Targets Of Compounds Research Articles

Podocarpane and cleistanthane diterpenoids from Strophioblachia glandulosa: Structural elucidation, anti-hypertrophy activity and network pharmacology

In the present investigation, fourteen unprecedented podocarpane diterpenoids strophiolosas A-J, L-N and P (1–10, 12–14, 16), two new cleistanthane derivatives strophiolosas Q-R (17–18), two new dibenzopyroan-ones and one new tetralone strophiolosas S-U (19–21), were isolated from the whole plant of Strophioblachia glandulosa. The structures were elucidated via various spectroscopic analysis, quantum chemistry calculations, and X-ray diffraction. Bioactivity test indicated that compounds 5 and 17 possessed promising anti-cardiac hypertrophy effect in vitro (IC50 values of 16.50 and 9.67 μM). Additionally, through network pharmacology prediction, PARP1 may be a potential target of compound 17, mediating its anti-hypertrophic effects through multiple pathways.

Omeprazole and its analogs exhibit insecticidal potencies as inhibitors of insect choline acetyltransferase

Choline acetyltransferase (ChAT) is crucial for acetylcholine synthesis and regulates diverse functions in numerous biological processes. Omeprazole, an inhibitor on human ChAT, was evaluated here on insect ChAT as a potential inhibitor, as well as its insecticidal potency on Nilaparvata lugens, a major insect pest on rice. The evaluation also included omeprazole analogs and α-NETA, in order to explore a superior leading compound targeting on insect ChAT. In toxicity test, α-NETA and omeprazole exhibited insecticidal activity, among which omeprazole exhibited activity with a mortality of around 50 % on N. lugens nymphs at 0.4 mg/mL. In vitro crude enzyme assays showed that omeprazole acted as an inhibitor on insect ChAT with a high selectivity and exciting potency compared with α-NETA and control. Three residues (Tyr84, Val95, Tyr589) was critical in N. lugens ChAT for interacting with its substrate choline through molecular docking, and it also revealed that omeprazole exhibited a higher binding affinity toward ChAT catalytic tunnel compared with α-NETA. Based on this, we screened omeprazole analogs for their affinity to N. lugens ChAT, and two compounds stood out. The 5-hydroxy omeprazole had the highest binding affinity by prediction, and 5-O-desmethyl omeprazole was with the lowest binding affinity. The toxicity bioassay and enzyme activity test were then performed on these two compounds. Aligned with the docking results, 5-hydroxy omeprazole showed a strong inhibitory effect and insecticidal activity. In summary, omeprazole and 5-hydroxy omeprazole could serve as lead compounds for insecticides targeting on insect ChAT, a novel target.

Precision Activity-Based α-Amylase Probes for Dissection and Annotation of Linear and Branched-Chain Starch-Degrading Enzymes.

α-Amylases are the workhorse enzymes of starch degradation. They are central to human health, including as targets for anti-diabetic compounds, but are also the key enzymes in the industrial processing of starch for biofuels, corn syrups, brewing and detergents. Dissection of the activity, specificity and stability of α-amylases is crucial to understanding their biology and allowing their exploitation. Yet, functional characterization lags behind DNA sequencing and genomics; and new tools are required for rapid analysis of α-amylase function. Here, we design, synthesize and apply new branched α-amylase activity-based probes. Using both α-1,6 branched and unbranched α-1,4 maltobiose activity-based probes we were able to explore the stability and substrate specificity of both a panel of human gut microbial α-amylases and a panel of industrially relevant α-amylases. We also demonstrate how we can detect and annotate the substrate specificity of α-amylases in the complex cell lysate of both a prominent gut microbe and a diverse compost sample by in-gel fluorescence and mass spectrometry. A toolbox of starch-active activity-based probes will enable rapid functional dissection of α-amylases. We envisage activity-based probes contributing to better selection and engineering of enzymes for industrial application as well as fundamental analysis of enzymes in human health.

An integrated analysis of network pharmacology and GEO database to decode the active component and the underlying mechanism of Yiwei decoction in non-small cell lung cancer

Treating non‑small‑cell lung cancer (NSCLC) is challenging and demands therapies with minimal side effects to enhance patient quality of life. Yiwei Decoction (YWD) shows potential for NSCLC treatment,but further research is necessary for full comprehension about active compounds, molecular targets, and mechanisms. Using TCMSP and BATMAN‑TCM, the study identified YWD’s active components and targets, and analyzed NSCLC differential genes from the GEO database.NSCLC targets from GeneCard, NCBI, and DisGeNET were combined with differential genes to identify component targets. A PPI network showed overlapping targets, while GO and KEGG analyses assessed relevant pathways. Molecular docking validated the connection between the main compound and core target in the “active ingredient‑target‑pathway” network. The study identified 193 targets for 20 active YWD components and 197 NSCLC‑related targets, with 14 overlaps.GO analysis revealed that YWD affects 146 biological processes, including cell proliferation and protein kinase binding. KEGG analysis identified 58 pathways related to inflammation, cell survival, and cancer, clarifying YWD’s role in NSCLC treatment. Network analysis and molecular docking indicated that n‑coumaroyltyramine and quercetin effectively bind to CCND1 and EGFR, underscoring their therapeutic contributions. The study suggests that YWD may target CCND1, EGFR, and TP53, impacting HIF‑1, JAK‑STAT, and other stress‑related pathways in NSCLC.

Recent Advances in Polymeric Nano Formulations Using Phenolic Compound Targeting Anti Inflammation

Recent Advances in Polymeric Nano Formulations Using Phenolic Compound Targeting Anti Inflammation

Bioinformatics combined with network pharmacology and experimental validation to identify key biomarkers of hepatocellular carcinoma and corresponding compounds in Radix Astragali and Pueraria Mirifica.

The occurrence and death rates of primary hepatocellular carcinoma (HCC) are increasing, and there remains a shortage of effective oral medications with minimal side effects. We aim to identify potential biomarkers and compounds from Radix Astragali (RA) and Pueraria Mirifica (PM) to treat liver cancer and improve prognosis. Differentially expressed genes (DEGs) associated with HCC were identified by bioinformatics analysis of three datasets, GSE112791, GSE101685, and GSE45114. Using public databases to predict the bioactive components and possible targets of RA and PM. Target crossover from Gene Expression Omnibus (GEO) and public databases were used to identify potential biomarkers for HCC. Subsequently, validation and prognostic value analyses were performed using the Gene Expression Profile Interaction Analysis (GEPIA) platform. The Cytoscape software created a network of "compound targets" to pinpoint compounds linked to the biomarkers. Molecular docking techniques were utilized to validate the connection between these compounds and the identified biomarkers. Ultimately, the HepG2 liver cancer cell line was chosen to assess the inhibitory effect of Hederagenin (HDG) and to confirm the expression of ADH1B through Western blot analysis. In this study, four key biomarkers (NR1I2, ADH1B, NQO1, GHR) were identified. Molecular docking showed that these four core targets could form stable conformations with the corresponding compounds. As the drug concentration decreases, the inhibitory effect on HepG2 diminishes, and the survival rate of HepG2 cells significantly declines following the administration of 100 µmol/L HDG. Compared to the control, the expression of ADH1B protein is significantly increased in HepG2 cells treated with 100 µmol/L HDG. The study identified four key biomarkers (ADH1B, GHR, NQO1, NR1I2) that have prognostic ability for HCC. This study provides biomarkers and potential targeted monomeric medicines for treating HCC.

Natural compounds modulate the mechanism of action of tumour-associated macrophages against colorectal cancer: a review.

Colorectal cancer (CRC) exhibits a substantial morbidity and mortality rate, with its aetiology and pathogenesis remain elusive. It holds significant importance within the tumour microenvironment (TME) and exerts a crucial regulatory influence on tumorigenesis, progression, and metastasis. TAMs possess the capability to foster CRC pathogenesis, proliferation, invasion, and metastasis, as well as angiogenesis, immune evasion, and tumour resistance. Furthermore, TAMs can mediate the prognosis of CRC. In this paper, we review the mechanisms by which natural compounds target TAMs to exert anti-CRC effects from the perspective of the promotional effects of TAMs on CRC, mainly regulating the polarization of TAMs, reducing the infiltration and recruitment of TAMs, enhancing the phagocytosis of macrophages, and regulating the signalling pathways and cytokines, and discuss the potential value and therapeutic strategies of natural compounds-targeting the TAMs pathway in CRC clinical treatment.

Discovery of 1,2,4-Triazole-3-thione Derivatives as Potent and Selective DCN1 Inhibitors for Pathological Cardiac Fibrosis and Remodeling.

DCN1, a critical co-E3 ligase during the neddylation process, is overactivated in many diseases, such as cancers, heart failure as well as fibrotic diseases, and has been regarded as a new target for drug development. Herein, we designed and synthesized a new class of 1,2,4-triazole-3-thione-based DCN1 inhibitors based the hit HD1 identified from high-throughput screening and optimized through numerous structure-activity-relationship (SAR) explorations. HD2 (IC50= 2.96 nM) was finally identified and represented a highly potent and selective DCN1 inhibitor with favorable PK properties and low toxicity. Amazingly, HD2 effectively relieved Ang II/TGFβ-induced cardiac fibroblast activation in vitro, and reduced ISO-induced cardiac fibrosis as well as remodeling in vivo, which was linked to the inhibition of cullin 3 neddylation and its substrate Nrf2 accumulation. Our findings unveil a novel 1,2,4-triazole-3-thione-based derivative HD2, which can be recognized as a promising lead compound targeting DCN1 for cardiac fibrosis and remodeling.

Network Pharmacology and Molecular Dynamics Simulations Reveal the Mechanism of Total Alkaloid Components in Anisodus Tanguticus (Maxim.) Pascher in Treating Inflammation and Pain.

This study aimed to elucidate the mechanism that total alkaloids in Anisodus tanguticus (AT)(Maxim.) Pascher played anti-inflammatory and analgesic effects. In this paper, the anti-inflammatory effect in the total alkaloids of AT was confirmed via lipopolysaccharide (LPS)-induced inflammation model in RAW 264.7 cells and the main components of AT were immediately analyzed by UPLC/MS. Disease targets were obtained in GeneCards and DisGeNET. Targets of major compounds were searched in ETCM, TCMSP and other databases. The protein-protein interaction (PPI) network was constructed using STRING database, and Cytoscape was used for core targets screening. GO and KEGG enrichment analysis were performed using Daivid database. Sailvina was used for molecular docking. Molecular dynamics simulation analysis was performed using the Amber 20 program. The results showed that the main components in AT were anisodamine, atropine, fabiatrin, scopolamine, scopoletin and scopolin, possibly exerting anti-inflammatory and analgesic effects through pathways such as EGFR tyrosine kinase inhibitor resistance and IL-17 signaling pathway. Fabiatrin and scopolin could be potential drugs with good anti-inflammatory and analgesic effects.

Cell components of tumor microenvironment in lung adenocarcinoma: Promising targets for small-molecule compounds.

Lung cancer is one of the most lethal tumors in the world with a 5-year overall survival rate of less than 20%, mainly including lung adenocarcinoma (LUAD). Tumor microenvironment (TME) has become a new research focus in the treatment of lung cancer. The TME is heterogeneous in composition and consists of cellular components, growth factors, proteases, and extracellular matrix. The various cellular components exert a different role in apoptosis, metastasis, or proliferation of lung cancer cells through different pathways, thus contributing to the treatment of adenocarcinoma and potentially facilitating novel therapeutic methods. This review summarizes the research progress on different cellular components with cell-cell interactions in the TME of LUAD, along with their corresponding drug candidates, suggesting that targeting cellular components in the TME of LUAD holds great promise for future theraputic development.

Exploring the Anti-Diabetic Potential of <i>Cichorium intybus</i> through Integrated Network Pharmacology Analysis and Molecular Docking Validation

Background: The major global health concern known as Type 2 Diabetes Mellitus (T2DM) ischaracterized by increased blood sugar level and insulin resistance. It is a common and complicated metabolic illness that needs to be understood from many angles in order to be predicted and treated effectively. Aim: Therefore, in his study, we aim to reveal the accurate and in-depth roots to predict the progression of diabetes and its management. Methods: A workable compound-target-pathway network pharmacology model and molecular docking studies were created by combining compound screening and target prediction. This model enabled researchers to systematically anticipate potential compounds and the mechanisms of Cichorium intybus anti-diabetic actions. Results: The results of the network pharmacology study were subsequently verified by using molecular docking, which effectively identified several active compounds of C. intybus and several targets that support anti-diabetes. For analytical purposes, four primary active chemicals are considered here: myricetin, cyanidin, quercitrin, and chicoric acid. These compounds act on targets such as alpha-amylase (1B2Y) and alpha-glucosidase (3W37). Here network pharmacology is used to build an interactive, complete network of genes relevant to diabetes, proteins, and pathways then validation is done through docking. Docking score of all 5 active compounds for both the targets alpha-glucosidase (PDB:3W37) and alpha-amylase (PDB:1B2Y) are considered. So, compound quercetin and cyanidin with both targets show the strongest binding affinities and interactions. Conclusion: Thus, this research successfully concludes the prediction of the active chemicals and targets of C. intybus for the treatment of diabetes. It offers fresh perspectives on the pharmacological and molecular foundations of C. intybus.

The quick screening of binding compounds and proteins for drug discovery and pharmacological research

In drug discovery and pharmacological research, early identification of target molecules for compounds with pharmacological effects is crucial. However, this process often requires significant effort and can be rate-limiting, thereby slowing down research progress. This paper introduces a simplified and rapid method for quick screening of binding compounds or proteins. Utilizing Affinity Selection Mass Spectrometry (ASMS), this technique efficiently detects compound-target binding through size-exclusion chromatography and mass spectrometry. ASMS offers high sensitivity and specificity, making it ideal for accurate identification of binding interactions. We have further enhanced ASMS to handle membrane proteins without solubilization, creating Binder Selection Technology (BST). BST allows screening against both soluble and challenging membrane proteins such as GPCRs and SLC transporters. By using cell membrane fractions or organelle fractions with high target molecule expression, BST efficiently identifies potential binding compounds. This innovative method constructs a comprehensive database of binding compounds for various targets, facilitating rapid hypothesis testing and pharmacological evaluation. Additionally, BST screens 17,000 proteins, including membrane proteins, using wheat germ cell-free and animal cell expression systems. This approach allows exploration of binding interactions without labeling compounds or immobilizing proteins, preserving their native state. BST is powerful for identifying targets of compounds with known pharmacological effects but unknown targets in animal or cell-based assays. By utilizing BST, researchers can overcome bottlenecks in early drug discovery, significantly enhancing research speed and success rates. This method represents a major advancement, providing an efficient and effective way to identify and validate target molecules in drug discovery.

New compounds target oral cancer cells without harming normal tissue

New compounds target oral cancer cells without harming normal tissue

Flavonoids in Astragali Radix Functions as Regulators of CDK2, VEGFA and MYC in Osteoporosis and Type 1 Diabetes Mellitus

Background: People with type 1 diabetes mellitus (T1DM) are significantly more likely to have osteoporosis (OP). Astragali Radix is a Chinese herbal medicine containing various active ingredients, and several clinical trials have been reported to use it to treat OP and T1DM, respectively. Objective: To evaluate the targets and potential mechanisms of Astragali Radix administration on OP and T1DM. Methods: The targets of Astragali Radix were identified using the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. The OP and T1DM datasets were downloaded from the Gene Expression Omnibus (GEO) database. The weighted gene correlation network analysis (WGCNA) method was used to identify the co-expression genes associated with OP and T1DM. In addition, the common gene targets of OP and T1DM were screened using two public databases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using the R tool. After the validation of key genes, molecular docking was performed to visualize small molecule-protein interactions. Results: The compound target network mainly contained 17 compounds and 147 corresponding targets. There were 561 GO items and 154 signaling pathways in KEGG, mainly including the AGE-RAGE signaling pathway in diabetic complications and osteoclast differentiation. The results of molecular docking showed that flavonoids were the top compound of Astragali Radix, which had a high affinity with CDK2, VEGFA, and MYC. Conclusion: Flavonoids in Astragali Radix may regulate multiple signaling pathways through MYC, CDK2, and VEGFA, which may play a therapeutic role in OP and T1DM.

Cryo-EM reveals transition states of the Acinetobacter baumannii F1-ATPase rotary subunits γ and ε, unveiling novel compound targets.

Priority 1: critical WHO pathogen Acinetobacter baumannii depends on ATP synthesis and ATP:ADP homeostasis and its bifunctional F1FO-ATP synthase. While synthesizing ATP, it regulates ATP cleavage by its inhibitory ε subunit to prevent wasteful ATP consumption. We determined cryo-electron microscopy structures of the ATPase active A. baumannii F1-αßγεΔ134-139 mutant in four distinct conformational states, revealing four transition states and structural transformation of the ε's C-terminal domain, forming the switch of an ATP hydrolysis off- and an ATP synthesis on-state based. These alterations go in concert with altered motions and interactions in the catalytic- and rotary subunits of this engine. These A. baumannii interacting sites provide novel pathogen-specific targets for inhibitors, with the aim of ATP depletion and/or ATP synthesis and growth inhibition. Furthermore, the presented diversity to other bacterial F-ATP synthases extends the view of structural elements regulating such a catalyst.

Mechanistic exploration of bioactive constituents in Gnetum gnemon for GPCR-related cancer treatment through network pharmacology and molecular docking

G Protein-Coupled Receptors (GPCRs) are integral membrane proteins that have gained considerable attention as drug targets, particularly in cancer treatment. In this study, we explored the capacity of bioactive compounds derived from Gnetum gnemon (GG) for the development of of pharmaceuticals targeting GPCRs within the context of cancer therapy. Integrated approach combined network pharmacology and molecular docking to identify and validate the underlying pharmacological mechanisms. We retrieved targets for GG-derived compounds and GPCRs-related cancer from databases. Subsequently, we established a protein-protein interaction (PPI) network by mapping the shared targets. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were employed to predict the mechanism of action of these targets. Molecular docking was conducted to validate our findings. We identified a total of 265 targets associated with GG-derived bioactive compounds for the treatment of GPCRs-related cancer. Functional enrichment analysis revealed the promising therapeutic effects of these targets on GPCRs-related cancer pathways. The PPI network analysis identified hub targets, including MAPK3, SRC, EGFR, STAT3, ESR1, MTOR, CCND1, and PPARG, which demonstrate as treatment targets for GPCRs-related cancer using GG-derived compounds. Additionally, molecular docking experiments demonstrated the strong binding affinity of gnetin A, gnetin C, (-)-viniferin, and resveratrol dimer, thus inhibiting MAPK3, SRC, EGFR, and MTOR. Survival analysis established the clinical prognostic relevance of identified hub genes in cancer. This study presents a novel approach for comprehending the therapeutic mechanisms of GG-derived active compounds and thereby paving the way for their prospective clinical applications in the field of cancer treatment.

Molecular Targets of Plant-Derived Bioactive Compounds in Oral Squamous Cell Carcinoma.

With a significant increase in both incidence and mortality, oral cancer-particularly oral squamous cell carcinoma (OSCC)-is one of the main causes of death in developing countries. Even though there is evidence of advances in surgery, chemotherapy, and radiotherapy, the overall survival rate for patients with OSCC has improved, but by a small percentage. This may be due, on the one hand, to the fact that the disease is diagnosed when it is at a too-advanced stage, when metastases are already present. This review explores the therapeutic potential of natural herbal products and their use as adjuvant therapies in the treatment of oral cancer from online sources in databases (PubMed, Web of Science, Google Scholar, Research Gate, Scopus, Elsevier). Even if classic therapies are known to be effective, they often produce many serious side effects and can create resistance. Certain natural plant compounds may offer a complementary approach by inducing apoptosis, suppressing tumor growth, and improving chemotherapy effectiveness. The integration of these compounds with conventional treatments to obtain remarkable synergistic effects represents a major point of interest to many authors. This review highlights the study of molecular mechanisms and their efficiency in in vitro and in vivo models, as well as the strategic ways in which drugs can be administered to optimize their use in real contexts. This review may have a significant impact on the oncology community, creating new inspirations for the development of more effective, safer cancer therapies with less toxic potential.

Sinulariapeptide F, a new peptide from culture broth of marine-derived fungus Simplicillium sp. SCSIO 41222.

One new compound named sinulariapeptide F (1) together with one known butyrolactone (2) and seven known peptides (3-9) were isolated from the fungus Simplicillium sp. SCSIO 41222. Their structures and absolute configurations were established using HRESIMS, NMR spectroscopy (1H, 13C, HSQC, HMBC) and marfey's method. All of these compounds were assessed their inhibitory activity of acetylcholinesterase (AChE) and pancreatic lipase (PL). Compounds 4 and 6 were selected to test for the inhibitory activity against programmed cell death-1 (PD-1)/ programmed cell death-ligand 1 (PD-L1). The results indicated that compound 4 displayed potent inhibition activity against PD-1/ PD-L1 with an IC50 value of 0.656 μM. Furthermore, the docking analysis demonstrated the interactions between 4 and proteins, suggesting PD-L1 to be a probable target for compound 4.

The Influence of the Estrous Cycle on Neuropeptide S Receptor-Mediated Behaviors.

The Neuropeptide S receptor (NPSR) has been identified as a potential therapeutic target for anxiety and post-traumatic stress disorder. Central administration of Neuropeptide S (NPS) in male mice produces anxiolytic-like effects, hyperlocomotion, and memory enhancement. Currently, the literature is limited in the number of studies investigating the effects of NPS in female test subjects despite females facing a higher prevalence of anxiety-related pathology, as well as greater risk for adverse effects while taking psychoactive drugs. Moreover, no previous studies have considered the influence of estrous cycle on the effects of NPS. The current study investigates whether NPS-mediated behavioral phenotypes seen in males translate to females, and whether they are affected by estrous cycle stage. Female C57BL/6NCr mice were intracerebroventricularly (ICV) cannulated and underwent behavioral paradigms to test locomotion, anxiety, and memory. Estrous cycle stage was determined through examination of vaginal cytology. Our results provide evidence that NPS-mediated behaviors are influenced by the estrous cycle. Administration of NPS decreased anxiety-like behaviors more robustly when the female mice were in high estrogen stages of the estrous cycle. Therefore, the desired anxiolytic-like effects of targeting the NPSR are intact in female mice. However, these effects may to be influenced by the stage of the estrous cycle. The NPSR remains a strong potential drug target for new anxiolytic compounds and based on our initial observations further studies exploring the interaction of estrous cycle and the NPS-system are warranted. Significance Statement The neuropeptide S (NPS) receptor has been identified as a potential target for treating anxiety, a condition that is most prevalent in females. Therefore, the potential interaction of estrous cycle with the NPS-system described in the current study is an important first step in understanding the function of the NPS-system in females.

A pH-Sensitive cRGD-PEG-siRNA Conjugated Compound Targeting Glioblastoma.

Glioblastoma ranks among the most prevalent primary intracranial tumors, characterized by high mortality and poor prognosis. Chemotherapy remains a key treatment strategy for gliomas, though most current drugs suffer from limited efficacy and significant toxicity. This study focuses on a cRGD-siEGFR coupling compound synthesized in a previous stage. Prior research indicated that cRGD-siEGFR molecules exhibited certain targeting and antitumor properties but faced issues of inadequate targeting, low efficacy, and high renal toxicity. To enhance antitumor efficacy and mitigate side effects, a pH-responsive, long-circulating, and highly targeted siRNA delivery system, the cRGD-PEG-siEGFR conjugate, was developed. The targeting, antitumor effects, and biological distribution of cRGD-PEG-siEGFR were examined. The results demonstrated that cRGD-PEG-siEGFR was effectively taken up by αvβ3-positive U87MG cells, specifically silenced EGFR gene expression, and exhibited antitumor effects. In normal physiological conditions, it avoided uptake by normal cells, thereby reducing side effects. Furthermore, in vivo biodistribution experiments revealed that cRGD-PEG-siEGFR, compared to cRGD-siEGFR, significantly decreased renal accumulation and exhibited prolonged circulation. Consequently, cRGD-PEG-siRNA emerges as a promising drug candidate with attributes of long circulation, high targeting, pH responsiveness, and substantial antitumor efficacy.