Biomolecules

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ISSN / EISSN : 2218273X / 2218273X
Current Publisher: MDPI (10.3390)
Total articles ≅ 1,427
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Alexey Egorov, Maya Rubtsova, Vitaly Grigorenko, Igor Uporov, Alexander Veselovsky
Published: 11 December 2019
by MDPI
Biomolecules, Volume 9; doi:10.3390/biom9120854

Abstract:Bacterial resistance to β-lactams, the most commonly used class of antibiotics, poses a global challenge. This resistance is caused by the production of bacterial enzymes that are termed β-lactamases (βLs). The evolution of serine-class A β-lactamases from penicillin-binding proteins (PBPs) is related to the formation of the Ω-loop at the entrance to the enzyme’s active site. In this loop, the Glu166 residue plays a key role in the two-step catalytic cycle of hydrolysis. This residue in TEM–type β-lactamases, together with Asn170, is involved in the formation of a hydrogen bonding network with a water molecule, leading to the deacylation of the acyl–enzyme complex and the hydrolysis of the β-lactam ring of the antibiotic. The activity exhibited by the Ω-loop is attributed to the positioning of its N-terminal residues near the catalytically important residues of the active site. The structure of the Ω-loop of TEM-type β-lactamases is characterized by low mutability, a stable topology, and structural flexibility. All of the revealed features of the Ω-loop, as well as the mechanisms related to its involvement in catalysis, make it a potential target for novel allosteric inhibitors of β-lactamases.
Jan Aaseth, Valeria Nurchi, Ole Andersen
Published: 11 December 2019
by MDPI
Biomolecules, Volume 9; doi:10.3390/biom9120856

Abstract:Follow-up studies after the Chernobyl and Fukushima accidents have shown that 137Cs and 131I made up the major amount of harmful contaminants in the atmospheric dispersion and fallout. Other potential sources for such radionuclide exposure may be terrorist attacks, e.g., via contamination of drinking water reservoirs. A primary purpose of radionuclide mobilization is to minimize the radiation dose. Rapid initiation of treatment of poisoned patients is imperative after a contaminating event. Internal contamination with radioactive material can expose patients to prolonged radiation, thus leading to short- and long-term clinical consequences. After the patient’s emergency conditions are addressed, the treating physicians and assisting experts should assess the amount of radioactive material that has been internalized. This evaluation should include estimation of the radiation dose that is delivered and the specific radionuclides inside the body. These complex assessments warrant the reliance on a multidisciplinary approach that incorporates regional experts in radiation medicine and emergencies. Regional hospitals should have elaborated strategies for the handling of radiation emergencies. If radioactive cesium is a significant pollutant, Prussian blue is the approved antidote for internal detoxification. Upon risks of radioiodine exposure, prophylactic or immediate treatment with potassium iodide tablets is recommended. Chelators developed from calcium salts have been studied for gastrointestinal trapping and enhanced mobilization after strontium exposure.
Tomas Sneideris, Andrius Sakalauskas, Rebecca Sternke-Hoffmann, Alessia Peduzzo, Mantas Ziaunys, Alexander Buell, Vytautas Smirnovas
Published: 11 December 2019
by MDPI
Biomolecules, Volume 9; doi:10.3390/biom9120855

Abstract:Millions of people around the world suffer from amyloid-related disorders, including Alzheimer’s and Parkinson’s diseases. Despite significant and sustained efforts, there are still no disease-modifying drugs available for the majority of amyloid-related disorders, and the overall failure rate in clinical trials is very high, even for compounds that show promising anti-amyloid activity in vitro. In this study, we demonstrate that even small changes in the chemical environment can strongly modulate the inhibitory effects of anti-amyloid compounds. Using one of the best-established amyloid inhibitory compounds, epigallocatechin-3-gallate (EGCG), as an example, and two amyloid-forming proteins, insulin and Parkinson’s disease-related α -synuclein, we shed light on the previously unexplored sensitivity to solution conditions of the action of this compound on amyloid fibril formation. In the case of insulin, we show that the classification of EGCG as an amyloid inhibitor depends on the experimental conditions select, on the method used for the evaluation of the efficacy, and on whether or not EGCG is allowed to oxidise before the experiment. For α -synuclein, we show that a small change in pH value, from 7 to 6, transforms EGCG from an efficient inhibitor to completely ineffective, and we were able to explain this behaviour by the increased stability of EGCG against oxidation at pH 6.
Natalia V. Zhukova
Published: 11 December 2019
by MDPI
Biomolecules, Volume 9; doi:10.3390/biom9120857

Abstract:The n-3 and n-6 polyunsaturated fatty acid (PUFA) families are essential for important physiological processes. Their major source are marine ecosystems. The fatty acids (FAs) from phytoplankton, which are the primary producer of organic matter and PUFAs, are transferred into consumers via food webs. Mollusk FAs have attracted the attention of researchers that has been driven by their critical roles in aquatic ecology and their importance as sources of essential PUFAs. The main objective of this review is to focus on the most important factors and causes determining the biodiversity of the mollusk FAs, with an emphasis on the key relationship of these FAs with the food spectrum and trophic preference. The marker FAs of trophic sources are also of particular interest. The discovery of new symbioses involving invertebrates and bacteria, which are responsible for nutrition of the host, deserves special attention. The present paper also highlights recent research into the molecular and biochemical mechanisms of PUFA biosynthesis in marine mollusks. The biosynthetic capacities of marine mollusks require a well-grounded evaluation.
Francis Opoku, Penny P. Govender, Ofentse J. Pooe, Mthokozisi B.C. Simelane
Published: 11 December 2019
by MDPI
Biomolecules, Volume 9; doi:10.3390/biom9120861

Abstract:To date, Plasmodium falciparum is one of the most lethal strains of the malaria parasite. P. falciparum lacks the required enzymes to create its own purines via the de novo pathway, thereby making Plasmodium falciparum hypoxanthine-guanine-xanthine phosphoribosyltransferase (PfHGXPT) a crucial enzyme in the malaria life cycle. Recently, studies have described iso-mukaadial acetate and ursolic acid acetate as promising antimalarials. However, the mode of action is still unknown, thus, the current study sought to investigate the selective inhibitory and binding actions of iso-mukaadial acetate and ursolic acid acetate against recombinant PfHGXPT using in-silico and experimental approaches. Recombinant PfHGXPT protein was expressed using E. coli BL21 cells and homogeneously purified by affinity chromatography. Experimentally, iso-mukaadial acetate and ursolic acid acetate, respectively, demonstrated direct inhibitory activity towards PfHGXPT in a dose-dependent manner. The binding affinity of iso-mukaadial acetate and ursolic acid acetate on the PfHGXPT dissociation constant (KD), where it was found that 0.0833 µM and 2.8396 µM, respectively, are indicative of strong binding. The mode of action for the observed antimalarial activity was further established by a molecular docking study. The molecular docking and dynamics simulations show specific interactions and high affinity within the binding pocket of Plasmodium falciparum and human hypoxanthine-guanine phosphoribosyl transferases. The predicted in silico absorption, distribution, metabolism and excretion/toxicity (ADME/T) properties predicted that the iso-mukaadial acetate ligand may follow the criteria for orally active drugs. The theoretical calculation derived from ADME, molecular docking and dynamics provide in-depth information into the structural basis, specific bonding and non-bonding interactions governing the inhibition of malarial. Taken together, these findings provide a basis for the recommendation of iso-mukaadial acetate and ursolic acid acetate as high-affinity ligands and drug candidates against PfHGXPT.
Heidrun Draut, Thomas Liebenstein, Gerrit Begemann
Published: 11 December 2019
by MDPI
Biomolecules, Volume 9; doi:10.3390/biom9120860

Abstract:Retinoic acid (RA) signaling is an important regulator of chordate development. RA binds to nuclear RA receptors that control the transcriptional activity of target genes. Controlled local degradation of RA by enzymes of the Cyp26a gene family contributes to the establishment of transient RA signaling gradients that control patterning, cell fate decisions and differentiation. Several steps in the lineage leading to the induction and differentiation of neuromesodermal progenitors and bone-producing osteogenic cells are controlled by RA. Changes to RA signaling activity have effects on the formation of the bones of the skull, the vertebrae and the development of teeth and regeneration of fin rays in fish. This review focuses on recent advances in these areas, with predominant emphasis on zebrafish, and highlights previously unknown roles for RA signaling in developmental processes.
Xiurong Xu, Yongfeng Lou, Kebin Yang, Xuemeng Shan, Chenglei Zhu, Zhimin Gao
Published: 11 December 2019
by MDPI
Biomolecules, Volume 9; doi:10.3390/biom9120862

Abstract:: Homeobox (HB) genes play critical roles in regulating various aspects of plant growth and development. However, little is known about HB genes in bamboo. In this study, a total of 115 HB genes (PeHB001‒PeHB115) were identified from moso bamboo (Phyllostachys edulis) and grouped into 13 distinct classes (BEL, DDT, HD-ZIP I‒IV, KNOX, NDX, PHD, PINTOX, PLINC, SAWADEE, and WOX) based on the conserved domains and phylogenetic analysis. The number of members in the different classes ranged from 2 to 24, and they usually varied in terms of exon‒intron distribution pattern and length. There were 20 conserved motifs found in 115 PeHBs, with motif 1 being the most common. Gene ontology (GO) analysis showed that PeHBs had diverse molecular functions, with 19 PeHBs being annotated as having xylem development, xylem, and phloem pattern formation functions. Co-expression network analysis showed that 10 of the 19 PeHBs had co-expression correlations, and three members of the KNOX class were hub proteins that interacted with other transcription factors (TFs) such as MYB, bHLH, and OVATE, which were associated with lignin synthesis. Yeast two-hybridization results further proved that PeHB037 (BEL class) interacted with PeHB057 (KNOX class). Transcriptome expression profiling indicated that all PeHBs except PeHB017 were expressed in at least one of the seven tissues of moso bamboo, and 90 PeHBs were expressed in all the tissues. The qRT-PCR results of the 19 PeHBs showed that most of them were upregulated in shoots as the height increased. Moreover, a KNOX binding site was found in the promoters of the key genes involved in lignin synthesis such as Pe4CL, PeC3H, PeCCR, and PeCOMT, which had positive expression correlations with five KNOX genes. Similar results were found in winter bamboo shoots with prolonged storage time, which was consistent with the degree of lignification. These results provide basic data on PeHBs in moso bamboo, which will be helpful for future functional research on PeHBs with positive regulatory roles in the process of lignification.
Mariola Kozlowska, Anna Zbikowska, Katarzyna Marciniak-Lukasiak, Malgorzata Kowalska
Published: 11 December 2019
by MDPI
Biomolecules, Volume 9; doi:10.3390/biom9120858

Abstract:This study aimed at determining the effect of aqueous ethanolic extracts from lemon balm, hyssop and nettle, and butylated hydroxyanisole (BHA) on properties of shortbread cookies. This was achieved by instrumental measurements of color and sensory properties of the cookies directly after baking and by determination of peroxide (PV) and p-anisidine (p-AnV) values, and specific extinction coefficients (K232 and K268 values) for fat extracted from the cookies stored for 3 months at room temperature. Increase of the herbal extracts’ concentration from 0.02% to 0.2% in the cookies caused a reduction of L* (the brightness) and a* values (the red coordinate), while b* values (the yellow coordinate) increased when the cookies were enriched with lemon balm and nettle extracts. Among the cookies studied, those prepared with BHA and 0.1 and 0.2% addition of lemon balm extracts were characterized by the highest scores for aroma, taste, and overall acceptability. Incorporation of BHA and 0.02% hyssop extract into the cookies caused a decrease of PV values (the peroxide value) for fat extracted from the cookies after 3 months of their storage compared to a (control) sample without additives and produced the lowest K232 values. Changes in the p-AnV values for the fat samples studied occurred gradually and slowly during the storage and the obtained values were lower compared to the control sample. All of the studied fat samples also showed a higher ability to scavenge DPPH radicals than the control sample. Considering both PV and p-AnV values as indicators of fat oxidation, BHA protected fat extracted from cookies against oxidation better than the herbal extracts used.
Murali Ganesan, Moses New-Aaron, Raghubendra Dagur, Edward Makarov, Weimin Wang, Kusum Kharbanda, Srivatsan Kidambi, Larisa Poluektova, Natalia Osna
Published: 10 December 2019
by MDPI
Biomolecules, Volume 9; doi:10.3390/biom9120851

Abstract:In an era of improved survival due to modern antiretroviral therapy, liver disease has become a major cause of morbidity and mortality, resulting in death in 15–17% of human immunodeficiency virus (HIV)-infected patients. Alcohol enhances HIV-mediated liver damage and promotes the progression to advanced fibrosis and cirrhosis. However, the mechanisms behind these events are uncertain. Here, we hypothesize that ethanol metabolism potentiates accumulation of HIV in hepatocytes, causing oxidative stress and intensive apoptotic cell death. Engulfment of HIV-containing apoptotic hepatocytes by non-parenchymal cells (NPCs) triggers their activation and liver injury progression. This study was performed on primary human hepatocytes and Huh7.5-CYP cells infected with HIV-1ADA, and major findings were confirmed by pilot data obtained on ethanol-fed HIV-injected chimeric mice with humanized livers. We demonstrated that ethanol exposure potentiates HIV accumulation in hepatocytes by suppressing HIV degradation by lysosomes and proteasomes. This leads to increased oxidative stress and hepatocyte apoptosis. Exposure of HIV-infected apoptotic hepatocytes to NPCs activates the inflammasome in macrophages and pro-fibrotic genes in hepatic stellate cells. We conclude that while HIV and ethanol metabolism-triggered apoptosis clears up HIV-infected hepatocytes, continued generation of HIV-expressing apoptotic bodies may be detrimental for progression of liver inflammation and fibrosis due to constant activation of NPCs.
Irene Jiménez-Munguía, Arseniy Fedorov, Inna Abdulaeva, Kirill Birin, Yury Ermakov, Oleg Batishchev, Yulia Gorbunova, Valerij Sokolov
Published: 10 December 2019
by MDPI
Biomolecules, Volume 9; doi:10.3390/biom9120853

Abstract:Photosensitizers (PSs) represent a group of molecules capable of generating reactive oxygen species (ROS), such as singlet oxygen (SO); thus, they are considered to be promising agents for anti-cancer therapy. The enhancement of the photodynamic efficiency of these compounds requires increasing the PS activity in the cancer cell milieu and exactly at the target cells. In the present work, we report the synthesis, lipid membrane binding and photodynamic activity of three novel cationic PSs based on β-imidazolyl-substituted porphyrin and its Zn(II) and In(III) complexes (1H2, 1Zn and 1In). Comparison of the behavior of the investigated porphyrins at the bilayer lipid membrane (BLM) demonstrated the highest adsorption for the 1In complex and the lowest one for 1Zn. The photodynamic efficiency of these porphyrins was evaluated by determining the oxidation rate of the styryl dye, di-4-ANEPPS, incorporated into the lipid membrane. These rates were proportional to the surface density (SD) of the porphyrin molecules at the BLM and were roughly the same for all three porphyrins. This indicates that the adsorption of these porphyrins at the BLM determines their photodynamic efficiency rather than the extinction or quantum yield of singlet oxygen.