Learning size-adaptive molecular substructures for explainable drug–drug interaction prediction by substructure-aware graph neural network

Drug–drug interactions (DDIs) can trigger unexpected pharmacological effects on the body, and the causal mechanisms are often unknown. Graph neural networks (GNNs) have been developed to better understand DDIs. However, identifying key substructures that contribute most to the DDI prediction is a challenge for GNNs. In this study, we presented a substructure-aware graph neural network, a message passing neural network equipped with a novel substructure attention mechanism and a substructure–substructure interaction module (SSIM) for DDI prediction (SA-DDI). Specifically, the substructure attention was designed to capture size- and shape-adaptive substructures based on the chemical intuition that the sizes and shapes are often irregular for functional groups in molecules. DDIs are fundamentally caused by chemical substructure interactions. Thus, the SSIM was used to model the substructure–substructure interactions by highlighting important substructures while de-emphasizing the minor ones for DDI prediction. We evaluated our approach in two real-world datasets and compared the proposed method with the state-of-the-art DDI prediction models. The SA-DDI surpassed other approaches on the two datasets. Moreover, the visual interpretation results showed that the SA-DDI was sensitive to the structure information of drugs and was able to detect the key substructures for DDIs. These advantages demonstrated that the proposed method improved the generalization and interpretation capability of DDI prediction modeling.

SA-DDI is designed to learn size-adaptive molecular substructures for drug–drug interaction prediction and can provide explanations that are consistent with pharmacologists.     

Sargassum fusiforme Polysaccharide-Based Hydrogel Microspheres Enhance Crystal Violet Dye Adsorption Properties

In this study, a polysaccharide-based hydrogel microsphere (SFP/SA) was prepared using S. fusiforme polysaccharide (SFP) and sodium alginate (SA). Fourier transform infrared spectroscopy (FT-IR) demonstrated that SFP was effectively loaded onto the hydrogel microsphere. Texture profile analysis (TPA) and differential scanning calorimetry (DSC) showed that, with the increase of SFP concentration, the hardness of SFP/SA decreased, while the springiness and cohesiveness of SFP/SA increased, and the thermal stability of SFP/SA improved. The equilibrium adsorption capacity of SFP/SA increased from 8.20 mg/g (without SFP) to 67.95 mg/g (SFP accounted 80%) without swelling, and from 35.05 mg/g (without SFP) to 81.98 mg/g (SFP accounted 80%) after 24 h swelling. The adsorption of crystal violet (CV) dye by SFP/SA followed pseudo-first order and pseudo-second order kinetics (both with R² > 0.99). The diffusion of intraparticle in CV dye was not the only influencing factor. Moreover, the adsorption of CV dye for SFP/SA (SFP accounted 60%) fit the Langmuir and Temkin isotherm models. SFP/SA exhibited good regenerative adsorption capacity. Its adsorption rate remained at > 97% at the 10th consecutive cycle while SFP accounted for 80%. The results showed that the addition of Sargassum fusiforme polysaccharide could increase the springiness, cohesiveness and thermal stability of the hydrogel microsphere, as well as improve the adsorption capacity of crystal violet dye.     

Structural and Functional Analysis of the Pyridoxal Phosphate Homeostasis Protein YggS from Fusobacterium nucleatum

Pyridoxal 5′-phosphate (PLP) is the active form of vitamin B6, but it is highly reactive and poisonous in its free form. YggS is a PLP-binding protein found in bacteria and humans that mediates PLP homeostasis by delivering PLP to target enzymes or by performing a protective function. Several biochemical and structural studies of YggS have been reported, but the mechanism by which YggS recognizes PLP has not been fully elucidated. Here, we report a functional and structural analysis of YggS from Fusobacterium nucleatum (FnYggS). The PLP molecule could bind to native FnYggS, but no PLP binding was observed for selenomethionine (SeMet)-derivatized FnYggS. The crystal structure of FnYggS showed a type III TIM barrel fold, exhibiting structural homology with several other PLP-dependent enzymes. Although FnYggS exhibited low (<35%) amino acid sequence similarity with previously studied YggS proteins, its overall structure and PLP-binding site were highly conserved. In the PLP-binding site of FnYggS, the sulfate ion was coordinated by the conserved residues Ser201, Gly218, and Thr219, which were positioned to provide the binding moiety for the phosphate group of PLP. The mutagenesis study showed that the conserved Ser201 residue in FnYggS was the key residue for PLP binding. These results will expand the knowledge of the molecular properties and function of the YggS family.     

Optimized Selection of Water Resource Allocation Schemes Based on Improved Connection Entropy in Beijing’s Southern Plain

Increased urbanization has caused problems such as increasing water consumption and the continuous deterioration of the groundwater environment. It is necessary to consider the groundwater quality in the water resource optimization system and increase the rate of reclaimed water development to reduce the amount of groundwater exploitation and achieve sustainable development of water resources. This study used the Daxing District, a region of Beijing’s southern plain, as an example to evaluate water quality by analyzing water quality data of surface and groundwater from 2012 to 2016 and actual water-use schemes from 2006 to 2016. Three groundwater extraction modes were set up based on NO₃–N concentrations, water resources were optimized under three extraction modes, and water resource optimization schemes were determined based on the improved connection entropy. The results show that (1) the surface water quality was poor, and the proportion of V₄ type water in the indexes of NH₃–N and chemical oxygen demand (COD) was the largest. The surface water can only be used for agricultural irrigation. The pollution sources contributing most to NH₃–N and COD were domestic and agricultural pollution sources. (2) The groundwater quality was good. The NO₃–N index was primarily type I–III water, accounting for 95.20% of the total samples. Severe NH₃–N pollution areas were mainly in the northern region, and most regional groundwater can be used for various purposes. (3) Taking 2016 as an example, three groundwater exploitation modes were set to optimize water resource allocation, and the results showed that the rate of groundwater development and NO₃–N pollution decreased significantly after optimization. (4) Connection entropy is an evaluation method that combines connection numbers and entropy, including identify, difference, and opposition entropy. As connection entropy being a kind of complete entropy, which can reflect the difference of the system in different states, based on the improved connection entropy, the connection entropies of optimal water resource allocation and actual water-use schemes were calculated. The connection entropy of groundwater exploitation mode 3 was less than that of groundwater exploitation modes 1 and 2 and actual water-use schemes from 2006 to 2016. Therefore, exploitation mode 3’s water resource optimization scheme was recommended. In the paper, satisfactory results have been obtained. As a kind of complete entropy, connection entropy has great research value in dealing with complex hydrological problems. This study’s research methods and outcomes can provide methodological and theoretical lessons for water management in freshwater-deficient areas.     

Na2S-Mediated One-Pot Selective Deoxygenation of α-Hydroxyl Carbonyl Compounds including Natural Products

A practical method for the deoxygenation of α-hydroxyl carbonyl compounds under mild reaction conditions is reported here. The use of cheap and easy-to-handle Na₂S·9H₂O as the reductant in the presence of PPh₃ and N-chlorosuccinimide (NCS) enables the selective dehydroxylation of α-hydroxyl carbonyl compounds, including ketones, esters, amides, imides and nitrile groups. The synthetic utility is demonstrated by the late-stage deoxygenation of bioactive molecule and complex natural products.     

Effect of Different Processing Methods on the Chemical Constituents of Scrophulariae Radix as Revealed by 2D NMR-Based Metabolomics

Scrophulariae Radix (SR) is one of the oldest and most frequently used Chinese herbs for oriental medicine in China. Before clinical use, the SR should be processed using different methods after harvest, such as steaming, “sweating”, and traditional fire-drying. In order to investigate the difference in chemical constituents using different processing methods, the two-dimensional (2D) ¹H-¹³C heteronuclear single quantum correlation (¹H-¹³C HSQC)-based metabolomics approach was applied to extensively characterize the difference in the chemical components in the extracts of SR processed using different processing methods. In total, 20 compounds were identified as potential chemical markers that changed significantly with different steaming durations. Seven compounds can be used as potential chemical markers to differentiate processing by sweating, hot-air drying, and steaming for 4 h. These findings could elucidate the change of chemical constituents of the processed SR and provide a guide for the processing. In addition, our protocol may represent a general approach to characterizing chemical compounds of traditional Chinese medicine (TCM) and therefore might be considered as a promising approach to exploring the scientific basis of traditional processing of TCM.     

Facile Fabrication of 1-Methylimidazole/Cu Nanozyme with Enhanced Laccase Activity for Fast Degradation and Sensitive Detection of Phenol Compounds

Facile construction of functional nanomaterials with laccase-like activity is important in sustainable chemistry since laccase is featured as an efficient and promising catalyst especially for phenolic degradation but still has the challenges of high cost, low activity, poor stability and unsatisfied recyclability. In this paper, we report a simple method to synthesize nanozymes with enhanced laccase-like activity by the self-assembly of copper ions with various imidazole derivatives. In the case of 1-methylimidazole as the ligand, the as-synthesized nanozyme (denoted as Cu-MIM) has the highest yield and best activity among the nanozymes prepared. Compared to laccase, the K_m of Cu-MIM nanozyme to phenol is much lower, and the v_max is 6.8 times higher. In addition, Cu-MIM maintains excellent stability in a variety of harsh environments, such as high pH, high temperature, high salt concentration, organic solvents and long-term storage. Based on the Cu-MIM nanozyme, we established a method for quantitatively detecting phenol concentration through a smartphone, which is believed to have important applications in environmental protection, pollutant detection and other fields.     

ACTIVE CONTROL OF A FLEXIBLE CANTILEVER PLATE WITH MULTIPLE TIME DELAYS

Active control of a flexible cantilever plate with multiple time delays is investigated using the discrete optimal control method. A controller with multiple time delays is presented. In this controller, time delay effect is incorporated in the mathematical model of the dynamic system throughout the control design and no approximations and assumptions are made in the controller derivation, so the system stability is easily guaranteed. Furthermore, this controller is available for both small time delays and large time delays. The feasibility and efficiency of the proposed controller are verified through numerical simulations in the end of this paper.     

TRANSIENT TORSIONAL WAVE IN FINITE HOLLOW CYLINDER WITH INITIAL AXIAL STRESS

An analytical solution is obtained for transient torsional vibration of a finite hollow cylinder with initial axial stress. The cylinder is subjected to dynamic shearing stress at the internal surface and is fixed at the external surface. The basic equations are presented and the solution is obtained by means of Fourier series expansion technique and the separation of variables method. The effects of the initial stress on the natural frequencies and transient torsional responses are presented and discussed.     

HIGH-FREQUENCY VIBRATIONS OF CORRUGATED CYLINDRICAL PIEZOELECTRIC SHELLS

Coupled extensional and flexural cylindrical vibrations of a corrugated cylindrical piezoelectric shell consisting of multiple pieces of circular cylindrical surfaces smoothly connected along their generatrix are studied. To validate the results for the case of relatively thick shells or equivalently high-frequency modes with short wavelengths, existing analysis is extended by considering shear deformation and rotatory inertia. An analytical solution is obtained. Based on the solution, resonant frequencies and mode shapes are calculated.