach, especially coarse-grained (CG) MD suitable for macromolecules, is becoming increasingly important for elucidating their dynamics and behavior. In fact, CG-MD simulation has succeeded in qualitatively reproducing numerous biological processes for various biomolecules such as conformational changes and protein folding with reasonable calculation costs. However, CG-MD simulations strongly depend on various parameters, and selecting an appropriate parameter set is necessary to reproduce a particular biological process. Because exhaustive examination of all candidate parameters is inefficient, it is important to identify successful parameters. Furthermore, the successful region, in which the desired process is reproducible, is essential for describing the detailed mechanics of functional processes and environmental sensitivity and robustness. We propose an efficient search method for identifying the successful region by using two machine learning techniques, Bayesian optimization and active learning. We evaluated its performance using F1-ATPase, a biological rotary motor, with CG-MD simulations. We successfully identified the successful region with lower computational costs (12.3% in the best case) without sacrificing accuracy compared to exhaustive search. This method can accelerate not only parameter search but also biological discussion of the detailed mechanics of functional processes and environmental sensitivity based on MD simulation studies. Full article

(This article belongs to the Special Issue Application of Artificial Intelligence for Medical Research)

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14 pages, 517 KiB

Open AccessArticle

High-Density Lipoprotein Particles and Their Relationship to Posttransplantation Diabetes Mellitus in Renal Transplant Recipients

by Sara Sokooti, Tamas Szili-Torok, Jose L. Flores-Guerrero, Maryse C. J. Osté, António W. Gomes-Neto, Jenny E. Kootstra-Ros, Hiddo J.L. Heerspink, Margery A. Connelly, Stephan J. L. Bakker and Robin P. F. Dullaart

Biomolecules 2020, 10(3), 481; https://doi.org/10.3390/biom10030481 - 21 Mar 2020

Cited by 10 | Viewed by 4017

Abstract

High concentrations of high-density lipoprotein (HDL) cholesterol are likely associated with a lower risk of posttransplantation diabetes mellitus (PTDM). However, HDL particles vary in size and density with yet unestablished associations with PTDM risk. The aim of our study was to determine the [...] Read more.

High concentrations of high-density lipoprotein (HDL) cholesterol are likely associated with a lower risk of posttransplantation diabetes mellitus (PTDM). However, HDL particles vary in size and density with yet unestablished associations with PTDM risk. The aim of our study was to determine the association between different HDL particles and development of PTDM in renal transplant recipients (RTRs). We included 351 stable outpatient adult RTRs without diabetes at baseline evaluation. HDL particle characteristics and size were measured by nuclear magnetic resonance (NMR) spectroscopy. During 5.2 (IQR, 4.1‒5.8) years of follow-up, 39 (11%) RTRs developed PTDM. In multivariable Cox regression analysis, levels of HDL cholesterol (hazard ratio [HR] 0.61, 95% confidence interval [CI] 0.40–0.94 per 1SD increase; p = 0.024) and of large HDL particles (HR 0.68, 95% CI 0.50–0.93 per log 1SD increase; p = 0.017), as well as larger HDL size (HR 0.58, 95% CI 0.36–0.93 per 1SD increase; p = 0.025) were inversely associated with PTDM development, independently of relevant covariates including, age, sex, body mass index, medication use, transplantation-specific parameters, blood pressure, triglycerides, and glucose. In conclusion, higher concentrations of HDL cholesterol and of large HDL particles and greater HDL size were associated with a lower risk of PTDM development in RTRs, independently of established risk factors for PTDM development. Full article

(This article belongs to the Special Issue High-Density Lipoprotein (HDL): The Role of Reverse Cholesterol Transport in Human Health and Disease)

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11 pages, 873 KiB

Open AccessCommunication

Fluorogenic and Bioorthogonal Modification of RNA Using Photoclick Chemistry

by Katja Krell and Hans-Achim Wagenknecht

Biomolecules 2020, 10(3), 480; https://doi.org/10.3390/biom10030480 - 21 Mar 2020

Cited by 9 | Viewed by 4050

Abstract

A bromoaryltetrazole-modified uridine was synthesized as a new RNA building block for bioorthogonal, light-activated and postsynthetic modification with commercially available fluorescent dyes. It allows “photoclick”-type modifications by irradiation with light (300 nm LED) at internal and terminal positions of presynthesized RNA with maleimide-conjugated [...] Read more.

A bromoaryltetrazole-modified uridine was synthesized as a new RNA building block for bioorthogonal, light-activated and postsynthetic modification with commercially available fluorescent dyes. It allows “photoclick”-type modifications by irradiation with light (300 nm LED) at internal and terminal positions of presynthesized RNA with maleimide-conjugated fluorophores in good yields. The reaction was evidenced for three different dyes. During irradiation, the emission increases due to the formation of an intrinsically fluorescent pyrazoline moiety as photoclick product. The fluorogenecity of the photoclick reaction was significantly enhanced by energy transfer between the pyrazoline as the reaction product (poor emitter) and the photoclicked dye as the strong emitter. The RNA-dye conjugates show remarkable fluorescent properties, in particular an up to 9.4 fold increase of fluorescence, which are important for chemical biology and fluorescent imaging of RNA in cells. Full article

(This article belongs to the Special Issue Novel Approaches in Biomolecule Labeling)

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23 pages, 3002 KiB

Open AccessArticle

1H-Imidazole-2,5-Dicarboxamides as NS4A Peptidomimetics: Identification of a New Approach to Inhibit HCV-NS3 Protease

by Abdelsattar M. Omar, Mahmoud A. Elfaky, Stefan T. Arold, Sameh H. Soror, Maan T. Khayat, Hani Z. Asfour, Faida H. Bamane and Moustafa E. El-Araby

Biomolecules 2020, 10(3), 479; https://doi.org/10.3390/biom10030479 - 21 Mar 2020

Cited by 5 | Viewed by 5028

Abstract

The nonstructural (NS) protein NS3/4A protease is a critical factor for hepatitis C virus (HCV) maturation that requires activation by NS4A. Synthetic peptide mutants of NS4A were found to inhibit NS3 function. The bridging from peptide inhibitors to heterocyclic peptidomimetics of NS4A has [...] Read more.

The nonstructural (NS) protein NS3/4A protease is a critical factor for hepatitis C virus (HCV) maturation that requires activation by NS4A. Synthetic peptide mutants of NS4A were found to inhibit NS3 function. The bridging from peptide inhibitors to heterocyclic peptidomimetics of NS4A has not been considered in the literature and, therefore, we decided to explore this strategy for developing a new class of NS3 inhibitors. In this report, a structure-based design approach was used to convert the bound form of NS4A into 1H-imidazole-2,5-dicarboxamide derivatives as first generation peptidomimetics. This scaffold mimics the buried amino acid sequence Ile-25` to Arg-28` at the core of NS4A_21`–33` needed to activate the NS3 protease. Some of the synthesized compounds (Coded MOC) were able to compete with and displace NS4A_21`–33` for binding to NS3. For instance, N⁵-(4-guanidinobutyl)-N²-(n-hexyl)-1H-imidazole-2,5-dicarboxamide (MOC-24) inhibited the binding of NS4A_21`–33` with a competition half maximal inhibitory concentration (IC₅₀) of 1.9 ± 0.12 µM in a fluorescence anisotropy assay and stabilized the denaturation of NS3 by increasing the aggregation temperature (40% compared to NS4A_21`–33`). MOC-24 also inhibited NS3 protease activity in a fluorometric assay. Molecular dynamics simulations were conducted to rationalize the differences in structure–activity relationship (SAR) between the active MOC-24 and the inactive MOC-26. Our data show that MOC compounds are possibly the first examples of NS4A peptidomimetics that have demonstrated promising activities against NS3 proteins. Full article

(This article belongs to the Collection Molecular Docking and Structure-Based Virtual Screenings as Efficient Tools in Bioorganic and Medicinal Chemistry)

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17 pages, 3298 KiB

Open AccessArticle

PIRT the TRP Channel Regulating Protein Binds Calmodulin and Cholesterol-Like Ligands

by Nicholas J. Sisco, Dustin D. Luu, Minjoo Kim and Wade D. Van Horn

Biomolecules 2020, 10(3), 478; https://doi.org/10.3390/biom10030478 - 21 Mar 2020

Cited by 5 | Viewed by 4544

Abstract

Transient receptor potential (TRP) ion channels are polymodal receptors that have been implicated in a variety of pathophysiologies, including pain, obesity, and cancer. The capsaicin and heat sensor TRPV1, and the menthol and cold sensor TRPM8, have been shown to be modulated by [...] Read more.

Transient receptor potential (TRP) ion channels are polymodal receptors that have been implicated in a variety of pathophysiologies, including pain, obesity, and cancer. The capsaicin and heat sensor TRPV1, and the menthol and cold sensor TRPM8, have been shown to be modulated by the membrane protein PIRT (Phosphoinositide-interacting regulator of TRP). The emerging mechanism of PIRT-dependent TRPM8 regulation involves a competitive interaction between PIRT and TRPM8 for the activating phosphatidylinositol 4,5-bisphosphate (PIP₂) lipid. As many PIP₂ modulated ion channels also interact with calmodulin, we investigated the possible interaction between PIRT and calmodulin. Using microscale thermophoresis (MST), we show that calmodulin binds to the PIRT C-terminal α-helix, which we corroborate with a pull-down experiment, nuclear magnetic resonance-detected binding study, and Rosetta-based computational studies. Furthermore, we identify a cholesterol-recognition amino acid consensus (CRAC) domain in the outer leaflet of the first transmembrane helix of PIRT, and with MST, show that PIRT specifically binds to a number of cholesterol-derivatives. Additional studies identified that PIRT binds to cholecalciferol and oxytocin, which has mechanistic implications for the role of PIRT regulation of additional ion channels. This is the first study to show that PIRT specifically binds to a variety of ligands beyond TRP channels and PIP₂. Full article

(This article belongs to the Special Issue Advances in Membrane Proteins)

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20 pages, 1137 KiB

Open AccessReview

The Role of Nicotinamide in Cancer Chemoprevention and Therapy

by Ilias P. Nikas, Stavroula A. Paschou and Han Suk Ryu

Biomolecules 2020, 10(3), 477; https://doi.org/10.3390/biom10030477 - 20 Mar 2020

Cited by 96 | Viewed by 17806

Abstract

Nicotinamide (NAM) is a water-soluble form of Vitamin B3 (niacin) and a precursor of nicotinamide-adenine dinucleotide (NAD⁺) which regulates cellular energy metabolism. Except for its role in the production of adenosine triphosphate (ATP), NAD⁺ acts as a substrate for several [...] Read more.

Nicotinamide (NAM) is a water-soluble form of Vitamin B3 (niacin) and a precursor of nicotinamide-adenine dinucleotide (NAD⁺) which regulates cellular energy metabolism. Except for its role in the production of adenosine triphosphate (ATP), NAD⁺ acts as a substrate for several enzymes including sirtuin 1 (SIRT1) and poly ADP-ribose polymerase 1 (PARP1). Notably, NAM is an inhibitor of both SIRT1 and PARP1. Accumulating evidence suggests that NAM plays a role in cancer prevention and therapy. Phase III clinical trials have confirmed its clinical efficacy for non-melanoma skin cancer chemoprevention or as an adjunct to radiotherapy against head and neck, laryngeal, and urinary bladder cancers. Evidence for other cancers has mostly been collected through preclinical research and, in its majority, is not yet evidence-based. NAM has potential as a safe, well-tolerated, and cost-effective agent to be used in cancer chemoprevention and therapy. However, more preclinical studies and clinical trials are needed to fully unravel its value. Full article

(This article belongs to the Special Issue Nicotinamide in Health and Diseases)

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20 pages, 981 KiB

Open AccessReview

Actionable Potentials of Less Frequently Mutated Genes in Colorectal Cancer and Their Roles in Precision Medicine

by Ryia Illani Mohd Yunos, Nurul Syakima Ab Mutalib, Francis Yew Fu Tieng, Nadiah Abu and Rahman Jamal

Biomolecules 2020, 10(3), 476; https://doi.org/10.3390/biom10030476 - 20 Mar 2020

Cited by 8 | Viewed by 5546

Abstract

Global statistics have placed colorectal cancer (CRC) as the third most frequently diagnosed cancer and the fourth principal cause of cancer-related deaths worldwide. Improving survival for CRC is as important as early detection. Personalized medicine is important in maximizing an individual’s treatment success [...] Read more.

Global statistics have placed colorectal cancer (CRC) as the third most frequently diagnosed cancer and the fourth principal cause of cancer-related deaths worldwide. Improving survival for CRC is as important as early detection. Personalized medicine is important in maximizing an individual’s treatment success and minimizing the risk of adverse reactions. Approaches in achieving personalized therapy in CRC have included analyses of specific genes with its clinical implications. Tumour genotyping via next-generation sequencing has become a standard practice to guide clinicians into predicting tumor behaviour, disease prognosis, and treatment response. Nevertheless, better prognostic markers are necessary to further stratify patients for personalized treatment plans. The discovery of new markers remains indispensable in providing the most effective chemotherapy in order to improve the outcomes of treatment and survival in CRC patients. This review aims to compile and discuss newly discovered, less frequently mutated genes in CRC. We also discuss how these mutations are being used to assist therapeutic decisions and their potential prospective clinical utilities. In addition, we will summarize the importance of profiling the large genomic rearrangements, gene amplification, and large deletions and how these alterations may assist in determining the best treatment option for CRC patients. Full article

(This article belongs to the Special Issue New Advances in Molecular Oncology)

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14 pages, 1121 KiB

Open AccessArticle

Consistency of the Tools That Predict the Impact of Single Nucleotide Variants (SNVs) on Gene Functionality: The BRCA1 Gene

by Javier Murillo, Flavio Spetale, Serge Guillaume, Pilar Bulacio, Ignacio Garcia Labari, Olivier Cailloux, Sebastien Destercke and Elizabeth Tapia

Biomolecules 2020, 10(3), 475; https://doi.org/10.3390/biom10030475 - 20 Mar 2020

Cited by 1 | Viewed by 2968

Abstract

Single nucleotide variants (SNVs) occurring in a protein coding gene may disrupt its function in multiple ways. Predicting this disruption has been recognized as an important problem in bioinformatics research. Many tools, hereafter p-tools, have been designed to perform these predictions and many [...] Read more.

Single nucleotide variants (SNVs) occurring in a protein coding gene may disrupt its function in multiple ways. Predicting this disruption has been recognized as an important problem in bioinformatics research. Many tools, hereafter p-tools, have been designed to perform these predictions and many of them are now of common use in scientific research, even in clinical applications. This highlights the importance of understanding the semantics of their outputs. To shed light on this issue, two questions are formulated, (i) do p-tools provide similar predictions? (inner consistency), and (ii) are these predictions consistent with the literature? (outer consistency). To answer these, six p-tools are evaluated with exhaustive SNV datasets from the BRCA1 gene. Two indices, called

K_{a l l}

and

K_{s t r o n g}

, are proposed to quantify the inner consistency of pairs of p-tools while the outer consistency is quantified by standard information retrieval metrics. While the inner consistency analysis reveals that most of the p-tools are not consistent with each other, the outer consistency analysis reveals they are characterized by a low prediction performance. Although this result highlights the need of improving the prediction performance of individual p-tools, the inner consistency results pave the way to the systematic design of truly diverse ensembles of p-tools that can overcome the limitations of individual members. Full article

(This article belongs to the Special Issue Bioinformatics and Precision Computational Biology: Selected Papers from the X International Conference on Bioinformatics #SoIBio+10)

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14 pages, 1190 KiB

Open AccessArticle

Glycerol as Alternative Co-Solvent for Water Extraction of Polyphenols from Carménère Pomace: Hot Pressurized Liquid Extraction and Computational Chemistry Calculations

by Nils Leander Huamán-Castilla, María Salomé Mariotti-Celis, Maximiliano Martínez-Cifuentes and José Ricardo Pérez-Correa

Biomolecules 2020, 10(3), 474; https://doi.org/10.3390/biom10030474 - 20 Mar 2020

Cited by 41 | Viewed by 7421

Abstract

Glycerol is a co-solvent for water extraction that has been shown to be highly effective for obtaining polyphenol extracts under atmospheric conditions. However, its efficacy under subcritical conditions has not yet been studied. We assessed different water-glycerol mixtures (15%, 32.5%, and 50%) in [...] Read more.

Glycerol is a co-solvent for water extraction that has been shown to be highly effective for obtaining polyphenol extracts under atmospheric conditions. However, its efficacy under subcritical conditions has not yet been studied. We assessed different water-glycerol mixtures (15%, 32.5%, and 50%) in a hot pressurized liquid extraction system (HPLE: 10 MPa) at 90 °C, 120 °C, and 150 °C to obtain extracts of low molecular weight polyphenols from Carménère grape pomace. Under the same extraction conditions, glycerol as a co-solvent achieved significantly higher yields in polyphenols than ethanol. Optimal extraction conditions were 150 °C, with 32.5% glycerol for flavonols and 50% for flavanols, stilbenes, and phenolic acids. Considering gallic acid as a model molecule, computational chemistry calculations were applied to explain some unusual extraction outcomes. Furthermore, glycerol, methanol, ethanol, and ethylene glycol were studied to establish an incipient structure–property relationship. The high extraction yields of gallic acid obtained with water and glycerol solvent mixtures can be explained not only by the additional hydrogen bonds between glycerol and gallic acid as compared with the other alcohols, but also because the third hydroxyl group allows the formation of a three-centered hydrogen bond, which intensifies the strongest glycerol and gallic acid hydrogen bond. The above occurs both in neutral and deprotonated gallic acid. Consequently, glycerol confers to the extraction solvent a higher solvation energy of polyphenols than ethanol. Full article

(This article belongs to the Special Issue Biomolecules from Plant Residues)

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14 pages, 3613 KiB

Open AccessFeature PaperArticle

An Alternatively Translated Connexin 43 Isoform, GJA1-11k, Localizes to the Nucleus and Can Inhibit Cell Cycle Progression

by Irina Epifantseva, Shaohua Xiao, Rachel E. Baum, André G. Kléber, TingTing Hong and Robin M. Shaw

Biomolecules 2020, 10(3), 473; https://doi.org/10.3390/biom10030473 - 20 Mar 2020

Cited by 26 | Viewed by 5026

Abstract

Connexin 43 (Cx43) is a gap junction protein that assembles at the cell border to form intercellular gap junction (GJ) channels which allow for cell–cell communication by facilitating the rapid transmission of ions and other small molecules between adjacent cells. Non-canonical roles of [...] Read more.

Connexin 43 (Cx43) is a gap junction protein that assembles at the cell border to form intercellular gap junction (GJ) channels which allow for cell–cell communication by facilitating the rapid transmission of ions and other small molecules between adjacent cells. Non-canonical roles of Cx43, and specifically its C-terminal domain, have been identified in the regulation of Cx43 trafficking, mitochondrial preconditioning, cell proliferation, and tumor formation, yet the mechanisms are still being explored. It was recently identified that up to six truncated isoforms of Cx43 are endogenously produced via alternative translation from internal start codons in addition to full length Cx43, all from the same mRNA produced by the gene GJA1. GJA1-11k, the 11kDa alternatively translated isoform of Cx43, does not have a known role in the formation of gap junction channels, and little is known about its function. Here, we report that over expressed GJA1-11k, unlike the other five truncated isoforms, preferentially localizes to the nucleus in HEK293FT cells and suppresses cell growth by limiting cell cycle progression from the G₀/G₁ phase to the S phase. Furthermore, these functions are independent of the channel-forming full-length Cx43 isoform. Understanding the apparently unique role of GJA1-11k and its generation in cell cycle regulation may uncover a new target for affecting cell growth in multiple disease models. Full article

(This article belongs to the Special Issue Trafficking of Cardiac Ion Channels – Mechanisms and Alterations Leading to Disease)

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15 pages, 758 KiB

Open AccessReview

The Impact of Mutant p53 in the Non-Coding RNA World

by Silvia Di Agostino

Biomolecules 2020, 10(3), 472; https://doi.org/10.3390/biom10030472 - 19 Mar 2020

Cited by 23 | Viewed by 4970

Abstract

Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), micro RNAs (miRNAs), and extracellular RNAs (exRNAs) are new groups of RNAs with regulation activities that have low or no protein-coding ability. Emerging evidence suggests that deregulated expression of these non-coding RNAs is associated with the [...] Read more.

Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), micro RNAs (miRNAs), and extracellular RNAs (exRNAs) are new groups of RNAs with regulation activities that have low or no protein-coding ability. Emerging evidence suggests that deregulated expression of these non-coding RNAs is associated with the induction and progression of diverse tumors throughout epigenetic, transcriptional, and post-transcriptional modifications. A consistent number of non-coding RNAs (ncRNAs) has been shown to be regulated by p53, the most important tumor suppressor of the cells frequently mutated in human cancer. It has been shown that some mutant p53 proteins are associated with the loss of tumor suppressor activity and the acquisition of new oncogenic functions named gain-of-function activities. In this review, we highlight recent lines of evidence suggesting that mutant p53 is involved in the expression of specific ncRNAs to gain oncogenic functions through the creation of a complex network of pathways that influence each other. Full article

(This article belongs to the Special Issue Recent Advances in p53)

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21 pages, 4375 KiB

Open AccessArticle

Development of Novel ¹¹¹-In-Labelled DOTA Urotensin II Analogues for Targeting the UT Receptor Overexpressed in Solid Tumours

by Benjamin Poret, Laurence Desrues, Marc-André Bonin, Martin Pedard, Martine Dubois, Richard Leduc, Romain Modzelewski, Pierre Decazes, Fabrice Morin, Pierre Vera, Hélène Castel, Pierre Bohn and Pierrick Gandolfo

Biomolecules 2020, 10(3), 471; https://doi.org/10.3390/biom10030471 - 19 Mar 2020

Cited by 3 | Viewed by 4287

Abstract

Overexpression of G protein-coupled receptors (GPCRs) in tumours is widely used to develop GPCR-targeting radioligands for solid tumour imaging in the context of diagnosis and even treatment. The human vasoactive neuropeptide urotensin II (hUII), which shares structural analogies with somatostatin, interacts with a [...] Read more.

Overexpression of G protein-coupled receptors (GPCRs) in tumours is widely used to develop GPCR-targeting radioligands for solid tumour imaging in the context of diagnosis and even treatment. The human vasoactive neuropeptide urotensin II (hUII), which shares structural analogies with somatostatin, interacts with a single high affinity GPCR named UT. High expression of UT has been reported in several types of human solid tumours from lung, gut, prostate, or breast, suggesting that UT is a valuable novel target to design radiolabelled hUII analogues for cancer diagnosis. In this study, two original urotensinergic analogues were first conjugated to a DOTA chelator via an aminohexanoic acid (Ahx) hydrocarbon linker and then -hUII and DOTA-urantide, complexed to the radioactive metal indium isotope to successfully lead to radiolabelled DOTA-Ahx-hUII and DOTA-Ahx-urantide. The ¹¹¹In-DOTA-hUII in human plasma revealed that only 30% of the radioligand was degraded after a 3-h period. DOTA-hUII and DOTA-urantide exhibited similar binding affinities as native peptides and relayed calcium mobilization in HEK293 cells expressing recombinant human UT. DOTA-hUII, not DOTA-urantide, was able to promote UT internalization in UT-expressing HEK293 cells, thus indicating that radiolabelled ¹¹¹In-DOTA-hUII would allow sufficient retention of radioactivity within tumour cells or radiolabelled DOTA-urantide may lead to a persistent binding on UT at the plasma membrane. The potential of these radioligands as candidates to target UT was investigated in adenocarcinoma. We showed that hUII stimulated the migration and proliferation of both human lung A549 and colorectal DLD-1 adenocarcinoma cell lines endogenously expressing UT. In vivo intravenous injection of ¹¹¹In-DOTA-hUII in C57BL/6 mice revealed modest organ signals, with important retention in kidney. ¹¹¹In-DOTA-hUII or ¹¹¹In-DOTA-urantide were also injected in nude mice bearing heterotopic xenografts of lung A549 cells or colorectal DLD-1 cells both expressing UT. The observed significant renal uptake and low tumour/muscle ratio (around 2.5) suggest fast tracer clearance from the organism. Together, DOTA-hUII and DOTA-urantide were successfully radiolabelled with ¹¹¹Indium, the first one functioning as a UT agonist and the second one as a UT-biased ligand/antagonist. To allow tumour-specific targeting and prolong body distribution in preclinical models bearing some solid tumours, these radiolabelled urotensinergic analogues should be optimized for being used as potential molecular tools for diagnosis imaging or even treatment tools. Full article

(This article belongs to the Special Issue Novel Approaches in Biomolecule Labeling)

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16 pages, 3545 KiB

Open AccessArticle

Why Does Knocking Out NACHO, But Not RIC3, Completely Block Expression of α7 Nicotinic Receptors in Mouse Brain?

by Anish Deshpande, Remitha M. Vinayakamoorthy, Brijesh K. Garg, Jaya Prakash Thummapudi, Gauri Oza, Ketaki Adhikari, Aayush Agarwal, Parnika Dalvi, Swetha Iyer, Sarulatha Thulasi Raman, Vijay Ramesh, Akshitha Rameshbabu, Alexandra Rezvaya, Sneha Sukumaran, Sweta Swaminathan, Bhargav Tilak, Zhiyuan Wang, Phu V. Tran and Ralph H. Loring

Biomolecules 2020, 10(3), 470; https://doi.org/10.3390/biom10030470 - 19 Mar 2020

Cited by 14 | Viewed by 6928

Abstract

Alpha7 nicotinic acetylcholine receptors (α7nAChRs) are interesting not only because of their physiological effects, but because this receptor requires chaperones to traffic to cell surfaces (measured by alpha-bungarotoxin [αBGT] binding). While knockout (KO) animals and antibodies that react across species exist for tmem35a [...] Read more.

Alpha7 nicotinic acetylcholine receptors (α7nAChRs) are interesting not only because of their physiological effects, but because this receptor requires chaperones to traffic to cell surfaces (measured by alpha-bungarotoxin [αBGT] binding). While knockout (KO) animals and antibodies that react across species exist for tmem35a encoding the protein chaperone NACHO, commercially available antibodies against the chaperone RIC3 that allow Western blots across species have not been generally available. Further, no effects of deleting RIC3 function (ric3 KO) on α7nAChR expression are reported. Finally, antibodies against α7nAChRs have shown various deficiencies. We find mouse macrophages bind αBGT but lack NACHO. We also report on a new α7nAChR antibody and testing commercially available anti-RIC3 antibodies that react across species allowing Western blot analysis of in vitro cultures. These antibodies also react to specific RIC3 splice variants and single-nucleotide polymorphisms. Preliminary autoradiographic analysis reveals that ric3 KOs show subtle αBGT binding changes across different mouse brain regions, while tmem35a KOs show a complete loss of αBGT binding. These findings are inconsistent with effects observed in vitro, as RIC3 promotes αBGT binding to α7nAChRs expressed in HEK cells, even in the absence of NACHO. Collectively, additional regulatory factors are likely involved in the in vivo expression of α7nAChRs. Full article

(This article belongs to the Special Issue Acetylcholine and Acetylcholine Receptors: Textbook Knowledge and New Data)

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44 pages, 437 KiB

Open AccessReview

Detection of Pathognomonic Biomarker PrP^Sc and the Contribution of Cell Free-Amplification Techniques to the Diagnosis of Prion Diseases

by Hasier Eraña, Jorge M. Charco, Ezequiel González-Miranda, Sandra García-Martínez, Rafael López-Moreno, Miguel A. Pérez-Castro, Carlos M. Díaz-Domínguez, Adrián García-Salvador and Joaquín Castilla

Biomolecules 2020, 10(3), 469; https://doi.org/10.3390/biom10030469 - 19 Mar 2020

Cited by 10 | Viewed by 5043

Abstract

Transmissible spongiform encephalopathies or prion diseases are rapidly progressive neurodegenerative diseases, the clinical manifestation of which can resemble other promptly evolving neurological maladies. Therefore, the unequivocal ante-mortem diagnosis is highly challenging and was only possible by histopathological and immunohistochemical analysis of the brain [...] Read more.

Transmissible spongiform encephalopathies or prion diseases are rapidly progressive neurodegenerative diseases, the clinical manifestation of which can resemble other promptly evolving neurological maladies. Therefore, the unequivocal ante-mortem diagnosis is highly challenging and was only possible by histopathological and immunohistochemical analysis of the brain at necropsy. Although surrogate biomarkers of neurological damage have become invaluable to complement clinical data and provide more accurate diagnostics at early stages, other neurodegenerative diseases show similar alterations hindering the differential diagnosis. To solve that, the detection of the pathognomonic biomarker of disease, PrP^Sc, the aberrantly folded isoform of the prion protein, could be used. However, the amounts in easily accessible tissues or body fluids at pre-clinical or early clinical stages are extremely low for the standard detection methods. The solution comes from the recent development of in vitro prion propagation techniques, such as Protein Misfolding Cyclic Amplification (PMCA) and Real Time-Quaking Induced Conversion (RT-QuIC), which have been already applied to detect minute amounts of PrP^Sc in different matrixes and make early diagnosis of prion diseases feasible in a near future. Herein, the most relevant tissues and body fluids in which PrP^Sc has been detected in animals and humans are being reviewed, especially those in which cell-free prion propagation systems have been used with diagnostic purposes. Full article

(This article belongs to the Special Issue Prion Disease Biomarkers: Recent Advances)

17 pages, 1482 KiB

Open AccessFeature PaperReview

The Role of Torsin AAA+ Proteins in Preserving Nuclear Envelope Integrity and Safeguarding Against Disease

by Anthony J. Rampello, Sarah M. Prophet and Christian Schlieker

Biomolecules 2020, 10(3), 468; https://doi.org/10.3390/biom10030468 - 19 Mar 2020

Cited by 22 | Viewed by 6045

Abstract

Torsin ATPases are members of the AAA+ (ATPases associated with various cellular activities) superfamily of proteins, which participate in essential cellular processes. While AAA+ proteins are ubiquitously expressed and demonstrate distinct subcellular localizations, Torsins are the only AAA+ to reside within the nuclear [...] Read more.

Torsin ATPases are members of the AAA+ (ATPases associated with various cellular activities) superfamily of proteins, which participate in essential cellular processes. While AAA+ proteins are ubiquitously expressed and demonstrate distinct subcellular localizations, Torsins are the only AAA+ to reside within the nuclear envelope (NE) and endoplasmic reticulum (ER) network. Moreover, due to the absence of integral catalytic features, Torsins require the NE- and ER-specific regulatory cofactors, lamina-associated polypeptide 1 (LAP1) and luminal domain like LAP1 (LULL1), to efficiently trigger their atypical mode of ATP hydrolysis. Despite their implication in an ever-growing list of diverse processes, the specific contributions of Torsin/cofactor assemblies in maintaining normal cellular physiology remain largely enigmatic. Resolving gaps in the functional and mechanistic principles of Torsins and their cofactors are of considerable medical importance, as aberrant Torsin behavior is the principal cause of the movement disorder DYT1 early-onset dystonia. In this review, we examine recent findings regarding the phenotypic consequences of compromised Torsin and cofactor activities. In particular, we focus on the molecular features underlying NE defects and the contributions of Torsins to nuclear pore complex biogenesis, as well as the growing implications of Torsins in cellular lipid metabolism. Additionally, we discuss how understanding Torsins may facilitate the study of essential but poorly understood processes at the NE and ER, and aid in the development of therapeutic strategies for dystonia. Full article

(This article belongs to the Special Issue AAA+ Proteins in Health and Disease: Structure, Physiological Function, and Mechanisms of Action)

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24 pages, 7724 KiB

Open AccessArticle

HO-1 Interactors Involved in the Colonization of the Bone Niche: Role of ANXA2 in Prostate Cancer Progression

by Nicolás Anselmino, Juan Bizzotto, Pablo Sanchis, Sofia Lage-Vickers, Emiliano Ortiz, Pia Valacco, Alejandra Paez, Estefania Labanca, Roberto Meiss, Nora Navone, Javier Cotignola, Elba Vazquez and Geraldine Gueron

Biomolecules 2020, 10(3), 467; https://doi.org/10.3390/biom10030467 - 18 Mar 2020

Cited by 16 | Viewed by 4808

Abstract

Background: Prostate cancer (PCa) dissemination shows a tendency to develop in the bone, where heme oxygenase 1 (HO-1) plays a critical role in bone remodeling. Previously by LC/ESI-MSMS, we screened for HO-1 interacting proteins and identified annexin 2 (ANXA2). The aim of this [...] Read more.

Background: Prostate cancer (PCa) dissemination shows a tendency to develop in the bone, where heme oxygenase 1 (HO-1) plays a critical role in bone remodeling. Previously by LC/ESI-MSMS, we screened for HO-1 interacting proteins and identified annexin 2 (ANXA2). The aim of this study was to analyze the relevance of ANXA2/HO-1 in PCa and bone metastasis. Methods: We assessed ANXA2 levels using a co-culture transwell system of PC3 cells (pre-treated or not with hemin, an HO-1 specific inducer) and the pre-osteoclastic Raw264.7 cell line. Results: Under co-culture conditions, ANXA2 mRNA levels were significantly modulated in both cell lines. Immunofluorescence analysis unveiled a clear ANXA2 reduction in cell membrane immunostaining for Raw264.7 under the same conditions. This effect was supported by the detection of a decrease in Ca²⁺ concentration in the conditioned medium. HO-1 induction in tumor cells prevented both, the ANXA2 intracellular relocation and the decrease in Ca²⁺ concentration. Further, secretome analysis revealed urokinase (uPA) as a key player in the communication between osteoclast progenitors and PC3 cells. To assess the clinical significance of ANXA2/HO-1, we performed a bioinformatics analysis and identified that low expression of each gene strongly associated with poor prognosis in PCa regardless of the clinico-pathological parameters assessed. Further, these genes appear to behave in a dependent manner. Conclusions: ANXA2/HO-1 rises as a critical axis in PCa. Full article

(This article belongs to the Special Issue Therapeutic Significance of Heme Oxygenase Induction or Inhibition)

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14 pages, 7851 KiB

Open AccessArticle

Exploring the Gelation Mechanisms and Cytocompatibility of Gold (III)-Mediated Regenerated and Thiolated Silk Fibroin Hydrogels

by Chavee Laomeephol, Helena Ferreira, Supansa Yodmuang, Rui L. Reis, Siriporn Damrongsakkul and Nuno M. Neves

Biomolecules 2020, 10(3), 466; https://doi.org/10.3390/biom10030466 - 18 Mar 2020

Cited by 13 | Viewed by 4939

Abstract

Accelerating the gelation of silk fibroin (SF) solution from several days or weeks to minutes or few hours is critical for several applications (e.g., cell encapsulation, bio-ink for 3D printing, and injectable controlled release). In this study, the rapid gelation of SF induced [...] Read more.

Accelerating the gelation of silk fibroin (SF) solution from several days or weeks to minutes or few hours is critical for several applications (e.g., cell encapsulation, bio-ink for 3D printing, and injectable controlled release). In this study, the rapid gelation of SF induced by a gold salt (Au³⁺) as well as the cytocompatibility of Au³⁺-mediated SF hydrogels are reported. The gelation behaviors and mechanisms of regenerated SF and thiolated SF (tSF) were compared. Hydrogels can be obtained immediately after mixing or within three days depending on the types of silk proteins used and amount of Au³⁺. Au³⁺-mediated SF and tSF hydrogels showed different color appearances. The color of Au-SF hydrogels was purple-red, whereas the Au-tSF hydrogels maintained their initial solution color, indicating different gelation mechanisms. The reduction of Au³⁺ by amino groups and further reduction to Au by tyrosine present in SF, resulting in a dityrosine bonding and Au nanoparticles (NPs) production, are proposed as underlying mechanisms of Au-SF gel formation. Thiol groups of the tSF reduced Au³⁺ to Au⁺ and formed a disulfide bond, before a formation of Au⁺-S bonds. Protons generated during the reactions between Au³⁺ and SF or tSF led to a decrease of the local pH, which affected the chain aggregation of the SF, and induced the conformational transition of SF protein to beta sheet. The cytocompatibility of the Au-SF and tSF hydrogels was demonstrated by culturing with a L929 cell line, indicating that the developed hydrogels can be promising 3D matrices for different biomedical applications. Full article

(This article belongs to the Special Issue Biological Biomaterials for Regenerative Medicine)

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15 pages, 22139 KiB

Open AccessArticle

2,3,4′,5-Tetrahydroxystilbene-2-O-β-D-Glucoside (THSG) Activates the Nrf2 Antioxidant Pathway and Attenuates Oxidative Stress-Induced Cell Death in Mouse Cochlear UB/OC-2 Cells

by Tien-Yuan Wu, Jia-Ni Lin, Zi-Yao Luo, Chuan-Jen Hsu, Jen-Shu Wang and Hung-Pin Wu

Biomolecules 2020, 10(3), 465; https://doi.org/10.3390/biom10030465 - 18 Mar 2020

Cited by 15 | Viewed by 4756

Abstract

Oxidative stress plays a critical role in the pathogenesis of hearing loss, and 2,3,4′,5-tetrahydroxystilbene-2-O-β-D-glucoside (THSG) exerts antioxidant effects by inhibiting reactive oxygen species (ROS) generation. With the aim of developing new therapeutic strategies for oxidative stress, this study investigated the protective [...] Read more.

Oxidative stress plays a critical role in the pathogenesis of hearing loss, and 2,3,4′,5-tetrahydroxystilbene-2-O-β-D-glucoside (THSG) exerts antioxidant effects by inhibiting reactive oxygen species (ROS) generation. With the aim of developing new therapeutic strategies for oxidative stress, this study investigated the protective mechanism of THSG in vitro using a normal mouse cochlear cell line (UB/OC-2). The THSG and ascorbic acid have similar free radical scavenger capacities. H₂O₂, but not THSG, reduced the UB/OC-2 cell viability. Moreover, H₂O₂ might induce apoptosis and autophagy by inducing morphological changes, as visualized by microscopy. As evidenced by Western blot analysis and monodansylcadaverine (MDC) staining, THSG might decrease H₂O₂-induced autophagy. According to a Western blotting analysis and Annexin V/PI and JC-1 staining, THSG might protect cells from H₂O₂-induced apoptosis and stabilize the mitochondrial membrane potential. Furthermore, THSG enhanced the translocation of nucleus factor erythroid 2-related factor 2 (Nrf2) into the nucleus and increased the mRNA and protein expression of antioxidant/detoxifying enzymes under H₂O₂-induced oxidative stress conditions. Collectively, our findings demonstrate that THSG, as a scavenging agent, can directly attenuate free radicals and upregulate antioxidant/detoxifying enzymes to protect against oxidative damage and show that THSG protects UB/OC-2 cells from H₂O₂-induced autophagy and apoptosis in vitro. Full article

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Biomolecules, Volume 10, Issue 3 (March 2020) – 145 articles

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