Synthesis and structure-activity relationship study of pyrrolidine-oxadiazoles as anthelmintics against Haemonchus contortus

Systems biology of Haemonchus contortus - Advancing biotechnology for parasitic nematode control

Parasitic nematodes represent a substantial global burden, impacting animal health, agriculture and economies worldwide. Of these worms, Haemonchus contortus - a blood-feeding nematode of ruminants - is a major pathogen and a model for molecular and applied parasitology research. This review synthesises some key advances in understanding the molecular biology, genetic diversity and host-parasite interactions of H. contortus, highlighting its value for comparative studies with the free-living nematode Caenorhabditis elegans. Key themes include recent developments in genomic, transcriptomic and proteomic technologies and resources, which are illuminating critical molecular pathways, including the ubiquitination pathway, protease/protease inhibitor systems and the secretome of H. contortus. Some of these insights are providing a foundation for identifying essential genes and exploring their potential as targets for novel anthelmintics or vaccines, particularly in the face of widespread anthelmintic resistance. Advanced bioinformatic tools, such as machine learning (ML) algorithms and artificial intelligence (AI)-driven protein structure prediction, are enhancing annotation capabilities, facilitating and accelerating analyses of gene functions, and biological pathways and processes. This review also discusses the integration of these tools with cutting-edge single-cell sequencing and spatial transcriptomics to dissect host-parasite interactions at the cellular level. The discussion emphasises the importance of curated databases, improved culture systems and functional genomics platforms to translate molecular discoveries into practical outcomes, such as novel interventions. New research findings and resources not only advance research on H. contortus and related nematodes but may also pave the way for innovative solutions to the global challenges with anthelmintic resistance.

Unveiling the research directions for pyrrolidine-based small molecules as versatile antidiabetic and anticancer agents

The pyrrolidine moiety, a five-membered saturated nitrogen-containing heterocycle, emerged as a crucial pharmacophore in medicinal chemistry due to its distinctive physicochemical properties, including hydrophilicity, basicity, and structural rigidity. Extensive modifications of pyrrolidine derivatives yielded novel compounds with pronounced antidiabetic and anticancer activities. The structural investigation of pyrrolidine-based molecules demonstrated that substitutions at the N1, 3rd, and 5th positions offer significant opportunities for optimizing biological activity and enhancing target-specific interactions. The synthesis of pyrrolidine-based molecules has been explored in literature; however, structural, target interaction analysis, and pharmacological aspects warranted for the development of targeted small molecule versatile antidiabetic and anticancer agents are lacking. The review addresses this gap by emphasizing the developments in pyrrolidine-based small molecules via structural and target interaction analysis, highlighting their antidiabetic and anticancer activities, and offering a comprehensive perspective on the development of targeted therapeutics. The investigated structural features and pharmacological developments underscore the dual functionality of pyrrolidine-based drugs in managing disorders, such as diabetes and cancer, that share common pathological mechanisms, such as inflammation, oxidative stress, and metabolic dysregulation. This overlap has catalyzed the development of multifunctional pyrrolidine derivatives capable of targeting pathways integral to both conditions, providing a promising avenue for therapeutic innovation.

Prediction and Prioritisation of Novel Anthelmintic Candidates from Public Databases Using Deep Learning and Available Bioactivity Data Sets

The control of socioeconomically important parasitic roundworms (nematodes) of animals has become challenging or ineffective due to problems associated with widespread resistance in these worms to most classes of chemotherapeutic drugs (anthelmintics) currently available. Thus, there is an urgent need to discover and develop novel compounds with unique mechanisms of action to underpin effective parasite control programmes. Here, we evaluated an in silico (computational) approach to accelerate the discovery of new anthelmintics against the parasitic nematode Haemonchus contortus (barber's pole worm) as a model system. Using a supervised machine learning workflow, we trained and assessed a multi-layer perceptron classifier on a labelled dataset of 15,000 small-molecule compounds, for which extensive bioactivity data were previously obtained for H. contortus via high-throughput screening, as well as evidence-based datasets from the peer-reviewed literature. This model achieved 83% precision and 81% recall on the class of 'active' compounds during testing, despite a high imbalance in the training data, with only 1% of compounds carrying this label. The trained model was then used to infer nematocidal candidates by in silico screening of 14.2 million compounds from the ZINC15 database. An experimental assessment of 10 of these candidates showed significant inhibitory effects on the motility and development of H. contortus larvae and adults in vitro, with two compounds exhibiting high potency for further exploration as lead candidates. These findings indicate that the present machine learning-based approach could accelerate the in silico prediction and prioritisation of anthelmintic small molecules for subsequent in vitro and in vivo validations.

BioisoIdentifier: an online free tool to investigate local structural replacements from PDB

Within the realm of contemporary medicinal chemistry, bioisosteres are empirically used to enhance potency and selectivity, improve adsorption, distribution, metabolism, excretion and toxicity profiles of drug candidates. It is believed that bioisosteric know-how may help bypass granted patents or generate novel intellectual property for commercialization. Beside the synthetic expertise, the drug discovery process also depends on efficient in silico tools. We hereby present BioisoIdentifier (BII), a web server aiming to uncover bioisosteric information for specific fragment. Using the Protein Data Bank as source, and specific substructures that the user attempt to surrogate as input, BII tries to find suitable fragments that fit well within the local protein active site. BII is a powerful computational tool that offers the ligand design ideas for bioisosteric replacing. For the validation of BII, catechol is conceived as model fragment attempted to be replaced, and many ideas are successfully offered. These outputs are hierarchically grouped according to structural similarity, and clustered based on unsupervised machine learning algorithms. In summary, we constructed a user-friendly interface to enable the viewing of top-ranking molecules for further experimental exploration. This makes BII a highly valuable tool for drug discovery. The BII web server is freely available to researchers and can be accessed at http://www.aifordrugs.cn/index/ . Scientific Contribution: By designing a more optimal computational process for mining bioisosteric replacements from the publicly accessible PDB database, then deployed on a web server for throughly free access for researchers. Additionally, machine learning methods are applied to cluster the bioisosteric replacements searched by the platform, making a scientific contribution to facilitate chemists' selection of appropriate bioisosteric replacements. The number of bioisosteric replacements obtained using BII is significantly larger than the currently available platforms, which expanding the search space for effective local structural replacements.

Recent insights about pyrrolidine core skeletons in pharmacology

To overcome numerous health disorders, heterocyclic structures of synthetic or natural origin are utilized, and notably, the emergence of various side effects of existing drugs used for treatment or the resistance of disease-causing microorganisms renders drugs ineffective. Therefore, the discovery of potential therapeutic agents that utilize different modes of action is of utmost significance to circumvent these constraints. Pyrrolidines, pyrrolidine-alkaloids, and pyrrolidine-based hybrid molecules are present in many natural products and pharmacologically important agents. Their key roles in pharmacotherapy make them a versatile scaffold for designing and developing novel biologically active compounds and drug candidates. This review aims to provide an overview of recent advancements (especially during 2015-2023) in the exploration of pyrrolidine derivatives, emphasizing their significance as fundamental components of the skeletal structure. In contrast to previous reviews that have predominantly focused on a singular biological activity associated with these molecules, this review consolidates findings from various investigations encompassing a wide range of important activities (antimicrobial, antiviral, anticancer, anti-inflammatory, anticonvulsant, cholinesterase inhibition, and carbonic anhydrase inhibition) exhibited by pyrrolidine derivatives. This study is also anticipated to serve as a valuable resource for drug research and development endeavors, offering significant insights and guidance.

Biochanin A in murine Schistosoma mansoni infection: effects on inflammation, oxidative stress and fibrosis

Biochanin A (BCA) is a multifunctional natural compound that possesses anti-infective, anti-inflammatory, anti-oxidative and hepatoprotective effects. The aim of the study was to assess the therapeutic efficacy of BCA on Schistosoma mansoni-infected mice. Fifty mice were divided into six different groups as non-infected, non-infected BCA-treated, infected untreated, early infected BCA-treated (seven days post-infection (dpi)), late infected BCA-treated 60 dpi and infected praziquantel (PZQ)-treated groups. Parasitological, histopathological examination and immunohistochemical staining of transforming growth factor (TGF)-β, inducible nitric oxide synthase (iNOS) and cyclooxygenase (COX-2) were investigated in liver sections. Cytochrome P450 (CYP450) gene expression of S. mansoni was evaluated by quantitative real-time polymerase chain reaction (RT-qPCR). A single dose of BCA significantly reduced worm burden in early (82.14%) and late infection (77.74%), mean tissue egg load in early (7.27 ± 0.495) and late BCA administration (7.63 ± 0.435) and decreased granuloma size. CYP450 mRNA expression was significantly reduced in early BCA treatment as compared to late treatment which emphasizes that early administration of BCA had more pronounced effects on worms than late administration. Both early and late BCA administration led to significant reduction in inflammatory cytokines as TGF and iNOS. Although the reduction of TGF and iNOS in BCA-treated mice was superior to PZQ, no statistically significant differences were noted. However, a significant downregulation of COX2 was noted in hepatocytes as compared to both infected control and PZQ-treated mice. BCA has schistosomicidal, anti-inflammatory, antioxidant and anti-fibrotic effects and could be regarded as a potential drug in schistosomiasis treatment.

Synthesis and Biological Evaluation of Novel Phthalide Analogs-1,2,4-Oxadiazole Hybrids as Potential Anti-Inflammatory Agents

A series of novel pathalide-1,2,4-oxadiazole analogs were synthesized for discovering novel anti-inflammatory agents. After the assessment of their cytotoxicity in vitro, all compounds had been screened for their anti-inflammatory activity by evaluating their inhibitory effect on LPS-induced NO production in RAW 264.7 macrophages. SARs had been concluded, and finally compound E13 was found to be the most potent compound. This compound could also significantly decrease the production of iNOS and COX-2. Preliminary mechanism studies indicated that compound E13 could inhibit the TLR4/NF-κB and ERK/p38 signaling pathways. These findings indicate that E13 holds great potential to be a lead compound for discovering novel anti-inflammatory drugs.

New 1,2,4-oxadiazole/pyrrolidine hybrids as topoisomerase IV and DNA gyrase inhibitors with promising antibacterial activity

A series of hybridized pyrrolidine compounds with a 1,2,4-oxadiazole moiety were synthesized to develop effective molecules against the enzymes DNA gyrase and topoisomerase IV (Topo IV). Compounds 8-20 were developed based on a previously disclosed series of compounds from our lab, but with small structural modifications in the hopes of increasing the compounds' biological activity. In comparison to novobiocin, with IC₅₀  = 170 nM, the findings of the DNA gyrase inhibitory assay revealed that compounds 16 and 17 were the most potent of all synthesized derivatives, with IC₅₀ values of 180 and 210 nM, respectively. Compound 17 had the strongest inhibitory effect against Escherichia coli Topo IV of all the synthesized compounds, with an IC₅₀ value of 13 µM, which was comparable to novobiocin (IC₅₀  = 11 µM). Therefore, hybrids 16 and 17 appeared to be potential dual-target inhibitors. In the minimal inhibitory concentration (MIC) assays, compound 17 outperformed ciprofloxacin against E. coli, with an MIC of 55 ng/ml, compared to 60 ng/ml for ciprofloxacin. Finally, the docking study, along with the in vitro experiments, supports our promising approach to effectively develop potent leads for further optimization as dual DNA gyrase and Topo IV inhibitors.

Anthelmintic Activity of Antioxidants: In Vitro Effects on the Liver Fluke Opisthorchis felineus

Currently, molecular parasitologists are searching for new agents against trematodiases. Redox metabolism is important for parasites as far as long-lived adult parasites inside a mammalian host are exposed to redox challenges. Antioxidants have been poorly studied as anthelmintic agents, in particular against the foodborne trematodes. Study of in vitro anthelmintic activity of nonenzymatic natural and synthetic antioxidants of various chemical structures was performed using standard motility and mortality assays against juvenile and adult Opisthorchis felineus worms. Promising agents have been found among both natural and synthetic compounds. The mitochondria-targeted antioxidant SkQ1 [10-(6′-plastoquinonyl)decyltriphenylphosphonium] in motility assays was as effective (half-maximal inhibitory concentration [IC₅₀] 0.6–1.4 μM) as praziquantel (IC₅₀ 0.47–1.4 μM), and SkQ1 was significantly more effective than praziquantel in mortality assays. Moreover, extensive tegument damage of the adult fluke was revealed after SkQ1 treatment. Flavonoids manifested potency too, with IC₅₀ values in a micromolar range (5.1–17.4 μM). Other natural and synthetic compounds tested against helminths were significantly less effective than praziquantel. Results of our study indicate that SkQ1 and flavonoids have high anthelmintic activities against the liver flukes. We propose that structure–activity relationship research might be worthwhile based on the structures of the most effective substances.