A highly specific aptamer for the SARS-CoV-2 spike protein from the authentic strain.

DNA aptamers are oligonucleotides that specifically bind to target molecules, similar to how antibodies bind to antigens. We identified an aptamer named MEZ that is highly specific to the receptor-binding domain, RBD, of the SARS-CoV-2 spike protein from the Wuhan-Hu-1 strain. The SELEX procedure was utilized to enrich the initial 31-mer oligonucleotide library with the target aptamer. The aptamer identification was performed using the novel protocol based on nanopore sequencing developed in this study. The MEZ aptamer was chemically synthesized and tested for binding with the SARS-CoV-2 RBD of the spike protein from different strains. The Kd is 6.5 nM for the complex with the RBD from the Wuhan-Hu-1 strain, which is comparable with known aptamers; the advantage is that the MEZ aptamer is smaller than known analogs. The proposed aptamer is highly selective for the RBD protein from the Wuhan-Hu-1 strain and does not form complexes with the RBD from Beta, Delta and Omicron strains. Experimental and theoretical studies together revealed the molecular mechanism of aptamer binding. The aptamer occupies the same binding site as ACE2 when bound to the RBD. The 3'-end of the MEZ aptamer is important for complex formation and is responsible for the discrimination of the RBD protein from a specific strain. The 5'-end is responsible for the formation of a loop in the 3D structure of the aptamer, which is important for proper binding.

Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms.

We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work. They were derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of reacting with the catalytic cysteine residue in the MPro active site. The reaction mechanisms of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) simulations. The results show that all four compounds form covalent adducts with the catalytic cysteine Cys 145 of MPro. From the chemical perspective, the reactions of these four molecules with MPro follow three distinct mechanisms. The reactions are initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand is accompanied by the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir (which has a reactive nitrile group) leads to the formation of a covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site. Our results contribute to the ongoing search for efficient inhibitors of the SARS-CoV-2 enzymes.

Selectivity of Exhaled Breath Biomarkers of Lung Cancer in Relation to Cancer of Other Localizations.

Lung cancer is a leading cause of death worldwide, mostly due to diagnostics in the advanced stage. Therefore, the development of a quick, simple, and non-invasive diagnostic tool to identify cancer is essential. However, the creation of a reliable diagnostic tool is possible only in case of selectivity to other diseases, particularly, cancer of other localizations. This paper is devoted to the study of the variability of exhaled breath samples among patients with lung cancer and cancer of other localizations, such as esophageal, breast, colorectal, kidney, stomach, prostate, cervix, and skin. For this, gas chromatography-mass spectrometry (GC-MS) was used. Two classification models were built. The first model separated patients with lung cancer and cancer of other localizations. The second model classified patients with lung, esophageal, breast, colorectal, and kidney cancer. Mann-Whitney U tests and Kruskal-Wallis H tests were applied to identify differences in investigated groups. Discriminant analysis (DA), gradient-boosted decision trees (GBDT), and artificial neural networks (ANN) were applied to create the models. In the case of classifying lung cancer and cancer of other localizations, average sensitivity and specificity were 68% and 69%, respectively. However, the accuracy of classifying groups of patients with lung, esophageal, breast, colorectal, and kidney cancer was poor.

Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang.

We report the results of a computational study of the mechanism of the light-induced chemical reaction of chromophore hydration in the fluorescent protein Dreiklang, responsible for its switching from the fluorescent ON-state to the dark OFF-state. We explore the relief of the charge-transfer excited-state potential energy surface in the ON-state to locate minimum energy conical intersection points with the ground-state energy surface. Simulations of the further evolution of model systems allow us to characterize the ground-state reaction intermediate tentatively suggested in the femtosecond studies of the light-induced dynamics in Dreiklang and finally to arrive at the reaction product. The obtained results clarify the details of the photoswitching mechanism in Dreiklang, which is governed by the chemical modification of its chromophore.

Modeling photophysical properties of the bacteriophytochrome-based fluorescent protein IFP1.4.

An enhanced interest in the phytochrome-based fluorescent proteins is explained by their ability to absorb and emit light in the far-red and infra-red regions particularly suitable for bioimaging. The fluorescent protein IFP1.4 was engineered from the chromophore-binding domain of a bacteriophytochrome in attempts to increase the fluorescence quantum yield. We report the results of simulations of structures in the ground S0 and excited S1 electronic states of IFP1.4 using the methods of quantum chemistry and quantum mechanics/molecular mechanics. We construct different protonation states of the biliverdin (BV) chromophore in the red-absorbing form of the protein by moving protons from the BV pyrrole rings to a suitable acceptor within the system and show that these structures are close in energy but differ by absorption bands. For the first time, we report structures of the minimum energy conical intersection points S1/S0 on the energy surfaces of BV in the protein environment and describe their connection to the local minima in the excited S1 state. These simulations allow us to characterize the deactivation routes in IFP1.4.

First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route.

Structures and optical spectra of the green fluorescent protein (GFP) forms along the proton transfer route A→I→B are characterized by first-principles calculations. We show that in the ground electronic state the structure representing the wild-type (wt) GFP with the neutral chromophore (A-form) is lowest in energy, whereas the systems with the anionic chromophore (B- and I-forms) are about 1 kcal/mol higher. In the S65T mutant, the structures with the anionic chromophore are significantly lower in energy than the systems with the neutral chromophore. The role of the nearby amino acid residues in the chromophore-containing pocket is re-examined. Calculations reveal that the structural differences between the I- and B-forms (the former has a slightly red-shifted absorption relative to the latter) are based not on the Thr203 orientation, but on the Glu222 position. In the case of wt-GFP, the hydrogen bond between the chromophore and the His148 residue stabilizes the structures with the deprotonated phenolic ring in the I- and B-forms. In the S65T mutant, concerted contributions from the His148 and Thr203 residues are responsible for a considerable energy gap between the lowest energy structure of the B type with the anionic chromophore from other structures.

Recent oceanic changes in the Arctic in the context of long-term observations.

This synthesis study assesses recent changes of Arctic Ocean physical parameters using a unique collection of observations from the 2000s and places them in the context of long-term climate trends and variability. Our analysis demonstrates that the 2000s were an exceptional decade with extraordinary upper Arctic Ocean freshening and intermediate Atlantic water warming. We note that the Arctic Ocean is characterized by large amplitude multi-decadal variability in addition to a long-term trend, making the link of observed changes to climate drivers problematic. However, the exceptional magnitude of recent high-latitude changes (not only oceanic, but also ice and atmospheric) strongly suggests that these recent changes signify a potentially irreversible shift of the Arctic Ocean to a new climate state. These changes have important implications for the Arctic Ocean's marine ecosystem, especially those components that are dependent on sea ice or that have temperature-dependent sensitivities or thresholds. Addressing these and other questions requires a carefully orchestrated combination of sustained multidisciplinary observations and advanced modeling.

Trajectory of the Arctic as an integrated system.

Although much remains to be learned about the Arctic and its component processes, many of the most urgent scientific, engineering, and social questions can only be approached through a broader system perspective. Here, we address interactions between components of the Arctic system and assess feedbacks and the extent to which feedbacks (1) are now underway in the Arctic and (2) will shape the future trajectory of the Arctic system. We examine interdependent connections among atmospheric processes, oceanic processes, sea-ice dynamics, marine and terrestrial ecosystems, land surface stocks of carbon and water, glaciers and ice caps, and the Greenland ice sheet. Our emphasis on the interactions between components, both historical and anticipated, is targeted on the feedbacks, pathways, and processes that link these different components of the Arctic system. We present evidence that the physical components of the Arctic climate system are currently in extreme states, and that there is no indication that the system will deviate from this anomalous trajectory in the foreseeable future. The feedback for which the evidence of ongoing changes is most compelling is the surface albedo-temperature feedback, which is amplifying temperature changes over land (primarily in spring) and ocean (primarily in autumn-winter). Other feedbacks likely to emerge are those in which key processes include surface fluxes of trace gases, changes in the distribution of vegetation, changes in surface soil moisture, changes in atmospheric water vapor arising from higher temperatures and greater areas of open ocean, impacts of Arctic freshwater fluxes on the meridional overturning circulation of the ocean, and changes in Arctic clouds resulting from changes in water vapor content.

Correction to "Non-invasive Exhaled Breath and Skin Analysis to Diagnose Lung Cancer: Study of Age Effect on Diagnostic Accuracy".

[This corrects the article DOI: 10.1021/acsomega.2c06132.].

Quantum-based Modeling of Protein-ligand Interaction: The Complex of RutA with Uracil and Molecular Oxygen.

Modern quantum-based methods are employed to model interaction of the flavin-dependent enzyme RutA with the uracil and oxygen molecules. This complex presents the structure of reactants for the chain of chemical reactions of monooxygenation in the enzyme active site, which is important in drug metabolism. In this case, application of quantum-based approaches is an essential issue, unlike conventional modeling of protein-ligand interaction with force fields using molecular mechanics and classical molecular dynamics methods. We focus on two difficult problems to characterize the structure of reactants in the RutA-FMN-O2 -uracil complex, where FMN stands for the flavin mononucleotide species. First, location of a small O2 molecule in the triplet spin state in the protein cavities is required. Second, positions of both ligands, O2 and uracil, must be specified in the active site with a comparable accuracy. We show that the methods of molecular dynamics with the interaction potentials of quantum mechanics/molecular mechanics theory (QM/MM MD) allow us to characterize this complex and, in addition, to surmise possible reaction mechanism of uracil oxygenation by RutA.

Non-Invasive Lung Cancer Diagnostics through Metabolites in Exhaled Breath: Influence of the Disease Variability and Comorbidities.

Non-invasive, simple, and fast tests for lung cancer diagnostics are one of the urgent needs for clinical practice. The work describes the results of exhaled breath analysis of 112 lung cancer patients and 120 healthy individuals using gas chromatography-mass spectrometry (GC-MS). Volatile organic compound (VOC) peak areas and their ratios were considered for data analysis. VOC profiles of patients with various histological types, tumor localization, TNM stage, and treatment status were considered. The effect of non-pulmonary comorbidities (chronic heart failure, hypertension, anemia, acute cerebrovascular accident, obesity, diabetes) on exhaled breath composition of lung cancer patients was studied for the first time. Significant correlations between some VOC peak areas and their ratios and these factors were found. Diagnostic models were created using gradient boosted decision trees (GBDT) and artificial neural network (ANN). The performance of developed models was compared. ANN model was the most accurate: 82-88% sensitivity and 80-86% specificity on the test data.

Fluctuating Atlantic inflows modulate Arctic atlantification.

Enhanced warm, salty subarctic inflows drive high-latitude atlantification, which weakens oceanic stratification, amplifies heat fluxes, and reduces sea ice. In this work, we show that the atmospheric Arctic Dipole (AD) associated with anticyclonic winds over North America and cyclonic winds over Eurasia modulates inflows from the North Atlantic across the Nordic Seas. The alternating AD phases create a "switchgear mechanism." From 2007 to 2021, this switchgear mechanism weakened northward inflows and enhanced sea-ice export across Fram Strait and increased inflows throughout the Barents Sea. By favoring stronger Arctic Ocean circulation, transferring freshwater into the Amerasian Basin, boosting stratification, and lowering oceanic heat fluxes there after 2007, AD+ contributed to slowing sea-ice loss. A transition to an AD- phase may accelerate the Arctic sea-ice decline, which would further change the Arctic climate system.

Comparative vascular responses three months after paclitaxel and everolimus-eluting stent implantation in streptozotocin-induced diabetic porcine coronary arteries.

BACKGROUND: Diabetes remains a significant risk factor for restenosis/thrombosis following stenting. Although vascular healing responses following drug-eluting stent (DES) treatment have been characterized previously in healthy animals, comparative assessments of different DES in a large animal model with isolated features of diabetes remains limited. We aimed to comparatively assess the vascular response to paclitaxel-eluting (PES) and everolimus-eluting (EES) stents in a porcine coronary model of streptozotocin (STZ)-induced type I diabetes. METHOD: Twelve Yucatan swine were induced hyperglycemic with a single STZ dose intravenously to ablate pancreatic ß-cells. After two months, each animal received one XIENCE V® (EES) and one Taxus Liberte (PES) stent, respectively, in each coronary artery. After three months, vascular healing was assessed by angiography and histomorphometry. Comparative in vitro effects of everolimus and paclitaxel (10-5 M-10-12 M) after 24 hours on carotid endothelial (EC) and smooth muscle (SMC) cell viability under hyperglycemic (42 mM) conditions were assayed by ELISA. Caspase-3 fluorescent assay was used to quantify caspase-3 activity of EC treated with everolimus or paclitaxel (10-5 M, 10-7 M) for 24 hours. RESULTS: After 3 months, EES reduced neointimal area (1.60 ± 0.41 mm, p < 0.001) with trends toward reduced % diameter stenosis (11.2 ± 9.8%, p = 0.12) and angiographic late-loss (0.28 ± 0.30 mm, p = 0.058) compared to PES (neointimal area: 2.74 ± 0.58 mm, % diameter stenosis: 19.3 ± 14.7%, late loss: 0.55 ± 0.53 mm). Histopathology revealed increased inflammation scores (0.54 ± 0.21 vs. 0.08 ± 0.05), greater medial necrosis grade (0.52 ± 0.26 vs. 0.0 ± 0.0), and persistently elevated fibrin scores (1.60 ± 0.60 vs. 0.63 ± 0.41) with PES compared to EES (p < 0.05). In vitro, paclitaxel significantly increased (p < 0.05) EC/SMC apoptosis/necrosis at high concentrations (≥ 10-7 M), while everolimus did not affect EC/SMC apoptosis/necrosis within the dose range tested. In ECs, paclitaxel (10-5 M) significantly increased caspase-3 activity (p < 0.05) while everolimus had no effect. CONCLUSION: After 3 months, both DES exhibited signs of delayed healing in a STZ-induced diabetic swine model. PES exhibited greater neointimal area, increased inflammation, greater medial necrosis, and persistent fibrin compared to EES. Differential effects of everolimus and paclitaxel on vascular cell viability may potentially be a factor in regulating delayed healing observed with PES. Further investigation of molecular mechanisms may aid future development of stent-based therapies in treating coronary artery disease in diabetic patients.

How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur.

This work explores the level of transparency in reporting the details of computational protocols that is required for practical reproducibility of quantum mechanics/molecular mechanics (QM/MM) simulations. Using the reaction of an essential SARS-CoV-2 enzyme (the main protease) with a covalent inhibitor (carmofur) as a test case of chemical reactions in biomolecules, we carried out QM/MM calculations to determine the structures and energies of the reactants, the product, and the transition state/intermediate using analogous QM/MM models implemented in two software packages, NWChem and Q-Chem. Our main benchmarking goal was to reproduce the key energetics computed with the two packages. Our results indicate that quantitative agreement (within the numerical thresholds used in calculations) is difficult to achieve. We show that rather minor details of QM/MM simulations must be reported in order to ensure the reproducibility of the results and offer suggestions toward developing practical guidelines for reporting the results of biosimulations.

Non-invasive Exhaled Breath and Skin Analysis to Diagnose Lung Cancer: Study of Age Effect on Diagnostic Accuracy.

Development of simple, fast, and non-invasive tests for lung cancer diagnostics is essential for clinical practice. In this paper, exhaled breath and skin were studied as potential objects to diagnose lung cancer. The influence of age on the performance of diagnostic models was studied. Gas chromatography in combination with mass spectrometry (MS) was used to analyze the exhaled breath of 110 lung cancer patients and 212 healthy individuals of various ages. Peak area ratios of volatile organic compounds (VOCs) were used for data analysis instead of VOC peak areas. Various machine learning algorithms were applied to create diagnostic models, and their performance was compared. The best results on the test data set were achieved using artificial neural networks (ANNs): classification of patients with lung cancer and young healthy volunteers: 88 ± 4% sensitivity and 83 ± 3% specificity; classification of patients with lung cancer and old healthy individuals: 81 ± 3% sensitivity and 85 ± 1% specificity. The difference between performance of models based on young and old healthy groups was minor. The results obtained have shown that metabolic dysregulation driven by the disease biology is too high, which significantly overlaps the age effect. The influence of tumor localization and histological type on exhaled breath samples of lung cancer patients was studied. Statistically significant differences between some parameters in these samples were observed. A possibility of assessing the disease status by skin analysis in the Zakharyin-Ged zones using an electronic nose based on the quartz crystal microbalance sensor system was evaluated. Diagnostic models created using ANNs allow us to classify the skin composition of patients with lung cancer and healthy subjects of different ages with a sensitivity of 69 ± 2% and a specificity of 68 ± 8% for the young healthy group and a sensitivity of 74 ± 7% and a specificity of 66 ± 6% for the old healthy group. Primary results of skin analysis in the Zakharyin-Ged zones for the lung cancer diagnosis have shown its utility, but further investigation is required to confirm the results obtained.

Development and Processing of New Composite Materials Based on High-Performance Semicrystalline Polyimide for Fused Filament Fabrication (FFF) and Their Biocompatibility.

Samples of composite materials based on high-performance semicrystalline polyimide R-BAPB (based on the dianhydride R: 1,3-bis-(3',4,-dicarboxyphenoxy)benzene and diamine BAPB: 4,4'-bis-(4″-aminophenoxy)diphenyl)) filled with carbon nanofibers and micron-sized discrete carbon fibers were obtained by FFF printing for the first time. The viscosity of melts of the composites based on R-BAPB, thermal, mechanical characteristics of the obtained composite samples, their internal structure, and biocompatibility were studied. Simultaneously with FFF printing, samples were obtained by injection molding. The optimal concentrations of carbon fillers in polyimide R-BAPB for their further use in FFF printing were determined. The effect of the incorporation of carbon fillers on the porosity of the printed samples was investigated. It was shown that the incorporation of carbon nanofibers reduces the porosity of the printed samples, which leads to an increase in deformation at break. Modification of polyimide with discrete carbon fibers increases the strength and Young's modulus sufficiently but decreases the deformation at break. The cytotoxicity analysis showed that the obtained composite materials are bioinert.

Distribution of coding apoptotic gene polymorphisms in women with extreme phenotypes of breast cancer predisposition and tolerance.

AIMS AND BACKGROUND: Comparison of subjects with extreme phenotypes of cancer susceptibility and tolerance allows to detect low-penetrance gene-disease interactions with a relatively small study size. METHODS AND STUDY DESIGN: We analyzed the distribution of 19 coding apoptotic gene polymorphisms (Bid Gly10Ser; Casp2 Leu141Val; Casp5 Ala90Thr and Val318Leu; Casp7 Glu255Asp; Casp8 His302Asp; Casp9 Val28Ala, His173Arg and Arg221Gln; Casp10 Ile479Leu; Faim Thr117Ala and Ser127Leu; DR4 Arg141His, Thr209Arg, Ala228Glu and Lys441Arg; Survivin Lys129Glu; TNFR1 Gln121Arg; XIAP Pro423Gln) in 121 breast cancer patients with clinical features of a hereditary predisposition (family history and/or early onset and/or bilaterality) and 142 elderly tumor-free women. RESULTS: None of the individual single nucleotide polymorphisms (SNPs) demonstrated an association with breast cancer risk. The analysis of gene interactions revealed that the combination of XIAP Pro423Gln (rs5956583) AA genotype with Casp7 Glu255Asp (rs2227310) CG genotype appeared to prevail in "supercases" relative to "supercontrols" (25/121 [21%] vs 11/142 [8%], P = 0.002). We attempted to validate this association in the second round of case-control analysis, which involved 519 randomly selected breast cancer patients and 509 age-matched healthy women, but no difference was detected upon this comparison. CONCLUSIONS: Coding apoptotic gene polymorphisms do not play a major role in BC predisposition. The results of this investigation may be considered while designing future studies on breast cancer-associated candidate SNPs.

Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2.

The role of protonation states of the chromophore and its neighboring amino acid side chains of the reversibly switching fluorescent protein rsEGFP2 upon photoswitching is characterized by molecular modeling methods. Numerous conformations of the chromophore-binding site in computationally derived model systems are obtained using the quantum chemistry and QM/MM approaches. Excitation energies are computed using the extended multiconfigurational quasidegenerate perturbation theory (XMCQDPT2). The obtained structures and absorption spectra allow us to provide an interpretation of the observed structural and spectral properties of rsEGFP2 in the active ON and inactive OFF states. The results demonstrate that in addition to the dominating anionic and neutral forms of the chromophore, the cationic and zwitterionic forms may participate in the photoswitching of rsEGFP2. Conformations and protonation forms of the Glu223 and His149 side chains in the chromophore-binding site play an essential role in stabilizing specific protonation forms of the chromophore.

Study of confounding factors influence on lung cancer diagnostics effectiveness using gas chromatography-mass spectrometry analysis of exhaled breath.

Aim: The purpose of this study was to estimate volatile organic compounds (VOCs) ability to distinguish exhaled breath samples of lung cancer patients and healthy volunteers and to assess the effect of smoking status and gender on parameters. Patients & methods: Exhaled breath samples of 40 lung cancer patients and 40 healthy individuals were analyzed using gas chromatography-mass spectrometry. Influence of other factors on the exhaled breath VOCs profile was investigated. Results: Some parameters correlating with the disease status were affected by other factors. Excluding these parameters allows creating a logistic regression diagnostic model with 83% sensitivity and 81% specificity. Conclusion: Influence of other factors on the exhaled breath VOCs profile has to be taken into account to avoid misleading results.

Exhaled breath analysis using GC-MS and an electronic nose for lung cancer diagnostics.

Exhaled breath analysis is an interesting and promising approach for the diagnostics of various diseases. Being non-invasive, convenient and simple, this approach has tremendous potential utility for further translation into clinical practice. In this study, gas chromatography-mass spectrometry (GC-MS) and quartz microbalance sensor-based "electronic nose" were applied for analysis of the exhaled breath of 40 lung cancer patients and 40 healthy individuals. It was found that the electronic nose was unable to distinguish the samples of different groups. However, the application of GC-MS allowed identifying statistically significant differences in compound peak areas and their ratios for investigated groups. Diagnostic models were created using random forest classifier based on peak areas and their ratios with the sensitivity and specificity of peak areas (ratios) of 85.7-96.5% (75.0-93.1%) and 73.3-85.1% (90.0-92.5%) on training data and 63.6-75.0% (72.7-100.0%) and 50.0-69.2% (76.9-84.6%) on test data, respectively. The exhaled breath samples of lung cancer patients and healthy volunteers could be distinguished by GC-MS with the use of individual compounds, but application of their ratios could help to determine specific differences between investigated groups and the level the influence of individual metabolism features alternating from one person to another as well as daily instrument reproducibility deviations. The electronic nose has to be significantly improved to apply it to lung cancer diagnostics of exhaled breath analysis and the influence of water vapour has to be lowered to increase the sensitivity of the sensors to detect lung cancer biomarkers.