Proteome interrogation using gold nanoprobes to identify targets of arctigenin in fish parasites

Structure-based discovery of potent myosin inhibitors to guide antiparasite drug development

Monogenea, a prevalent parasite in aquaculture, poses significant threats to the industry, leading to substantial losses. Current preventive measures have proven insufficient, necessitating the development of novel and effective anti-parasitic drugs. In this investigation, we obtained the full-length myosin cDNA sequence by analyzing three-generation transcriptome data, revealing a 5817-base sequence encoding 1938 amino acids. Subsequently, we modeled and analyzed the characteristics of the secondary and tertiary of myosin, pinpointing the crucial functional region within the motor domain (amino acids 1-768). The prokaryotic expression of this domain yielded a protein of 87.44 kDa, confirmed as myosin by Western Blotting. Molecular docking identified ASN439 as the key amino acid residue involved in arctigenin and myosin binding, a result corroborated by site-directed mutagenesis, affirming the active cavity of this interaction. Chalcone and shikonin were chosen from a virtual sieve of molecular library of natural drugs based on the active cavity. Chalcone and shikonin exhibited EC50 values of 1.085 mg/L and 0.371 mg/L, respectively, with corresponding IC50 values for myosin of 0.44 mM and 0.14 mM. Given its superior activity and structure, shikonin was selected for further optimization of drug molecule design, culminating in the discovery of 1,4-naphthoquinone as a potent antiparasitic agent. This compound demonstrated an EC50 of 0.047 mg/L, LC50 of 0.23 mg/L, and a TI index of 4.893. These findings collectively highlight the potential of shikonin and 1,4-naphthoquinone as alternative compounds to control Gyrodactylus infections. Further optimization of medicinal chemistry holds promise for the development of more potent 1,4-naphthoquinone analogues, offering prospects for future anthelmintic control through combinatorial or replacement strategies.

Virus-like Iron-Gold Heterogeneous Nanoparticles for Drug Target Screening

Drug-target recognition has great impacts on revealing mechanisms of pharmacological activities, especially drug resistance and off-target effects. In recent years, chemoproteomics has been widely used for drug target screening and discovery due to its high-throughput, high accuracy, and sensitivity. However, there still remain challenges on how to efficiently and unambiguously track target proteins from complex biological matrices. Herein, we report a drug target screening method based on virus-like iron-gold heterogeneous nanoparticles (Au@Fe3O4 NPs). The unique structure of Au@Fe3O4 NPs not only maintains the magnetism of Fe3O4 NPs to facilitate protein enrichment and purification, but also increases drug modification by introducing more active sites on the surface of Au NPs. After coincubating the drug modified NPs with the cell lysate, the high loading of drug on the surface of Au@Fe3O4 NPs was beneficial for capturing target proteins with low abundance. This well-designed heterogeneous nanomaterial provides a novel strategy for improving the efficiency and accuracy of affinity-based proteomics.

Target protein identification of andrographolide based on isomer approach

The target identification of natural products is one of the most challenging issues in the standardized application of traditional Chinese medicine. It is widely recognized that magnetic nanoparticles (MNPs) could function as a tool that capture the target proteins of active molecule. However, the false positives caused by non-specific adsorption should not be ignored. Here, we reported a functionalized MNPs technique that could enrich the target proteins of andrographolide (AG) based on isomers approach. We designed and characterized MNPs and isomers of AG. The combination of the two could be used as an ideal coupling, which provides a feasible method for the target proteins enrichment of AG. In addition, the target proteins were identified by HPLC-MS/MS. Moreover, bioinformatics analysis and systematic computational dockings were performed to search for the interactions between target proteins and AG. Six inflammation-related proteins, including CD4, IKBKB, PKN1, PKN2, YWHAB and YWHAH were proved to be the anti-inflammatory targets of AG. All of the results indicated this integrated system could benefit target identification of bioactive natural products.

Combining experimental strategies for successful target deconvolution

Investment in phenotypic drug discovery has led to increased demand for rapid and robust target deconvolution to aid successful drug development. Although methods for target identification and mechanism of action (MoA) discovery are flourishing, they typically lead to lists of putative targets. Validating which target(s) are involved in the therapeutic mechanism of a compound poses a significant challenge, requiring direct binding, target engagement, and functional studies in relevant physiological contexts. A combination of orthogonal approaches can allow target identification beyond the proteome as well as aid prioritisation for resource-intensive target validation studies.

Comparative Proteomics Analysis of Anisakis simplex s.s.-Evaluation of the Response of Invasive Larvae to Ivermectin

Ivermectin (IVM), an antiparasitic drug, has a positive effect against Anisakis simplex s.s. infection and has been used for the treatment and prevention of anisakiasis in humans. However, the molecular mechanism of action of IVM on A. simplex s.s. remains unknown. Herein, tandem mass tag (TMT) labeling and extensive liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis were used to identify the effect of IVM on the proteome of A. simplex s.s. in vitro. During the study, 3433 proteins, of which 1247 had at least two protein unique peptides, were identified. Comparative proteomics analysis revealed that 59 proteins were differentially regulated (DRPs) in IVM-treated larvae, of which 14 proteins were upregulated and 38 were downregulated after 12 h of culture, but after 24 h, 12 proteins were upregulated and 22 were downregulated. The transcription level of five randomly selected DRPs was determined by real-time PCR as a supplement to the proteomic data. The functional enrichment analysis showed that most of the DRPs were involved in oxidoreductase activity, immunogenicity, protein degradation, and other biological processes. This study has, for the first time, provided comprehensive proteomics data on A. simplex s.s. response to IVM and might deliver new insight into the molecular mechanism by which IVM acts on invasive larvae of A. simplex s.s.