Subject: Physical Sciences, Acoustics Keywords: spatial light modulators; laser trapping; holographic optical tweezers
Online: 26 March 2021 (15:10:07 CET)
Spatial light modulators (SLMs) have been widely used to achieve dynamic control of optical traps. Often, holographic optical tweezers have been presumed to provide nanometer or sub-nanometer positioning accuracy. It is known that some features concerning the digitalized structure of SLMs cause a loss in steering efficiency of the optical trap, but their effect on trap positioning accuracy has been scarcely analyzed. On the one hand, the SLM look-up-table, which we found to depend on laser power, produces positioning deviations when the trap is moved at the micron scale. On the other hand, phase quantization, which makes linear phase gratings become phase staircase profiles, leads to unexpected local errors in the steering angle. We have tracked optically-trapped microspheres with sub-nanometer accuracy to study the effects on trap positioning, which can be as high as 2 nm in certain cases. We have also implemented a correction strategy that enabled the reduction of errors down to 0.3 nm.
ARTICLE | doi:10.20944/preprints202103.0293.v1
Subject: Chemistry And Materials Science, Biomaterials Keywords: Metal-Organic Framework; MOF-801; Modulators; Ethanol; Marangoni Flow Effect
Online: 10 March 2021 (16:22:10 CET)
We report that ethanol, used together with water, plays a crucial role in tuning the structures of a zirconium-based Metal-Organic Framework, the 12-connected MOF-801, and the possible mechanisms of this modulating effect. By employing the cosolvent system of ethanol and water just under room temperature without the presence of a monotopic carboxylic acid as the modulator, MOF-801 in various morphologies of different sizes can be synthesized. The linear correlation between the ethanol/water ratio and the crystal sizes is also demonstrated. The growth mechanism is mainly explained by ethanol’s binding with the metal ion clusters and the Marangoni Flow Effect. Ethanol competes with the linker molecules in coordinating with the Zr metal clusters, a role similar to that of the modulators. The Marangoni Flow Effect, which dominates at a certain solvent ratio, further promotes the 1-D alignment of the MOF-801 crystals.
ARTICLE | doi:10.20944/preprints202307.0058.v1
Subject: Medicine And Pharmacology, Pharmacy Keywords: lactoperoxidase; Streptococcus mutans; biofilm; dental caries; lactoperoxidase system modulators; cariogenic biofilm
Online: 3 July 2023 (12:58:53 CEST)
The lactoperoxidase (LPO) system shows promise in the prevention of dental caries, a common chronic disease. This system has antimicrobial properties and is part of the non-specific antimicrobial immune system. Understanding the efficacy of the LPO system in the fight against biofilms could provide information on alternative strategies for the prevention and treatment of caries. In this study, the enzymatic system was modified using four different (pseudo)halide substrates (thiocyanate, thiocyanate-iodide mixture, selenocyanate, and iodide). The study evaluated the effects of such modifications on the ability of Streptococcus mutans to form a biofilm, the synthesis of insoluble polysaccharides, the synthesis of lactate, the consumption of glucose and sucrose, the concentrations of intracellular NAD+ and NADH and the efficiency of transmembrane glucose transport by phosphoenolpuryvate PEP-carbohydrate phosphotransferase (PTS). The results showed that the LPO-iodide system had the strongest inhibitory effect on biofilm growth and lactate synthesis (complete inhibition). This was associated with an increase in the NAD+/NADH ratio and an inhibition of glucose PTS activity. The LPO-selenocyanate system showed a moderate inhibitory effect on biofilm biomass growth and lactate synthesis. The other systems showed relatively small inhibition of lactate synthesis and glucose PTS but no effect on the growth of biofilm biomass. This study provides a basis for further research on the use of alternative substrates of the LPO system, particularly the LPO-iodide system, in the prevention and control of biofilm-related diseases.
ARTICLE | doi:10.20944/preprints202011.0333.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: peroxiporins; oxidative stress; hydrogen peroxide; water channels; Sigma1 receptors; Sigma1 receptor modulators; neurodegenerative diseases
Online: 12 November 2020 (09:33:34 CET)
Specific aquaporins (AQP), called peroxyporins, play a relevant role in controlling H2O2 permeability and ensure reactive oxygen species wasting during oxidative stress. Another target involved in oxidative stress is the Sigma1 Receptor (S1R), since its activation is triggered by oxidative or endoplasmic reticulum stress. Herein we evaluated the effect of S1R modulators on AQP-dependent water permeability in the presence and in the absence of oxidative stress. Applying stopped-flow light scattering and fluorescent probe methods, water and hydrogen peroxide permeability in Hela cells have been studied. Results evidenced that S1R agonists can restore water permeability in heat-stressed cells and the co-administration with a S1R antagonist totally counteracted the ability to restore the water permeability. All compounds except one were able to counteract the oxidative stress of HeLa cells specifically knocked down for S1R. Taken together, our results support the hypothesis that the investigated compounds act as dual aquaporin and Sigma1 receptor (DAS) modulators. The finding that small molecules can modulate both AQP and S1R opens a new direction toward the identification of innovative drugs able to regulate cell survival during oxidative stress in pathologic conditions, like cancer and degenerative diseases.
REVIEW | doi:10.20944/preprints202202.0316.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: Selenoprotein Glutathione Peroxidase 4 (GPX4); Reduced Glutathione (GSH); ferroptosis; lipid peroxidation; ferroptosis modulators; small molecules targeting GPX4
Online: 24 February 2022 (12:05:30 CET)
The selenoprotein glutathione peroxidase 4 (GPX4) is one of the main antioxidant mediators in the human body. Its central function involves the reduction of complex hydroperoxides into their respective alcohols often using reduced Glutathione (GSH) as a reducing agent. GPX4 has become a hotspot therapeutic target in biomedical research following its characterization as a chief regulator of ferroptosis, and its subsequent recognition as a specific pharmacological target for the treatment of an extensive variety of human diseases including cancers and neurodegenerative disorders. Several recent studies have provided insights into how GPX4 is distinguished from the rest of the glutathione peroxidase family, the unique biochemical properties of GPX4, how GPX4 is related to lipid peroxidation and ferroptosis, and how the enzyme may be modulated as a potential therapeutic target. This current report aims to review the literature underlying all these insights and present an up-to-date perspective on the current understanding of GPX4 as a potential therapeutic target.
ARTICLE | doi:10.20944/preprints201912.0374.v1
Subject: Biology And Life Sciences, Biophysics Keywords: alpha-fetoprotein; estrogens; selective estrogen receptor modulators; homology-based modeling; molecular docking; protein-ligand interaction; amino acid substitutions
Online: 29 December 2019 (08:08:23 CET)
Alpha-fetoprotein (AFP) is a major embryo- and tumor-associated protein capable of binding and transporting variety of hydrophobic ligands including estrogens. AFP has been shown to inhibit estrogen receptor (ER)-positive tumor growth and this can be attributed to its estrogen-binding ability. Despite AFP has long been investigated, its three-dimensional (3D) structure has not been experimentally resolved and molecular mechanisms underlying AFP-ligand interaction remain obscure. In our study we constructed homology-based 3D model of human AFP (HAFP) with the purpose to perform docking of ERα ligands, three agonists (17β-estradiol, estrone and diethylstilbestrol) and three antagonists (tamoxifen, afimoxifene and endoxifen) into the obtained structure. Based on ligand docked scoring function, we identified three putative estrogen- and antiestrogen-binding sites with different ligand binding affinities. Two high-affinity sites were located in (i) a tunnel formed within HAFP subdomains IB and IIA and (ii) opposite side of the molecule in a groove originating from cavity formed between domains I and III, while (iii) the third low-affinity site was found at the bottom of the cavity. 100 ns MD simulation allowed studying their geometries and showed that HAFP-estrogen interactions occur due to van der Waals forces, while both hydrophobic and electrostatic interactions were almost equally involved in HAFP-antiestrogen binding. MM/GBSA rescoring method estimated binding free energies (ΔGbind) and showed that antiestrogens have higher affinities to HAFP as compared to estrogens. We performed in silico point substitutions of amino acid residues to confirm their roles in HAFP-ligand interactions and showed that Thr132, Leu138, His170, Phe172, Ser217, Gln221, His266, His316, Lys453, and Asp478 residues along two disulfide bonds, Cys224-Cys270 and Cys269-Cys277 have key roles in both HAFP-estrogen and HAFP-antiestrogen binding. Data obtained in our study contribute to understanding mechanisms underlying protein-ligand interactions and anti-cancer therapy strategies based on ER-binding ligands.
REVIEW | doi:10.20944/preprints201906.0192.v1
Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: voltage-gated calcium channels; major depressive disorder; autism spectrum disorder; schizophrenia; bipolar disorder; attention-deficit and hyperactivity disorder; anxiety; calcium channel modulators; psychiatric disorders; auxiliary subunits; genetic risk variations
Online: 20 June 2019 (04:16:52 CEST)
Psychiatric disorders are mental, behavioral or emotional disorders. These conditions are prevalent, one in four adults suffer from any type of psychiatric disorders world-wide. It has always been observed that psychiatric disorders have a genetic component, however new methods to sequence full genomes of large cohorts have identified with high precision genetic risk loci for these conditions. Psychiatric disorders include, but are not limited to, bipolar disorder, schizophrenia, autism spectrum disorder, anxiety disorders, major depressive disorder, and attention-deficit and hyperactivity disorder. Several risk loci for psychiatric disorders fall within genes that encode for voltage-gated calcium channels (CaVs). Calcium entering through CaVs is key for multiple neuronal processes. In this review, we will summarize recent findings that link CaVs and their auxiliary subunits to psychiatric disorders. First, we will provide a general overview of CaVs structure, classification, function, expression and pharmacology. Next, we will summarize tools and databases to study risk loci associated with psychiatric disorders. We will examine functional studies of risk variations in CaV genes when available. We will review pharmacological evidence of the use of CaV modulators to treat psychiatric disorders. Our review will be of interest for those studying pathophysiological aspects of CaVs.