Maciassaunders6580

Macromolecular crowding influences protein mobility and stability in vivo. A precise description of the crowding effect on protein thermal stability requires the estimate of the combined effects of excluded volume, specific protein-environment interactions, as well as the thermal response of the crowders. Here, we explore an ideal model system, the lysozyme protein in powder state, to dissect the factors controlling the melting of the protein under extreme crowding. By deploying state-of-the art molecular simulations, supported by calorimetric experiments, we assess the role of the environment flexibility and of intermolecular electrostatic interactions. In particular, we show that the temperature-dependent flexibility of the macromolecular crowders, along with specific interactions, significantly alleviates the stabilizing contributions of the static volume effect.A metal-free Cs2CO3-promoted hydrothiolation of alkynes with aryl thioureas for stereoselective synthesis of (Z)-vinyl sulfides has been reported. Vinyl thioethers were obtained without a metal catalyst in good yields via anti-Markovnikov and cis addition. The protocol features a broad substrate scope of the starting materials, high atom economy, good yields, and exclusive stereoselectivity, showing potential synthetic value for the synthesis of a diversity of (Z)-vinyl thioethers.Machine learning classifiers trained on class imbalanced data are prone to overpredict the majority class. This leads to a larger misclassification rate for the minority class, which in many real-world applications is the class of interest. For binary data, the classification threshold is set by default to 0.5 which, however, is often not ideal for imbalanced data. Adjusting the decision threshold is a good strategy to deal with the class imbalance problem. In this work, we present two different automated procedures for the selection of the optimal decision threshold for imbalanced classification. A major advantage of our procedures is that they do not require retraining of the machine learning models or resampling of the training data. The first approach is specific for random forest (RF), while the second approach, named GHOST, can be potentially applied to any machine learning classifier. We tested these procedures on 138 public drug discovery data sets containing structure-activity data for a variety of pharmaceutical targets. We show that both thresholding methods improve significantly the performance of RF. We tested the use of GHOST with four different classifiers in combination with two molecular descriptors, and we found that most classifiers benefit from threshold optimization. GHOST also outperformed other strategies, including random undersampling and conformal prediction. Finally, we show that our thresholding procedures can be effectively applied to real-world drug discovery projects, where the imbalance and characteristics of the data vary greatly between the training and test sets.Single-nanoparticle inductively coupled plasma mass spectrometry (SP-ICP-MS) has demonstrated unique advantages for the detection of biological samples. However, methods for enzyme activity detection based on SP-ICP-MS technology have been rarely explored. Here we report the development of a novel SP-ICP-MS assay for uracil-DNA glycosylase (UDG) activity detection based on its ability to specifically recognize and remove uracil to induce the cleavage of the DNA probe. Our design allows the generation of single gold nanoparticles correlated to the specific enzymatic reaction for a highly sensitive SP-ICP-MS measurement. The developed assay enables sensitive UDG activity detection with a detection limit of 0.0003 U/mL. The cell lysate analysis by the developed assay reveals its applicability for the detection of UDG activity in real samples. It is envisioned that our design may provide a new paradigm for developing the SP-ICP-MS assay for enzyme activity detection in biological samples.Ozone is a powerful oxidant, most commonly used for oxidation of alkenes to carbonyls. The synthetic utility of other ozone-mediated reactions is hindered by its high reactivity and propensity to overoxidize organic molecules, including most solvents. This challenge can largely be mitigated by adsorbing both substrate and ozone onto silica gel, providing a solvent-free oxidation method. In this manuscript, a flow-based packed bed reactor approach is described that provides exceptional control of reaction temperature and time to achieve improved control and chemoselectivity over this challenging transformation. A powerful method to oxidize primary amines into nitroalkanes is achieved. Examples of pyridine, C-H bond, and arene oxidations are also demonstrated, confirming the system is generalizable to diverse ozone-mediated processes.Chrysin, one of the most pharmacologically active natural flavonoids, has been extracted from various plants. Mast cells are an important part of innate immunity-mediating anaphylaxis. Pseudo-allergic reactions are currently believed to be associated with the MAS-related GPR family member X2 (MrgX2). In this study, the anti-pseudo allergy effect of chrysin and its underlying mechanisms were studied in vitro and in vivo. Chrysin inhibited passive cutaneous anaphylaxis and systemic pseudo-allergy in vivo. LAD2 cell degranulation, calcium ion (Ca2+) influx, and adenosine 5'-triphosphate (ATP) content were significantly suppressed in a dose-dependent manner. Chrysin suppressed pseudo-allergic reactions through the PLC/IP3/Ca2+ and ERK/STAT3 serine 727 pathways downstream of MrgX2. Therefore, mitochondrial ATP, but not glycolysis, is vital for pseudo-allergic reactions mediated by MrgX2. This study provides new insights for the treatment of pseudo-allergy.There is an increasing demand for free-energy calculations using ab initio molecular dynamics these days. Metadynamics (MetaD) is frequently utilized to reconstruct the free-energy surface, but it is often computationally intractable for the first-principles calculations. Machine learning potentials (MLPs) have become popular alternatives. However, the training could be a long and arduous process before using them in practical applications. To accelerate MetaD use with MLPs for the free-energy calculation in an easy manner, we propose the adaptive machine learning potential-accelerated metadynamics (AMLP-MetaD). In this method, the MLP in the form of a Gaussian approximation potential (GAP) can adapt itself based on its uncertainty estimation, which decides whether to accept the model prediction or recalculate it with a reference method (usually density functional theory) for further training during the MetaD simulation. We demonstrate that the free-energy landscape similar to the ab initio one can be obtained using AMLP-MetaD with a 10-time speedup. Moreover, the quality of the free-energy results can be deeply improved using Δ-MLP, which is the GAP-corrected density functional tight binding in our case. We exemplify this novel method with two model systems, CO adsorption on the Pt13 cluster and the Pt(111) surface, which are of vital importance in heterogeneous catalysis. The successful application in these two tests highlights that our proposed method can be used in both cluster and periodic systems and for up to two collective variables.Fluorescence guided surgery (FGS) has been highlighted in the clinical site for guiding surgical procedures and providing the surgeon with a real-time visualization of the operating field. Selleck BX471 FGS is a powerful technique for precise surgery, particularly tumor resection; however, clinically approved fluorescent dyes have often shown several limitations during FGS, such as non-tumor-targeting, low in vivo stability, insufficient emission intensity, and low blood-brain barrier penetration. In this study, we disclose a fluorescent dye complex, peptide, and protein for the targeted visualization of human glioblastoma (GBM) cells and tissues. Our noble triple receptor-targeting fluorescent complex (named BSA-OXN-SIWV) consists of (i) dipolar oxazepine dye (OXN), which has high stability, low cytotoxicity, bright fluorescence, and two-photon excitable, (ii) tetra-peptide (SIWV) for the targeting of the caveolin-1 receptor, and (iii) bovine serum-albumin (BSA) protein for the targeting of albondin (gp60) and secreted protein acidic and rich in cysteine receptor. The photophysical properties and binding mode of BSA-OXN-SIWV were analyzed, and the imaging of GBM cell lines and human clinical GBM tissues were successfully demonstrated in this study. Our findings hold great promise for the application of BSA-OXN-SIWV to GBM identification and the surgery at clinical sites, as a new FGS agent.This article describes the discovery of novel potent muscarinic receptor antagonists identified during a search for more active histamine H3 receptor (H3R) ligands. The idea was to replace the flexible seven methylene linker with a semirigid 1,4-cyclohexylene or p-phenylene substituted group of the previously described histamine H3R antagonists ADS1017 and ADS1020. These simple structural modifications of the histamine H3R antagonist led to the emergence of additional pharmacological effects, some of which unexpectedly showed strong antagonist potency at muscarinic receptors. This paper reports the routes of synthesis and pharmacological characterization of guanidine derivatives, a novel chemotype of muscarinic receptor antagonists binding to the human muscarinic M2 and M4 receptors (hM2R and hM4R, respectively) in nanomolar concentration ranges. The affinities of the newly synthesized ADS10227 (1-4-4-[4-(phenoxymethyl)cyclohexyl]methylpiperazin-1-ylbut-1-yl-1-(benzyl)guanidine) at hM2R and hM4R were 2.8 nM and 5.1 nM, respectively.The proteins in the starchy endosperm of wheat determine wheat quality and exhibit a quantitative gradient decreasing from the outer to inner endosperm. Here, we investigate how protein-rich sub-aleurone cells contribute to the protein content and gradient by studying three cultivars, each cultivated at three levels of nitrogen (N)-fertilization. The observed increased protein content with increased N-fertilization was cultivar-dependent. Image analysis showed that the underlying protein gradient could be described by a declining biexponential curve, with protein contents up to 32.0% in the sub-aleurone. Cultivars did not differ in protein content in the center of the cheeks and only differed in the outer endosperm when N-fertilization is applied. N-Fertilization resulted in relatively higher increases in protein content in the outer compared to inner endosperm. Hence, sub-aleurone cells could affect the classification of cultivars by baking quality. Cultivar selection and N-fertilization could furthermore be promising techniques to produce protein-rich miller's bran.Interleukin 17 (IL-17) cytokines promote inflammatory pathophysiology in many autoimmune diseases, including psoriasis, multiple sclerosis, rheumatoid arthritis, and inflammatory bowel disease. Such broad involvement of IL-17 in various autoimmune diseases makes it an ideal target for drug discovery. Psoriasis is a chronic inflammatory disease characterized by numerous defective components of the immune system. Significantly higher levels of IL-17A have been noticed in lesions of psoriatic patients, if compared to non-lesion parts. Therefore, this paper is focused on the macrolide inspired macrocycles as potential IL-17A/IL-17RA modulators and covers the molecular design, synthesis, and in vitro profiling. Macrocycles are designed to diversify and enrich chemical space through different ring sizes and a variety of three-dimensional shapes. Inhibitors in the nM range were identified in both target-based and phenotypic assays. In vitro ADME as well as in vivo PK properties are reported.