Combinatorial Chemistry & High Throughput Screening - Volume 26, Issue 9, 2023

Background: Ageratina is an American genus of the tribe Eupatorieae (Asteraceae), comprising about 320 species. In Mexico, some species of this genus are highly valued for their medicinal properties, particularly A. pichinchensis, A. petiolaris, and A. grandifolia. Furthermore, herbal preparations of A. pichinchensis are available for treating several mycoses. Aims and Objective: The present review is aimed to summarize the chemical and pharmacological properties of 37 species of the Ageratina genus up to April, 2022. Methods: Data were recorded using online scientific databases, including Scopus, PubMed, Google Scholar, Taylor and Francis Imprints, National Center for Biotechnology Information, Science Direct, JSTOR, and SciFinder. The information was gathered from research articles, relevant books on herbal medicinal plants and the history of medicinal plants from Mexico, theses, reports, and web pages. Results: The specialized metabolites present in the Ageratina genus belong to different chemical classes, including flavonoids, benzyl benzoates, benzofurans, chromenes, and terpenoids. The chromenes, benzofurans, and benzyl benzoates are the metabolites most widespread in the genus. So far, the species more thoroughly investigated is A. adenophora. Ageratina has received little attention from the pharmacological point of view. The studies are limited to 10 species. Biological studies have been conducted on extracts and/or compounds isolated from plants collected mainly from China and Mexico. The results revealed that the extracts and metabolites possess several biological activities, including antiviral, antioxidant, antimicrobial, anti-inflammatory, antinociceptive, antifeedant, larvicidal, acaricidal, antidiabetic, antiprotozoal, and wound-healing properties. In the case of A. pichinchensis, A. petiolaris, and A. grandifolia, the pharmacological studies provided evidence for their use for treating gastrointestinal complaints and diabetes. Furthermore, herbal preparations of A. pichinchensis are now widely used for alleviating onychomycosis. A. adenophora, is the most investigated species, chemically and biologically; however, some hepatotoxicity effect has been recorded. Conclusion: This review recapitulates information on the Ageratina genus, highlighting the phytochemistry and biological activities of the species investigated. It is important to point out that the pharmacological potential of this large genus remains largely unexplored.

Background: Hairy agrimony (Agrimonia pilosa Ledeb.) is a traditional medicinal plant widely used in Eastern Europe and Eastern Asia. The plant is harvested as it comes into flower and could be dried for later usage. Hairy agrimony has been traditionally introduced to treat sore throat, abdominal pain, headache, mucoid dysentery, bloody and white discharge, parasites, and eczema. Objective: Since the 1950s, various experimental reports relating to phytochemical and pharmacological aspects have been observed, but an overview is now not available. The current paper emphasizes on in-depth information about the botanical description, traditional use, phytochemistry, and pharmacology. Methods: The collection of previous research is basically dependent on the reliable resources Sci- Finder, Google Scholar, ScienceDirect, reputation publishers, and thesis books. Results: A. pilosa was found to contain a variety of chemical classes. To date, more than 160 secondary metabolites have been separated, and the derivatives type flavonoids, phloroglucinols, tannins, isocoumarins, and triterpenoids are the main components. A. pilosa crude extracts and their isolates set a broad panel of pharmacological values, including anti-cancer, anti-microbial, antivirus, anti-oxidant, anti-inflammation, anti-diabetes, anti-osteosarcoma, anti-aging, anti-nociception, anti-adipogenesis, anti-leishmaniasis, estrogenic-like activity, neuroprotective and hepatoprotective activities, and vascular relaxation. Conclusion: In vitro and in vivo results also successfully explained the pharmacological mechanisms of A. pilosa constituents. More bioassay-guided phytochemical and clinical studies are necessary.

Background: Citrus grandis ‘Tomentosa,’ a fruit epicarp of C. grandis ‘Tomentosa’ or C. grandis (L.) Osbeck is widely used in health food and medicine. Based on our survey results, there are also rich essential oils with bioactivities in leaves, but the chemical compounds in this part and relevant pharmacological activities have never been studied systematically. Therefore, this study was to preliminarily decipher the pharmacological activities and mechanisms of the essential oil in leaves of C. grandis ‘Tomentosa’ by an integrated network pharmacology approach. Methods: Essential oil compositions from leaves ofC. grandis ‘Tomentosa’ were identified using GC-MS/MS. And then, the targets of these oil compositions were predicted and screened from TCMSP, SwissTargetPrediction, STITCH and SEA databases. STRING database was used to construct the protein-protein interaction networks, and the eligible protein targets were input into WebGestalt 2019 to carry out GO enrichment and KEGG pathway enrichment analysis. Based on the potential targets, disease enrichment information was obtained by TTD databases. Cytoscape software was used to construct the component-target-disease network diagrams. Results: Finally, 61 essential oil chemical components were identified by GC-MS/MS, which correspond to 679 potential targets. Biological function analysis showed 12, 19, and 12 GO entries related to biological processes, cell components and molecular functions, respectively. 43 KEGG pathways were identified, of which the most significant categories were terpenoid backbone biosynthesis, TNF signaling pathway and leishmaniasis. The component-target-disease network diagram revealed that the essential oil compositions in leaves of C. grandis ‘Tomentosa’ could treat tumors, immune diseases, neurodegenerative diseases and respiratory diseases, which were highly related to CHRM1, PTGS2, CASP3, MAP2K1 and CDC25B. Conclusion: This study may provide new insight into C. grandis ‘Tomentosa’ or C. grandis (L.) Osbeck and may provide useful information for future utilization and development.

Background and Aim: Major Depressive Disorder (MDD) is a common affective disorder. GuiPi decoction (GPD) is used to treat depression in China, Japan, and Korea. However, its effective ingredients and antidepressant mechanisms remain unclear. We attempted to reveal the potential mechanisms of GPD in the treatment of MDD by network pharmacology and molecular docking. In addition, we conducted an enzymatic activity assay to validate the results of molecular docking. Methods: GPD-related compounds and targets, and MDD-related targets were retrieved from databases and literature. The herb-compound-target network was constructed by Cytoscape. The protein- protein interaction network was built using the STRING database to find key targets of GPD on MDD. Enrichment analysis of shared targets was analyzed by MetaCore database to obtain the potential pathway and biological process of GPD on MDD. The main active compounds treating MDD were screened by molecular docking. The PDE4s inhibitors were screened and verified by an enzyme activity assay. Results: GPD contained 1222 ingredients and 190 potential targets for anti-MDD. Possible biological processes regulated by GPD were neurophysiological processes, blood vessel morphogenesis, Camp Responsive Element Modulator (CREM) pathway, and Androgen Receptor (AR) signaling crosstalk in MDD. Potential pathways in MDD associated with GPD include neurotransmission, cell differentiation, androgen signaling, and estrogen signaling. Fumarine, m-cresol, quercetin, betasitosterol, fumarine, taraxasterol, and lupeol in GPD may be the targets of SLC6A4, monoamine oxidase A (MAOA), DRD2, OPRM1, HTR3A, Albumin (ALB), and NTRK1, respectively. The IC50 values of trifolin targeting Phosphodiesterase (PDE) 4A and girinimbine targeting PDE4B1 were 73.79 μM and 31.86 μM, respectively. The IC50 values of girinimbine and benzo[a]carbazole on PDE4B2 were 51.62 μM and 94.61 μM, respectively. Conclusion: Different compounds in GPD may target the same protein, and the same component in GPD can target multiple targets. These results suggest that the effects of GPD on MDD are holistic and systematic, unlike the pattern of one drug-one target.

Objective: The study aims to explore the prognostic significance of zona pellucida glycoprotein 3 (ZP3) in hepatocellular carcinoma (HCC) tissues. Methods: The expression of ZP3 protein in HCC tissues was detected by immunohistochemistry (IHC) to study its effects on the clinicopathological characteristics and prognosis of HCC patients. The Cancer Genome Atlas (TCGA) database was used to confirm the expression of ZP3 in HCC tissues, and Gene set enrichment analysis (GSEA) was performed to obtain potential ZP3-related pathways in HCC. Results: IHC detection found that ZP3 had a high expression in HCC tissues and was associated with cirrhosis and hepatitis B virus infection in HCC patients (p<0.05). TCGA database also showed that ZP3 was up-regulated in HCC tissues. Further survival evaluation confirmed that ZP3 expression caused an impact on the overall survival time and disease-free survival time of HCC patients (p<0.05), implying a potential role in HCC prognosis. GSEA analysis indicated that the 187 differential gene sets were mainly involved in 10 signaling pathways, including 5 up-regulated and 5 down-regulated pathways. Conclusion: High expression of ZP3 in HCC tissues is found to have an important role in HCC development and prognosis.

Background and Objective: Traditional Chinese medicines that have inhibitory effects on the CYP3A4 enzymes were screened and their inhibitory effects were verified with in vitro bioassay. Methods: The computer virtual screening methods, including the CYP3A4 enzyme pharmacophore model and the molecular docking method, were used to rapidly screen the potential CYP3A4 inhibitors in the Traditional Chinese Medicine Database (TCMD), and then in vitro experiments were conducted to validate the computational data. Results: A total of 413 chemical components in TCMD that have potential inhibitory effects on the CYP3A4 enzyme were screened, and four kinds of traditional Chinese medicines (Abrus precatorius, Andrographis paniculata, Angelica pubescens f. biserrata and Lithospermum erythrorhizon) contained the most potential CYP3A4 inhibitors; The results of the in vitro experiments showed that these four traditional Chinese medicine extracts all had certain degrees of inhibition on the CYP3A4 enzyme, with IC50 values of 5.15, 14.97, 15.2, and 24.21 μg/ml, respectively. Conclusion: The extracts of Abrus precatorius, Andrographis paniculata, Angelica pubescens f. biserrata and Lithospermum erythrorhizon had certain inhibitory effects on the CYP3A4 enzyme, and attention should be paid to the possible adverse reactions when they were used in combination with the CYP3A4 enzyme-substrate drugs. A combination of computational approaches might be a useful tool to identify potential inhibitors of the CYP3A4 enzyme from traditional Chinese medicine.

Background: Streptococcus mutans is one of the bacteria that contributes to biofilm formation and causes dental caries. The inhibition of SrtA, gbpC, and Ag I/II is a promising target to be developed as an antibacterial. Ocimum basilicum is known to have antibacterial activity. Aim and Objective: The aim of this study is to evaluate the potential nevadensin as antibacterial against in-silico. Methods: Antibacterial analysis was carried out by disc diffusion and micro-dilution methods and the in-silico study was performed with ligand-protein docking. Results: The result showed that the MIC and MBC values of nevadensin are 900 and 7200 μg/mL, respectively. The binding energy of nevadensin to SrtA, gbpC, and Ag I/II were -4.53, 8.37, -6.12 kcal/mol, respectively. Conclusion: Nevadensin shows moderate activity as an antibacterial against S. mutans. Meanwhile, in silico studies showed it has the same binding strength as chlorhexidine in inhibiting SrtA, whereas to gbpC and Ag I/II, it has a weaker binding affinity. Therefore, nevadensin has the potential as a natural antibacterial against S. mutans by inhibiting SrtA.

Background: Depression is a typical outcome of the repair of posttraumatic stress disorder (PTSD). Based on network pharmacology and neuropharmacology experiments, this study aimed to explore how gastrodin (GAS) reverses depressive symptoms in traumatically stressed rats. Methods: GAS-related targets were predicted by SwissTargetPrediction; depression-related targets were collected from GeneCards and therapeutic target database (TTD); protein-protein interaction (PPI) network was constructed with its action mechanism being predicted by gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. The animal model of PTSD was replicated by single prolonged stress (SPS). The antidepressant effect of GAS was investigated by the forced swim test (FST) and tail suspension test (TST). The levels of tyrosine hydroxylase (TH) and corticotropin-releasing factor type I receptor (CRF1) in locus ceruleus (LC) and the expression of corticotropin-releasing factor (CRF) in the paraventricular nucleus of the hypothalamus (PVN) and central amygdala (CeA) were measured by immunofluorescence. Results: GAS significantly shortened the tail suspension and swimming immobility in SPS rats in TST and FST experiments (p < 0.05 or p < 0.01). The network analysis showed that the critical antidepressant targets of GAS were 86 targets such as GAPDH, CASP3 MMP9, HRAS, DPP4, and TH, which were significantly enriched in the pathways such as pathways neuroactive ligandreceptor interaction. High doses of GAS could significantly reduce the level of TH and CRF in CEA in the brain of rats with depressive symptoms (p < 0.01) and, at the same time, lower the expression of CRF in PVN (p < 0.05). Conclusion: The effect of GAS on depressive symptoms in SPS rats may be closely related to its reduction of CRF expression in PVN and CeA and inhibition of neuron (NE) synthesis in LC.

Background: Intervertebral Disc Degeneration (IDD) is a heterogeneous spinal disease whose underlying molecular mechanism is unclear. Objectives: This study aimed to identify, profile, and analyze microRNAs (miRNAs) related to IDD. Methods: Microarray Gene Expression IDD data (GSE63492) were downloaded from Gene Expression Omnibus datasets. We employed Weighted Gene Co-Expression Network Analysis (WGCNA) to construct a miRNA co-expression network, and the miRNAs related to the IDD stage were detected. The number of differentially expressed miRNAs between normal and degenerated nucleus pulposus tissues was calculated. Twenty-three clinical specimens were used to validate the expression of miRNAs using qRT-PCR. Results: WGCNA identified 48 miRNAs significantly related to the IDD stage, and 94 miRNAs that were significantly different between normal and degenerated nucleus pulposus tissues. We selected 32 overlapping miRNAs and identified 347 corresponding target genes. The integrative analysis revealed the biological function and pathways of these targeted genes. Analysis of clinical specimens validated that hsa-miR-4534 was upregulated in IDD, whereas hsa-miR-1827 and hsa-miR- 185-5p were downregulated in IDD. Conclusion: This study has identified a subset of miRNAs that are related to IDD pathogenesis and hub miRNAs that are keys to the IDD co-expression network, which may potentially be utilized as indicators for treatment.

Background: Isoindolin-1-ones are medicinally privileged heterocyclic compounds. Due to the interesting biological activities exhibited by these compounds, several synthetic and medicinal research groups have developed numerous synthetic approaches for these compounds. We have also previously reported two efficient approaches for the synthesis of the isoindolin-1-ones through iodoaminocyclization of alkynyl amides using n-BuLi and phosphazene superbases. Objective: This study aimed to construct a medium-size library of multi-substituted 3- methyleneisoindolin-1-ones and study its biological profile, specifically anti-cancer activity. Methods: Solution phase parallel synthesis was performed for the synthesis of the 3- methyleneisoindolin-1-ones library through n-BuLi-mediated iodoaminocyclization of 2.(1- Alkynyl)benzamides. The iodocyclized products were further derivatized through palladiumcatalyzed Sonogashira and Suzuki Miyaura couplings and N-alkylation reactions. In silico evaluation of the physicochemical and ADMET properties was performed to examine the drug-likeness of the library compounds. Selected isoindolin-1-one analogues were evaluated for in vitro antiproliferative activity in various human cancer cell lines (MCF-7, A-549, and U-373 MG). Results: A library of 46 multisubstituted 3-methyleneisoindolin-1-ones has been synthesized. The iodo-isoindolin-1-ones were synthesized in 66-76% yields through n-BuLi-mediated iodoaminocyclization of 2.(1-Alkynyl)benzamides. Further diversification afforded the diverse library members in yields of 40-96%. Two of the library compounds exhibited GI50 values of < 10 μM in the human breast cancer cell line (MCF-7). Conclusion: Isoindolin-1-one library was constructed through electrophilic cyclization. The diversification was successfully performed through various C-C and C-N bond formation reactions. The anti-proliferative activity of the library members appears to be arising from the interaction of the compounds with the protein kinase drug targets.

Introduction: Limited number of researches in the literature have been reported to examine degradation stability by regression methods. Monitoring storage stability of plant extracts containing phytochemicals has become a special field. Objective: This study aims to develop model equations to examine the stability of total phenolic material (TPM) and total anthocyanin (TA) in the sour cherry peel extract under several conditions, such as keeping the samples in a freezer (-20°C), refrigerator (4°C) and room temperature (25°C) conditions. In addition, two types of ambient conditions (under dark and light, respectively) were applied to observe the effect of sunlight on oxidation. Methods: The storage stability was monitored in terms of TPM and TA. 8 different polynomial regression equations were produced for the data obtained under each condition in order to define the deterioration of the TPM and TA during 60 days of the storage. Results: Keeping the samples in the light at ambient conditions was the least efficient for stability (~10 days), while the shelf life of the product could have been quite long with the storage in the freezer after opening the package of the product. Conclusions: The most suitable condition for both TPM and TA has been determined as -20°C with the calculation of degradation days as 157 and 115 (R^2 = 0.9874 / 0.9265, and average error rates = 0.207097% / 0.119541%).

Background: Osteoporosis is a prevalent disease for the aged population. Chinese herbderived natural compounds have anti-osteoporosis effects. Due to the complexity of chemical ingredients and natural products, it is necessary to develop a high-throughput approach with the integration of cheminformatics and deep-learning methods to explore their mechanistic action, especially herb/drug-gene interaction networks. Methods: Ten medicinal herbs for clinical osteoporosis treatment were selected. Chemical ingredients of the top 10 herbs were retrieved from the TCMIO database, and their predicted targets were obtained from the SEA server. Anti-osteoporosis clinical drugs and targets were collected from multidatabases. Chemical space, fingerprint similarity, and scaffold comparison of the compounds between herbs and clinical drugs were analyzed by RDKit and SKlearn. A network of herb-ingredient-target was constructed via Gephi, and GO and KEGG enrichment analyses were performed using clusterProfiler. Additionally, the bioactivity of compounds and targets was predicted by DeepScreening. Molecular docking of YYH flavonoids to HSD17B2 was accomplished by AutoDockTools. Results: Cheminformatics result depicts a pharmacological network consisting of 89 active components and 30 potential genes. The chemical structures of plant steroids, flavonoids, and alkaloids are key components for anti-osteoporosis effects. Moreover, bioinformatics result demonstrates that the active components of herbs mainly participate in steroid hormone biosynthesis and the TNF signaling pathway. Finally, deep-learning-based regression models were constructed to evaluate 22 anti-osteoporosis-related protein targets and predict the activity of 1350 chemical ingredients of the 10 herbs. Conclusion: The combination of cheminformatics and deep-learning approaches sheds light on the exploration of medicinal herbs mechanisms, and the identification of novel and active compounds from medical herbs in complex molecular systems.