A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods.

Computational drug repositioning, which involves identifying new indications for existing drugs, is an increasingly attractive research area due to its advantages in reducing both overall cost and development time. As a result, a growing number of computational drug repositioning methods have emerged. Heterogeneous network-based drug repositioning methods have been shown to outperform other approaches. However, there is a dearth of systematic evaluation studies of these methods, encompassing performance, scalability and usability, as well as a standardized process for evaluating new methods. Additionally, previous studies have only compared several methods, with conflicting results. In this context, we conducted a systematic benchmarking study of 28 heterogeneous network-based drug repositioning methods on 11 existing datasets. We developed a comprehensive framework to evaluate their performance, scalability and usability. Our study revealed that methods such as HGIMC, ITRPCA and BNNR exhibit the best overall performance, as they rely on matrix completion or factorization. HINGRL, MLMC, ITRPCA and HGIMC demonstrate the best performance, while NMFDR, GROBMC and SCPMF display superior scalability. For usability, HGIMC, DRHGCN and BNNR are the top performers. Building on these findings, we developed an online tool called HN-DREP (http://hn-drep.lyhbio.com/) to facilitate researchers in viewing all the detailed evaluation results and selecting the appropriate method. HN-DREP also provides an external drug repositioning prediction service for a specific disease or drug by integrating predictions from all methods. Furthermore, we have released a Snakemake workflow named HN-DRES (https://github.com/lyhbio/HN-DRES) to facilitate benchmarking and support the extension of new methods into the field.

Synthesis of Mesoporous and Hollow SiO2@ Eu(TTA)3phen with Enhanced Fluorescence Properties.

Lanthanide ions are extensively utilized in optoelectronic materials, owing to their narrow emission bandwidth, prolonged lifetime, and elevated fluorescence quantum yield. Inorganic non-metallic materials commonly serve as host matrices for lanthanide complexes, posing noteworthy challenges regarding loading quantity and fluorescence performance stability post-loading. In this investigation, an enhanced Stöber method was employed to synthesize mesoporous hollow silica, and diverse forms of SiO2@Eu(TTA)3phen (S@Eu) were successfully prepared. Transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDS), Fourier-transform infrared (FTIR) spectroscopy, and X-ray photoelectron spectroscopy (XPS) outcomes revealed the effective binding of silica with Eu(TTA)3phen through both physical adsorption and chemical bonding. This includes the formation of Si-O-C bonds between silica and the ligand, as well as Si-O-Eu bonds between silica and europium ions. Fluorescence tests demonstrated that the mesoporous SiO2@Eu(TTA)3phen(MS@Eu) composite exhibited the highest fluorescence intensity among the three structured silica composites, with a notable enhancement of 46.60% compared to the normal SiO2@Eu(TTA)3phen composite. The Brunauer-Emmett-Teller (BET) analysis indicated that the specific surface area plays a crucial role in influencing the fluorescence intensity of SiO2@Eu(TTA)3phen, whereby the prepared mesoporous hollow silica further elevated the fluorescence intensity by 61.49%. Moreover, SiO2@Eu(TTA)3phen demonstrated 11.11% greater cyclic stability, heightened thermal stability, and enhanced alkaline resistance relative to SiO2@Eu(TTA)3phen.

Dual Proton/Silver-Catalyzed Serial (5 + 2)-Cycloaddition and Nazarov Cyclization of (E)-2-Arylidene-3-hydroxyindanones with Conjugated Eneynes: Synthesis of Indanone-Fused Benzo[cd]azulenes.

A one-pot step-economic tandem process involving (5 + 2)-cycloaddition and Nazarov cyclization reactions has been reported for the facile synthesis of indanone-fused benzo[cd]azulenes from (E)-2-arylidene-3-hydroxyindanones and conjugated eneynes. This highly regio- and stereoselective bisannulation reaction is enabled by dual silver and Brønsted acid catalysis and opens up a new avenue for the construction of important bicyclo[5.3.0]decane skeletons.