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Glabridin is a natural isoflavone with estrogen receptor agonism and significant anti-tumor activity. Additionally, glabridin has a regulation effect on PI3K/AKT/mTOR pathway, but its exact target remains unclear. In this study, we evaluated the antitumor activity of glabridin against breast cancer and prostate cancer cells, and further clarified its targeting to PI3K. We found that glabridin could significantly inhibit the cell viability of human breast cancer and prostate cancer cell lines. It induced caspase activation cascade and cell apoptosis through decreasing the mitochondrial transmembrane potential and increasing the intracellular reactive oxygen species (ROS). Moreover, glabridin could attenuate epithelial-mesenchymal transition (EMT) progression by inhibiting cell migration. PharmMapper calculation showed that PI3Kγ might be the most potential target protein because of the highest Normal Fit score (0.9735) and z'-score (0.9797). Molecular docking and bio-layer interferometry (BLI) analysis further demonstrated the PI3Kγ targeting of glabridin. In vivo experiments showed that glabridin can effectively inhibit the tumor growth of breast cancer xenograft model, and does not show obvious hepatorenal toxicity. Moreover, glabridin could effectively promote the anti-proliferation and pro-apoptotic effects of tamoxifen on MDA-MB-231 cell and taxol on DU145 cell. Elucidating the targeting of glabridin to PI3K may lay a theoretical foundation for the structural derivatization of glabridin, which is expected to greatly promote the application and development of glabridin in the field of cancer therapy.

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Cancer is a rapidly growing non-communicable disease worldwide that is responsible for high mortality rates, which account for 9.6 million death in 2018. Dihydroartemisinin (DHA) is an active metabolite of artemisinin, an active principle present in the Chinese medicinal plant Artemisia annua used for malaria treatment. Dihydroartemisinin possesses remarkable and selective anticancer properties however the underlying mechanism of the antitumor effects of DHA from the structural point of view is still not yet elucidated. In the present study, we employed molecular docking simulation techniques using Autodock suits to access the binding properties of dihydroartemisinin to multiple protein targets implicated in cancer pathogenesis. Its potential targets with comprehensive pharmacophore were predicted using a PharmMapper database. The co-crystallised structures of the protein were obtained from a Protein Data Bank and prepared for molecular docking simulation. Out of the 24 selected protein targets, DHA has shown about 29% excellent binding to the targets compared to their co-crystallised ligand. Additionally, 75% of the targets identified for dihydroartemisinin binding are protein kinases, and 25% are non-protein kinases. Hydroxyl functional group of dihydroartemisinin contributed to 58.5% of the total hydrogen interactions, while pyran (12.2%), endoperoxide (9.8%), and oxepane (19.5%) contributed to the remaining hydrogen bonding. The present findings have elucidated the possible antitumor properties of dihydroartemisinin through the structural-based virtual studies, which provides a lead to a safe and effective anticancer agent useful for cancer therapy.Communicated by Ramaswamy H. Sarma.

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INTRODUCTION: The roots of Stephania succifera are used in traditional medicine for the treatment of several diseases. Research on this plant has mainly focused on bioactive alkaloids from the roots, and no previous work on compounds from the abundant leaves has yet been reported. OBJECTIVE: To identify and compare alkaloidal compounds in S. succifera roots and leaves and to predict the potential bioactivity of some alkaloids. METHODS: High-performance liquid chromatography with quadrupole time-of-flight tandem mass spectrometry (HPLC-QTOF-MS/MS) was employed to identify alkaloidal compounds from S. succifera. The potential targets and bioactivities of most alkaloids were predicted using the PharmMapper server. RESULTS: Fifty-six alkaloidal compounds, including protoberberine-, aporphine-, proaporphine-, benzylisoquinoline-, and lactam-type alkaloids, were identified or tentatively identified in S. succifera roots and leaves based on the HPLC-MS data. Forty-one compounds have not been previously reported in S. succifera and eight of them have not been previously reported in the literature. Twenty-four alkaloidal compounds were found in both roots and leaves. Twelve potential targets with different indications were predicted for some alkaloids. CONCLUSION: Comparison of chemical constituents and their potential bioactivities for S. succifera roots and leaves indicated that diverse bioactive alkaloids were present in the leaves as well as the roots. PharmMapper provided new directions for bioactivity screening. This study will be helpful for further understanding the medicinal components of S. succifera and the rational utilisation of plant resources.

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A new series of novel pyrazole-containing imide derivatives were synthesized and evaluated for their anticancer activities against A-549, Bel7402, and HCT-8 cell lines. Among these compounds A2, A4, A11 and A14 possessed high inhibition activity against A-549 cell lines with IC50 values at 4.91, 3.22, 27.43 and 18.14 µM, respectively, better than that of 5-fluorouracil (IC50=59.27 µM). A2, A4, and A11 also exhibited significant inhibitory activity towards HCT-8 and Bel7402 cell lines. Interestingly, the Heat Shock Protein 90α (Hsp90α, PDB ID: 1UYK) was found to be the potential drug target of these synthesized compounds with the aid of PharmMapper server (http://lilab.ecust.edu.cn/pharmmapper/) and docking module of Schrödinger (Maestro 10.2). Additionally, molecular dynamics simulation was performed out to explore the most likely binding mode of compound A2 with Hsp90α.Communicated by Ramaswamy H. Sarma.

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AIM/HYPOTHESIS: Diabetes is a hyperglycaemic disease treated by a set of allopathic drugs and natural biomolecules along with many variety of stem cell. We aim to investigate the role of these drugs in targeting common protein molecule in diabetes and its associated disease. We also aim to investigate the organ degeneration mechanistic pathway in diabetes. METHOD: We have generated diabetes using streptozotocin injection and treated them using bone marrow transplantation and curcumin administration. The organs were studied histopathologically and by immunofluorescence analysis while drugs were studied Pharmacogenomically. RESULT: Mice injected with streptozotocin have higher glucose and lower insulin, islet number/diameter, bone marrow cell number compared to control and bone marrow transplanted and curcumin administered mice. Histopathology staining demonstrates damaged morphology of pancreas, kidney, brain and cardiac muscle. Further, upon comparison of all allopathic and ayurvedic drugs used for diabetes several protein targets have been identified by reverse pharmacophore analysis using PharmMapper. VEGF, CDK2, insulin receptor, HSp90, eNOS, Fructose1,6 bisphosphatase, neprilysin, AchE, MAPK are several common protein targets of anti-diabetic drugs. CONCLUSION: This article demonstrates that VEGF and CDK2 are critical marker in organ damage in diabetes as well as organ regeneration.

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Heterocyclic 1,3-diazine nucleus is a valuable pharmacophore in the field of medicinal chemistry and exhibit a wide spectrum of biological activities. PharmMapper, a robust online tool used for establishing the target proteins based on reverse pharmacophore mapping. PharmMapper study is carried out to explore the pharmacological activity of 1,3-diazine derivatives using reverse docking program. PharmMapper, an open web server was used to recognize for all the feasible target proteins for the developed compounds through reverse pharmacophore mapping. The results were analyzed via molecular docking with maestro v11.5 (Schrodinger 2018-1) using GTPase HRas as possible target. The molecular docking studies displayed the binding behavior of 1,3-diazine within GTP binding pocket. From the docking study compounds s3 and s14 showed better docked score with anticancer potency against cancer cell line (HCT116). Hence, the GTPase HRas may be the possible target of 1,3-diazine derivatives for their anticancer activity where the retrieved information may be quite useful for developing rational drug designing. Furthermore the selected 1,3-diazine compounds were evaluated for their in vitro anticancer activity against murine macrophages cell line. 1,3-Diazine compounds exhibited good selectivity of the compounds towards the human colorectal carcinoma cell line instead of the murine macrophages. The toxicity study of the most active compounds was also performed on non cancerous HEK-293 cell line.

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To predict the targets of active ingredients of Kuihua Hugan Tablets by network pharmacology, and explore the "multi-component-multi-target-multi-pathway" hepatoprotective mechanism of action. First, through traditional Chinese medicine systems pharmacology(TCMSP) and TCM Database@Taiwan Database, main active ingredients of Kuihua Hugan Tablets were screened out based on oral bioavailability(OB), drug-likeness(DL) and effective half-lives(HL). The targets of active ingredients of Kuihua Hugan Tablets were predicted based on the PharmMapper method. Then, the prediction was conducted by screening the target genes associated with chronic hepatitis and early cirrhosis through CooLGeN and GeneCards databases. Target gene functions and signal pathways were analyzed by bioinformatics annotation database Metascape. Cytoscape software was used to construct the Kuihua Hugan Tablets ingredient-target and ingredient-target-pathway network. String database combined with Cytoscape software was used to construct the networks of component-target and component-target-pathway. STRING database was combined with Cytoscape software to draw protein-protein interaction(PPI) network and conduct network topology analysis. Finally, Systems Dock Web Site software was applied in verifying the molecular docking between active ingredients and potential protein targets. A total of 26 compounds and 509 potential targets were screened out from Kuihua Hugan Tablets in the experiment. The results of PPI network analysis indicated that albumin(ALB), insulin-like growth factor 1(IGF1), matrix metalloproteinase-9(MMP9), matrix metalloproteinase-2(MMP2), non-receptor tyrosine kinase proto-oncogene(SRC), estrogen receptor 1(ESR1) and cancer-signal transduction-inflammation-drugs metabolism-related biological processes and metabolic pathways were closely associated with the active ingredients in Kuihua Hugan Tablets. The effects of Kuihua Hugan Tablets in alleviating chronic hepatitis and early cirrhosis indicated the multi-component, multi-target, and multi-pathway characteristics of traditional Chinese medicines, providing new ideas for further research and development of Kuihua Hugan Tablets.

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To predict the targets of active ingredients of Kuihua Hugan Tablets by network pharmacology, and explore the "multi-component-multi-target-multi-pathway" hepatoprotective mechanism of action. First, through traditional Chinese medicine systems pharmacology(TCMSP) and TCM Database@Taiwan Database, main active ingredients of Kuihua Hugan Tablets were screened out based on oral bioavailability(OB), drug-likeness(DL) and effective half-lives(HL). The targets of active ingredients of Kuihua Hugan Tablets were predicted based on the PharmMapper method. Then, the prediction was conducted by screening the target genes associated with chronic hepatitis and early cirrhosis through CooLGeN and GeneCards databases. Target gene functions and signal pathways were analyzed by bioinformatics annotation database Metascape. Cytoscape software was used to construct the Kuihua Hugan Tablets ingredient-target and ingredient-target-pathway network. String database combined with Cytoscape software was used to construct the networks of component-target and component-target-pathway. STRING database was combined with Cytoscape software to draw protein-protein interaction(PPI) network and conduct network topology analysis. Finally, Systems Dock Web Site software was applied in verifying the molecular docking between active ingredients and potential protein targets. A total of 26 compounds and 509 potential targets were screened out from Kuihua Hugan Tablets in the experiment. The results of PPI network analysis indicated that albumin(ALB), insulin-like growth factor 1(IGF1), matrix metalloproteinase-9(MMP9), matrix metalloproteinase-2(MMP2), non-receptor tyrosine kinase proto-oncogene(SRC), estrogen receptor 1(ESR1) and cancer-signal transduction-inflammation-drugs metabolism-related biological processes and metabolic pathways were closely associated with the active ingredients in Kuihua Hugan Tablets. The effects of Kuihua Hugan Tablets in alleviating chronic hepatitis and early cirrhosis indicated the multi-component, multi-target, and multi-pathway characteristics of traditional Chinese medicines, providing new ideas for further research and development of Kuihua Hugan Tablets.

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BACKGROUND: Pyrimidine is an important pharmacophore in the field of medicinal chemistry and exhibit a broad spectrum of biological potentials. A study was carried out to identify the target protein of potent bis-pyrimidine derivatives using reverse docking program. PharmMapper, a robust online tool was used for identifying the target proteins based on reverse pharmacophore mapping. The murine macrophage (RAW 264.7) and human embryonic kidney (HEK-293) cancer cell line used for selectivity and safety study. METHODS: An open web server PharmMapper was used to identify the possible target of the developed compounds through reverse pharmacophore mapping. The results were analyzed and validated through docking with Schrodinger v9.6 using 10 protein GTPase HRas selected as possible target. The docking studies with Schrödinger validated the binding behavior of bis-pyrimidine compounds within GTP binding pocket. MTT and sulforhodamine assay were used as antiproliferative activity. RESULTS AND DISCUSSION: The protein was found one of the top scored targets of the compound 18, hence, the GTPase HRas protein was found crucial to be targeted for competing cancer. Toxicity study demonstrated the significant selectivity of most active compounds, 12, 16 and 18 showed negligible cell toxicity at their IC50 concentration. CONCLUSION: From the results, we may conclude that GTPase HRas as a possible target of studied bis-pyrimidine derivatives where the retrieved information may be quite useful for rational drug designing.

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Dolastatin 16 is a cyclic depsipeptide isolated from the marine invertebrates and cyanobacterium Lyngbya majuscula, however, its bioactivity has been a historical question. In this study, peptidyl-prolyl cis-trans isomerase FKBP1A (FKBP12) was predicted as a potential target of dolastatin 16 via PharmMapper as well as verified using chemical-protein interactome (CPI) and molecular docking. FKBP1A has been previously identified as a target for the natural polyketide FK506 (tacrolimus), an immune suppressor inhibiting the rejection of organ transplantation in clinical use. The comparison study via the reverse pharmacophore screening and molecular docking of dolastatin 16 and FK506 indicated the good consistency of analysis with the computational approach. As the results, the lowest binding energy of dolastatin 16-FKBP1A complex was -7.4 kcal/mol and FK506-FKBP1A complex was -8.7 kcal/mol. The ligand dolastatin 16 formed three hydrogen bonds vs. four of FK506, as well as seven hydrophobic interactions vs. six of FK506 within the active site residues. These functional residues are highly repetitive and consistent with previously reported active site of model of FK506-FKBP1A complex, and the pharmacophore model was shown feasibly matching with the molecular feature of dolastatin 16.

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OBJECTIVE: To predict the action targets of the hypoglycemic bioactive components of Gegen (Puerariae Lobatae Radix), and investigate the “multi-components, multi-targets and multi-pathways” mechanism. METHODS: Based on the network pharmacology, the reported 27 active ingredients in Gegen were used to predict the action target and reveal the action mechanism via reversed pharmacophore matching method, database mining, and some other methods. The PharmMapper database and DrugBank database were applied to screen the hypoglycemic drug targets approved by FDA. Additionlly, the information of these targets and their intentions were revealed by the String database. At last the ingredients-targets-pathways network was constructed via the Cytoscape software. RESULTS: Studies found that Gegen contained hypoglycemic components, such as:puerarin, 3'-hydroxypuerarin, 3'-methoxypuerarin, daidzein and so on. Their actions involved in 9 potential targets and 25 energy metabolism or signal transmutation relevant biological processes, e.g. insulin receptor, angiotensin-converting enzyme 2 (ACE2), and peroxisome proliferator-activated receptor γ (PPARγ). While the mainly metabolism and signal transmutation pathways were HIF-1 signaling pathway, renin-angiotensin system, FoxO signaling pathway, AMPK signaling pathway and so on. CONCLUSION: From the view of molecular network, this study applied provides network pharmacology methods and technologies to clarify the multi-components, multi-targets and multi-pathways of Gegen on the hypoglycemic effect, and it provides a theoretical basis and a clue for further exploration of the hypoglycemic mechanism of Gegen.

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Objective To predict the action targets of antitussive and expectorant active ingredients of Farfarae Flos (FF) to understand the “multi-components, multi-targets, and multi-pathways” mechanism. Methods Using network pharmacology, the main components in FF [chlorogenic acid, 3,5-O-dicaffeoylquinic acid, 3,4-O-dicaffeoylquinic acid, 4,5-O-dicaffeoylquinic acid, rutin, caffeic acid, quercetin, kampferol, hyperoside, β-sitosterol, tussilagone, and 7β-(3-Ethyl-ciscrotonoyloxy)-1α-(2-methylbutyryloxy)-3(14)- dehydro-Z-notonipetranone] reported in previous studies, were used to predict the targets of main active ingredients of FF according to the PharmMapper method. The prediction was made by screening of the antitussive and expectorant targets approved by the CooLGeN database and annotating the information of targets with the aid of MAS 3.0 biological molecular function software. Based on the molecular docking, the tight binding of active ingredients with potential protein targets was explored by Systems Dock Web Site. The Cytoscape software was used to construct the FF ingredients-targets-pathways network. Results The network analysis indicated that the active ingredients in FF involve 18 targets, such as IL-2, COX-2, and RNASE3, as well as the signal transduction-inflammation-energy metabolism relevant biological processes and metabolic pathways. Conclusion The antitussive and expectorant effect of FF showed the characteristics of traditional Chinese medicine in multi-components, multi-targets, and multi-pathways. This research provides a scientific basis for elucidation of the antitussive and expectorant pharmacological mechanism of FF.

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Pelargonium sidoides DC (Geraniaceae) is a medicinal plant indigenous to Southern Africa that has been widely evaluated for its use in the treatment of upper respiratory tract infections. In recent studies, the anti-proliferative potential of P. sidoides was shown, and several phenolic compounds were identified as the bioactive compounds. Little, however, is known regarding their anti-proliferative protein targets. In this study, the anti-proliferative mechanisms of P. sidoides through in silico target identification and network pharmacology methodologies were evaluated. The protein targets of the 12 phenolic compounds were identified using the target identification server PharmMapper and the server for predicting Drug Repositioning and Adverse Reactions via the Chemical-Protein Interactome (DRAR-CPI). Protein-protein and protein-pathway interaction networks were subsequently constructed with Cytoscape 3.4.0 to evaluate potential mechanisms of action. A total of 142 potential human target proteins were identified with the in silico target identification servers, and 90 of these were found to be related to cancer. The protein interaction network was constructed from 86 proteins involved in 209 interactions with each other, and two protein clusters were observed. A pathway enrichment analysis identified over 80 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched with the protein targets and included several pathways specifically related to cancer as well as various signaling pathways that have been found to be dysregulated in cancer. These results indicate that the anti-proliferative activity of P. sidoides may be multifactorial and arises from the collective regulation of several interconnected cell signaling pathways.

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Thiazolidinone derivatives have been found to exhibit a wide range of pharmacological activities. 2-Thiazolylimino-5-benzylidene-thiazolidin-4-one derivatives show antibacterial activity in in vitro tests which are comparable to marketed drugs. However, the target for this scaffold remains yet to be identified. In our work, we identified seven putative targets for this scaffold using web servers such as DRAR-CPI, PharmMapper, and TarFisDock and databases such as BindingDB and ChEMBL. Each of these servers used different algorithms and scoring functions for protein target identification. Further, these targets are substantiated by molecular docking analysis. Based on the docking studies, scaffold 2-thiazolylimino-5-benzylidene-thiazolidin-4-one is observed to exhibit affinity against diverse targets, particularly, towards COX-2, acetylcholinesterase, aldose reductase, and thyroid hormone receptor alpha. This study describes an initial probability that these proteins may be targeted by this scaffold.

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