A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries.

Identifying the interactome for a protein of interest is challenging due to the large number of possible binders. High-throughput experimental approaches narrow down possible binding partners but often include false positives. Furthermore, they provide no information about what the binding region is (e.g., the binding epitope). We introduce a novel computational pipeline based on an AlphaFold2 (AF) Competitive Binding Assay (AF-CBA) to identify proteins that bind a target of interest from a pull-down experiment and the binding epitope. Our focus is on proteins that bind the Extraterminal (ET) domain of Bromo and Extraterminal domain (BET) proteins, but we also introduce nine additional systems to show transferability to other peptide-protein systems. We describe a series of limitations to the methodology based on intrinsic deficiencies of AF and AF-CBA to help users identify scenarios where the approach will be most useful. Given the method's speed and accuracy, we anticipate its broad applicability to identify binding epitope regions among potential partners, setting the stage for experimental verification.

Sifting Through the Noise: A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries.

Identifying the interactome for a protein of interest is challenging due to the large number of possible binders. High-throughput experimental approaches narrow down possible binding partners, but often include false positives. Furthermore, they provide no information about what the binding region is (e.g. the binding epitope). We introduce a novel computational pipeline based on an AlphaFold2 (AF) Competition Assay (AF-CBA) to identify proteins that bind a target of interest from a pull-down experiment, along with the binding epitope. Our focus is on proteins that bind the Extraterminal (ET) domain of Bromo and Extraterminal domain (BET) proteins, but we also introduce nine additional systems to show transferability to other peptide-protein systems. We describe a series of limitations to the methodology based on intrinsic deficiencies to AF and AF-CBA, to help users identify scenarios where the approach will be most useful. Given the speed and accuracy of the methodology, we expect it to be generally applicable to facilitate target selection for experimental verification starting from high-throughput protein libraries.

Cardiotoxicity and ROS Protection Assessment of three Structure-Related N-Acylhydrazones with Potential for the Treatment of Neurodegenerative Diseases.

The senescence process is associated with accumulated oxidative damage and increased metal concentration in the heart and brain. Besides, abnormal metal-protein interactions have also been linked with the development of several conditions, including Alzheimer's and Parkinson's diseases. Over the years we have described a series of structure-related compounds with different activities towards models of such diseases. In this work, we evaluated the potential of three N-acylhydrazones (INHHQ: 8-hydroxyquinoline-2-carboxaldehyde isonicotinoyl hydrazone, HPCIH: pyridine-2-carboxaldehyde isonicotinoyl hydrazone and X1INH: 1-methyl-1H-imidazole-2-carboxaldehyde isonicotinoyl hydrazone) to prevent oxidative stress in cellular models, with the dual intent of being active on this pathway and also to confirm their lack of cardiotoxicity as an important step in the drug development process, especially considering that the target population often presents cardiovascular comorbidity. The 8-hydroxyquinoline-contaning compound, INHHQ, exhibits a significant cardioprotective effect against hydrogen peroxide and a robust antioxidant activity. However, this compound is the most toxic to the studied cell models and seems to induce oxidative damage on its own. Interestingly, although not possessing a phenol group in its structure, the new-generation 1-methylimidazole derivative X1INH showed a cardioprotective tendency towards H9c2 cells, demonstrating the importance of attaining a compromise between activity and intrinsic cytotoxicity when developing a drug candidate.

The effect of temperature on the synthesis of magnetite nanoparticles by the coprecipitation method.

Magnetic nanoparticles, such as magnetite (Fe3O4), exhibit superparamagnetic properties below 15 nm at room temperature. They are being explored for medical applications, and the coprecipitation technique is preferred for cost-effective production. This study investigates the impact of synthesis temperature on the nanoparticles' physicochemical characteristics. Two types of magnetic analysis were conducted. Samples T 40, T 50, and T 60 displayed superparamagnetic behavior, as evidenced by the magnetization curves. The experiments verified the development of magnetic nanoparticles with an average diameter of approximately dozens of nanometers, as determined by various measurement methods such as XDR, Raman, and TEM. Raman spectroscopy showed the characteristic bands of the magnetite phase at 319, 364, 499, and 680 cm-1. This was confirmed in the second analysis with the ZFC-FC curves, which showed that the samples' blocking temperatures were below ambient temperature. ZFC-FC curves revealed a similar magnetization of about 30 emu/g when applying a magnetic field of 5 kOe.

Protocol for production and purification of SARS-CoV-2 3CLpro.

3CLpro protease from SARS-CoV-2 is a primary target for COVID-19 antiviral drug development. Here, we present a protocol for 3CLpro production in Escherichia coli. We describe steps to purify 3CLpro, expressed as a fusion with the Saccharomyces cerevisiae SUMO protein, with yields up to 120 mg L-1 following cleavage. The protocol also provides isotope-enriched samples suitable for nuclear magnetic resonance (NMR) studies. We also present methods to characterize 3CLpro by mass spectrometry, X-ray crystallography, heteronuclear NMR, and a Förster-resonance-energy-transfer-based enzyme assay. For complete details on the use and execution of this protocol, please refer to Bafna et al.1.

Toxicological Effects of Fine Particulate Matter (PM2.5): Health Risks and Associated Systemic Injuries-Systematic Review.

Previous studies focused on investigating particulate matter with aerodynamic diameter ≤ 2.5 µm (PM2.5) have shown the risk of disease development, and association with increased morbidity and mortality rates. The current review investigate epidemiological and experimental findings from 2016 to 2021, which enabled the systemic overview of PM2.5's toxic impacts on human health. The Web of Science database search used descriptive terms to investigate the interaction among PM2.5 exposure, systemic effects, and COVID-19 disease. Analyzed studies have indicated that cardiovascular and respiratory systems have been extensively investigated and indicated as the main air pollution targets. Nevertheless, PM2.5 reaches other organic systems and harms the renal, neurological, gastrointestinal, and reproductive systems. Pathologies onset and/or get worse due to toxicological effects associated with the exposure to this particle type, since it can trigger several reactions, such as inflammatory responses, oxidative stress generation and genotoxicity. These cellular dysfunctions lead to organ malfunctions, as shown in the current review. In addition, the correlation between COVID-19/Sars-CoV-2 and PM2.5 exposure was also assessed to help better understand the role of atmospheric pollution in the pathophysiology of this disease. Despite the significant number of studies about PM2.5's effects on organic functions, available in the literature, there are still gaps in knowledge about how this particulate matter can hinder human health. The current review aimed to approach the main findings about the effect of PM2.5 exposure on different systems, and demonstrate the likely interaction of COVID-19/Sars-CoV-2 and PM2.5.

Silver-modified nitrogen-doped graphene quantum dots as a sensor for formaldehyde in milk using headspace micro-extraction on a single-drop of aqueous nanoparticles dispersion.

BACKGROUND: Fraudulent practices used to distort the quality of milk and derivatives include the addition of formaldehyde. RESULTS: A formaldehyde sensor was developed based on the luminescence of newly proposed N-doped graphene quantum dots modified with silver (N-GQDs-Ag) that were prepared using a simple method. A microdroplet of the nanoparticle dispersion was used to collect formaldehyde vapor by headspace single-drop micro-extraction (HS-SDME). After, the microdroplet was diluted in water, the nanoparticle photoluminescence quenching, caused by the analyte, was measured. The strong luminescent quenching allowed a detection limit at 1.7 × 10-4% w/v. Response was selective towards formaldehyde. SIGNIFICANCE: The method was effective and a cost-effective method for screening analysis of milk samples with matrix interferences minimized due to the nature of nanoparticle (prepared using Tollen's reagent) and due to the probing at the headspace of the sample cell. Results were statistically similar to those obtained using liquid chromatography.

Use of selective quenching of a photoluminescent probe based on a Eu(III) ß-diketonate complex for determination of methylmercury in produced water after liquid-liquid extraction.

An Eu(III) ß-diketonate complex was produced and employed as a photoluminescent probe to determine methylmercury (CH3Hg+). To establish its molecular structure, the Eu(III) complex was characterized by elemental (CHNS) and thermogravimetric analyses and infrared spectroscopy. After establishing robust conditions to use the Eu(III) complex as an analytical probe, it was employed for the analysis of produced water (PW) samples with the analytical response based on the luminescence suppression proportional to the concentration of CH3Hg+ (a linear model after normalization of the response within the concentration range from 0.2 µg L-1 up to 2.0 µg L-1). Selectivity was guaranteed by a simple liquid-liquid extraction of the analyte in dichloromethane, which also allowed a 50 times pre-concentration factor. The instrumental limit of quantification of 0.2 µg L-1 is equal to the limit established in Brazilian resolution for total mercury content in waters, but pre-concentration (50 times factor) improved the overall method limit of quantification down to 4 ng L-1. Recovery results agreed with the ones achieved using cold vapor atomic absorption spectrometry.

The use of hedgerows to mitigate pesticide exposure of a population living in a rural area.

Farmer populations living in houses inside vegetable gardens are exposed to indoor pesticide pollution. The pulverization drift and volatile pesticides transported by wind are important sources of indoor pollution, which can be mitigated by hedgerows. This study was the first attempt in Brazil to investigate the efficiency of six different hedgerow species in reducing pesticide residues in air. A fluorescent compound (p-aminobenzoic acid or PABA) was introduced in the sprayed pesticide fluid that traced the pesticide in the water. Samples were collected in Petri dishes positioned on stakes at different heights in front of and behind the hedgerows. Data indicated barrier efficiency of up to 99%. Simulation of nontarget drift contamination with herbicide concentrations exhibited reduced senescence effects on leaves and posed no threat to survival. Hedgerows are feasible, simple, and inexpensive techniques, which may be used easily by farmers, independent of external support and efficiently mitigating indoor pesticide pollution, thus protecting human health. Integr Environ Assess Manag 2022;18:19-24. © 2021 SETAC.

Assessment of the effects of seasonality on the ecotoxicity induced by the particulate matter using the animal model Caenorhabditis elegans.

The present work aimed to establish potential changes in the ecotoxicological effects on C. elegans induced by the exposure of coarse (PM10) and fine (PM2.5) particulate matter collected during dry and rainy periods. We also analyzed the probable influence on the change of a city's activities as the mega-events result in air quality. The element levels evaluation was performed on PM, on the solutions of exposure, and C. elegans after exposure. Biochemical essays were performed to evaluate damage to C. elegans. The results showed that infrastructure works increased the levels of pollutants, generating increases in the concentrations of PM2.5 and PM10. The biochemical results suggested effects mediated by different mechanisms, where PM2.5 induced an increase in antioxidant capacity with activation of the defense system and lipoperoxidation. Results suggest that PM10 reduces the antioxidant capacity and activates the glutathione S-transferase activity enzymatic action, but also induces lipoperoxidation in all groups of animals exposed to samples collected during the dry period of 2016. Individuals exposed to PM2.5 in 2017 wet and dry periods and PM10 in 2016 and 2017 dry periods shown a decrease in size compared to controls, while for fertility data, there was a decrease only in individuals exposed to PM2.5 in the periods that the highest levels of PM concentration. We conclude that despite the positive issues linked to the hosting of mega-events, their infrastructure requirements can compromise air quality and bring damage related to lipoperoxidation and physiological changes in the life cycle of biological systems, such as what happened to C. elegans exposed to tested extracts. Also, rainy events reduced the presence of these pollutants, washing the atmosphere.

Assessment of air quality changes during COVID-19 partial lockdown in a Brazilian metropolis: from lockdown to economic opening of Rio de Janeiro, Brazil.

Abstract: During the COVID-19 pandemic, restrictive measures are taken by several cities around the world, as well as Rio de Janeiro, reducing routine activities in large urban centers and primary pollutant emissions. This study aims to assess air quality during this partial lockdown through O3, CO, and PM10 concentrations and meteorological data collected in five air quality monitoring stations spread over the whole city, considering the substantial changes in city routine. The period evaluated starts in March 2020, when the partial lockdown was decreed, and ends in September 2020, when economic opening ended. Compared with 2019 data, CO concentration reduced significantly, as expected since the main source of these pollutants is vehicular traffic. O3 concentration increased, most probably as a consequence of the reduction in primary pollutants. On the other hand, PM10 concentration did not vary significantly. From June to September, pollutant concentrations increased responding to the economic opening. Thereby, the partial lockdown contributed to improving air quality in Rio de Janeiro City, which means that changes in work format may be an alternative to reduce atmospheric pollution in big cities, since home office contributes to mobility reductions, and consequently to vehicular emissions. Highlights: • Lockdown contributed to CO reduction and O3 increase.• Differences on rain profile explain low variation on PM10 concentrations.• Lockdown has been like a very long weekend concerning atmospheric pollution.• Home office and distance learning improve air quality. Supplementary Information: The online version contains supplementary material available at 10.1007/s11869-021-01127-2.

Magnetic Characterization by Scanning Microscopy of Functionalized Iron Oxide Nanoparticles.

This study aimed to systematically understand the magnetic properties of magnetite (Fe3O4) nanoparticles functionalized with different Pluronic F-127 surfactant concentrations (Fe3O4@Pluronic F-127) obtained by using an improved magnetic characterization method based on three-dimensional magnetic maps generated by scanning magnetic microscopy. Additionally, these Fe3O4 and Fe3O4@Pluronic F-127 nanoparticles, as promising systems for biomedical applications, were prepared by a wet chemical reaction. The magnetization curve was obtained through these three-dimensional maps, confirming that both Fe3O4 and Fe3O4@Pluronic F-127 nanoparticles have a superparamagnetic behavior. The as-prepared samples, stored at approximately 20 °C, showed no change in the magnetization curve even months after their generation, resulting in no nanoparticles free from oxidation, as Raman measurements have confirmed. Furthermore, by applying this magnetic technique, it was possible to estimate that the nanoparticles' magnetic core diameter was about 5 nm. Our results were confirmed by comparison with other techniques, namely as transmission electron microscopy imaging and diffraction together with Raman spectroscopy. Finally, these results, in addition to validating scanning magnetic microscopy, also highlight its potential for a detailed magnetic characterization of nanoparticles.

The aroylhydrazone INHHQ prevents memory impairment induced by Alzheimer's-linked amyloid-ß oligomers in mice.

Converging evidence indicates that neurotoxicity and memory impairment in Alzheimer's disease is induced by brain accumulation of soluble amyloid-ß oligomers (AßOs). Physiological metals are poorly distributed and concentrated in the senile plaques typical of Alzheimer's disease, where they may be coordinated to the amyloid-ß peptide (Aß). Indeed, zinc and copper increase Aß oligomerization and toxicity. Metal-protein attenuating compounds represent a class of agents proposed for Alzheimer's disease treatment, as they reduce abnormal interactions of metal ions with Aß, inhibit Aß oligomerization and prevent deleterious redox reactions in the brain. The present work investigates the protective action of an isoniazid-derived aroylhydrazone, INHHQ, on AßO-induced memory impairment. Systemic administration of a single dose of INHHQ (1 mg/kg) prevented both short-term and long-term memory impairment caused by AßOs in mice. In-vitro studies showed that INHHQ prevents Cu(Aß)-catalyzed production of reactive oxygen species. Although the mechanism of protection by INHHQ is not yet fully understood at a molecular level, the results reported herein certainly point to the value of aroylhydrazones as promising neuroprotective agents in Alzheimer's disease and related disorders.

Aroylhydrazones constitute a promising class of 'metal-protein attenuating compounds' for the treatment of Alzheimer's disease: a proof-of-concept based on the study of the interactions between zinc(II) and pyridine-2-carboxaldehyde isonicotinoyl hydrazone.

With the increasing life expectancy of the world's population, neurodegenerative diseases, such as Alzheimer's disease (AD), will become a much more relevant public health issue. This fact, coupled with the lack of efficacy of the available treatments, has been driving research directed to the development of new drugs for this pathology. Metal-protein attenuating compounds (MPACs) constitute a promising class of agents with potential application on the treatment of neurodegenerative diseases, such as AD. Currently, most MPACs are based on 8-hydroxyquinoline. Recently, our research group has described the hybrid aroylhydrazone containing the 8-hydroxyquinoline group INHHQ as a promising MPAC. By studying the known structure-related ligand HPCIH, which does not contain the phenol moiety, as a simplified chemical model for INHHQ, we aimed to clarify the real impact of the aroylhydrazone group for the MPAC activity of a compound with potential anti-Alzheimer's activity. The present work describes a detailed solution and solid-state study of the coordination of HPCIH with Zn2+ ions, as well as its in vitro binding-ability towards this metal in the presence of the Aß(1-40) peptide. Similar to INHHQ, HPCIH is able to efficiently compete with Aß(1-40) for Zn2+ ions, performing as expected for an MPAC. The similarity between the behaviors of both ligands is remarkable. Taken together, the data presented herein point to aroylhydrazones, such as the compounds HPCIH and the previously published INHHQ, as encouraging MPACs for the treatment of AD.

A moderate metal-binding hydrazone meets the criteria for a bioinorganic approach towards Parkinson's disease: Therapeutic potential, blood-brain barrier crossing evaluation and preliminary toxicological studies.

Alzheimer's and Parkinson's diseases share similar amyloidogenic mechanisms, in which metal ions might play an important role. In this last neuropathy, misfolding and aggregation of α-synuclein (α-Syn) are crucial pathological events. A moderate metal-binding compound, namely, 8-hydroxyquinoline-2-carboxaldehyde isonicotinoyl hydrazone (INHHQ), which was previously reported as a potential 'Metal-Protein Attenuating Compound' for Alzheimer's treatment, is well-tolerated by healthy Wistar rats and does not alter their major organ weights, as well as the tissues' reduced glutathione and biometal levels, at a concentration of 200mgkg-1. INHHQ definitively crosses the blood-brain barrier and can be detected in the brain of rats so late as 24h after intraperitoneal administration. After 48h, brain clearance is complete. INHHQ is able to disrupt, in vitro, anomalous copper-α-Syn interactions, through a mechanism probably involving metal ions sequestering. This compound is non-toxic to H4 (human neuroglioma) cells and partially inhibits intracellular α-Syn oligomerization. INHHQ, thus, shows definite potential as a therapeutic agent against Parkinson's as well.

Probing the Surface of a Laccase for Clues towards the Design of Chemo-Enzymatic Catalysts.

Systems featuring a multi-copper oxidase associated with transition-metal complexes can be used to perform oxidation reactions in mild conditions. Here, a strategy is presented for achieving a controlled orientation of a ruthenium-polypyridyl graft at the surface of a fungal laccase. Laccase variants are engineered with unique surface-accessible lysine residues. Distinct ruthenium-polypyridyl-modified laccases are obtained by the reductive alkylation of lysine residues precisely located relative to the T1 copper centre of the enzyme. In none of these hybrids does the presence of the graft compromise the catalytic efficiency of the enzyme on the substrate 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid). Furthermore, the efficiency of the hybrids in olefin oxidation coupled to the light-driven reduction of O2 is highly dependent on the location of the graft at the enzyme surface. Simulated RuII -CuII electron coupling values and distances fit well the observed reactivity and could be used to guide future hybrid designs.

Structural Solutions for Low-Cost Bamboo Frames: Experimental Tests and Constructive Assessments.

Experimental tests and constructive assessments are presented for a simple bamboo framed structure with innovative low-cost and low technology joints, specifically conceived for small buildings in developing countries. Two full scale one-storey bamboo frames have been designed by using the simplest joints solution among three different tested typologies. The entire building process is based on low-technology and natural materials: bamboo canes, wooden cylinders, plywood plates and canapé rods. The first full scale specimen (Unit A) is a one-storey single deck truss structure subjected to monotonic collapse test; the second full scale specimen (Unit B) is a one-storey double deck truss structure used to evaluate the construction time throughout assembling tests. The first full scale specimen showed ductility in collapse and ease in strengthening; the second one showed remarkable ease and speed in assembling structural elements. Finally several constructive solutions are suggested for the design of simple one-storey buildings; they are addressed to four purposes (housing, school, chapel, health center) by the composition of the proposed full scale bamboo frames. Ease of use and maintenance with a low level of technology contribute to application in developing countries although not exclusively.