Multiple Ligand Simultaneous Docking Research Articles

Abstract 1148: Bazedoxifene as a novel GP130 inhibitor for the treatment of triple-negative breast cancer

Abstract Triple negative breast cancer (TNBC) is the only subtype of breast cancer still lacking effective therapeutic options. Thus, finding novel targets and therapies to treat TNBC is an urgent clinical issue. IL-6 is one of the principal oncogenic mediators in breast cancer and systemic IL-6 levels correlates with poor prognosis, advanced disease, and metastases. Importantly, growth of TNBC cells are replied on autocrine cytokines including IL-6. Therefore, IL-6 signaling represents a novel approach with a potential to improve the therapeutic efficacy. To date, however, no small molecules that target IL-6 signaling are available for clinical cancer therapy. IL-6 binds to IL-6 Rα, then recruits GP130 to form the IL-6/IL-6 Rα/GP130 heterotrimer and triggers a signaling cascade downstream including JAK/STAT3, PI3-K/AKT/mTOR, and MEK/ERK. Therefore, it is possible to target IL-6 signaling by blocking IL-6 binds to GP130 or IL-6 Rα and thus inhibiting its signaling cascade downstream.To effectively target IL-6 signaling, we have utilized a novel drug discovery approach combining Multiple Ligand Simultaneous Docking and drug repurposing to target GP130, since its structure is more druggable than IL-6 Rα. We have identified a FDA-approved drug Bazedoxifene (for the prevention of the postmenopausal osteoporosis in postmenopausal women) with a novel function to inhibit IL-6 and GP130 protein-protein interactions and thus blocking IL-6 signaling cascade downstream. In this study, we examined the therapeutic effect of Bazedoxifene on TNBC, aiming to verify Bazedoxifene as a Novel IL-6/GP130 Inhibitor for TNBC treatments.Our data of western blot showed Bazedoxifene inhibited increased STAT3 phosphorylation induced by IL-6. In addition, Bazedoxifene inhibited phosphorylation of AKT and ERK in TNBC cells that were also produced by IL-6. Furthermore, combination of Bazedoxifene with paclitaxel exhibited more significant inhibition than single agent alone on cell viability in TNBC cells either in 2D or 3D culture model in vitro. Results of colony formation showed that Bazedoxifene could significantly inhibit cell survive and proliferation at 20 μM, which were more effective than Evista and SC144. Moreover, Bazedoxifene could inhibit cell migration. We tested the increased proliferation of TNBC cells using BrdU with the added IL-6, which were then inhibited by Bazedoxifene, demonstrating the Bazedoxifene could achieve a competed inhibition of IL6. The result of significant inhibition of tumor growth in vivo furtherly verified the therapeutic effects of Bazedoxifene. All results showed the significant therapeutic effects of Bazedoxifene in TNBC cells by competed blocking IL6 signaling. Thus, Bazedoxifene holds a great potential for TNBC therapy. Note: This abstract was not presented at the meeting. Citation Format: Jilai Tian, Yang Cao, Xiang Chen, Hui Xiao, Chenglong Li, Jiayuh Lin. Bazedoxifene as a novel GP130 inhibitor for the treatment of triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1148. doi:10.1158/1538-7445.AM2017-1148

Growth-suppressive activity of raloxifene on liver cancer cells by targeting IL-6/GP130 signaling.

BackgroundInterleukin-6 (IL-6) is a multifunctional cytokine, which is involved in the regulation of differentiation and growth of certain types of tumor cells. Constitutive activation of Signal Transducer and Activator of Transcription 3 (STAT3) induced by IL-6 is frequently detected in liver cancer and has emerged as a viable molecular target for liver cancer treatment. However, few inhibitors targeting up-streams of STAT3 are available for the therapy of liver cancer. We reported the discovery of EVISTA (Raloxifene HCl) as novel inhibitor of IL-6/GP130 protein-protein interactions (PPIs) using multiple ligand simultaneous docking (MLSD) and drug repositioning. The possible effect of Raloxifene in STAT3 signaling or liver cancer cells is still unclear.ResultsRaloxifene inhibited the P-STAT3 stimulated by IL-6, but not the induction of STAT1 and STAT6 phosphorylation by IFN-γ, IFN-α, and IL-4. Raloxifene inhibited STAT3 phosphorylation and resulted in the induction apoptosis on human liver cancer cell-lines. Raloxifene inhibited the targets of STAT3, such as Bcl-2, Bcl-xl and survivin and cell viability, cell migration, and colony formation in liver cancer cells. Further, daily administration of Raloxifene suppressed the Hep-G2 tumor growth in mice in vivo.Materials and MethodsThe inhibitory effect on STAT3 phosphorylation and activity as well as cell viability, migration, and colony forming ability by Raloxifene was examined in human liver cancer cells. Tumor growth was detected via mouse xenograft tumor mode.ConclusionsOur results suggest that Raloxifene is a potent IL-6/GP130 inhibitor and may be a chemoprevention agent for liver cancer by targeting persistent STAT3 signaling.

Discovery of an Orally Selective Inhibitor of Signal Transducer and Activator of Transcription 3 Using Advanced Multiple Ligand Simultaneous Docking.

Targeting signal transducer and activator of transcription 3 (STAT3) is a potential anticancer strategy. However, STAT3 inhibitors with good selectivity and bioavailability are rare. The aim of this study was to discover selective direct STAT3 inhibitors with good druglikeness. By the advanced multiple ligand simultaneous docking (AMLSD) method, compound 9 was designed as an orally bioavailable STAT3 inhibitor that presented superior druggability and selectivity compared with other representative STAT3 inhibitors. 9 directly and selectively inhibited the pY705 site of STAT3 with an affinity (Ki) of 440 nM. The IC50 of 9 for MDA-MB-231 breast cancer cells was 184-fold lower than its IC50 for MCF-10A normal breast epithelial cells. 9 in vivo induced significant antitumor responses (better than gefitinib), and its therapeutic index should be over 100, indicating good safety of 9.

Bazedoxifene as a Novel GP130 Inhibitor for Pancreatic Cancer Therapy.

The IL6/GP130/STAT3 pathway is crucial for tumorigenesis in multiple cancer types, including pancreatic cancer, and presents as a viable target for cancer therapy. We reported Bazedoxifene, which is approved as a selective estrogen modulator by FDA, as a novel inhibitor of IL6/GP130 protein-protein interactions using multiple ligand simultaneous docking and drug repositioning approaches. STAT3 is one of the major downstream effectors of IL6/GP130. Here, we observed Bazedoxifene inhibited STAT3 phosphorylation and STAT3 DNA binding, induced apoptosis, and suppressed tumor growth in pancreatic cancer cells with persistent IL6/GP130/STAT3 signaling in vitro and in vivo In addition, IL6, but not INFγ, rescued Bazedoxifene-mediated reduction of cell viability. Bazedoxifene also inhibited STAT3 phosphorylation induced by IL6 and IL11, but not by OSM or STAT1 phosphorylation induced by INFγ in pancreatic cancer cells, suggesting that Bazedoxifene inhibits the GP130/STAT3 pathway mediated by IL6 and IL11. Furthermore, Bazedoxifene combined with paclitaxel or gemcitabine synergistically inhibited cell viability and cell migration in pancreatic cancer cells. These results indicate that Bazedoxifene is a potential agent and can generate synergism when combined with conventional chemotherapy in human pancreatic cancer cells and tumor xenograft in mice. Therefore, our results support that Bazedoxifene as a novel inhibitor of GP130 signaling and may be a potential and safe therapeutic agent for human pancreatic cancer therapy. Mol Cancer Ther; 15(11); 2609-19. ©2016 AACR.

Abstract 4562: Inhibition of STAT3 signaling in human liver cancer cells using Evista

Abstract Liver cancer is one of the major causes of morbidity and mortality in China and also around the World. Constitutive activation of Signal Transducers and Activators of Transcription 3 (STAT3) signaling is frequently detected in human cancer including liver cancer and has emerged as a viable molecular target for liver cancer treatment. Novel therapeutic approaches of more effective treatments are much needed. To date, few STAT3 inhibitors are available for the therapy of liver cancer yet. Evista (Raloxifene HCI) is used for the prevention and treatment of osteoporosis and was approved for reducing the risk of invasive breast cancer in postmenopausal women with osteoporosis and in postmenopausal women at high risk for invasive breast cancer. We reported the discovery of Raloxifene as novel inhibitors of IL-6/GP130 protein­protein interactions (PPIs) using multiple ligand simultaneous docking (MLSD) and drug repositioning. The possible effect of Evista in STAT3 signaling or liver cancer cells is still unclear. The ability of Evista to inhibit STAT3 was tested. Evista inhibited the P-STAT3 stimulated by IL-6 but not the induction of STAT1, STAT2, and STAT4 phosphorylation by IFN-α and IL-4. Evista inhibited STAT3 phosphorylation and resulted in the induction apoptosis on human liver cancer cell lines HEPG2, 7721, and HUH-7 as evidenced by caspase-3 cleavage. Evista also inhibited the cell viability, cell migration and colony formation in liver cancer cells. Furthermore, administration daily of Evista suppressed the HEPG2 tumor growth in mice in vivo. In summary, our study is the first report indicating that Evista also exhibits biology activity against persistent STAT3 signaling in human liver cancer cells. These results suggest that Evista may also be a chemoprevention agent for liver cancer by targeting persistent STAT3 signaling. Citation Format: Yina Wang, Chongqiang Zhao, Haiyan Ma, Huameng Li, Jiagao Lu, Chenglong Li, Jiayuh Lin, Li Lin. Inhibition of STAT3 signaling in human liver cancer cells using Evista. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4562.

Multiple ligand simultaneous docking (MLSD): A novel approach to study the effect of inhibitors on substrate binding to PPO

Multiple ligand simultaneous docking, a computational approach is used to study the concurrent interactions between substrate and the macromolecule binding together in the presence of an inhibitor. The present investigation deals with the study of the effect of different inhibitors on binding of substrate to the protein Polyphenoloxidase (PPO). The protein was isolated from Mucuna pruriens and confirmed as tyrosinases involved in l-DOPA production. The activity was measured using different inhibitors at different concentrations taking catechol as substrate. A high-throughput binding study was conducted to compare the binding orientations of individual ligands and multiple ligands employing Autodock 4.2. The results of single substrate docking showed a better binding of urea with the binding energy of −3.48kJmol−1 and inter molecular energy of −3.48kJmol−1 while the results of MLSD revealed that ascorbic acid combined with the substrate showed better inhibition with a decreased binding energy of −2.37kJmol−1.

Abstract 4598: GP130 as a novel therapeutic target in il-6-dependent cancers

Abstract The IL-6/GP130 signaling pathway is critical for the survival and progression of cancer cells of multiple cancer types. We report here the new discovery of Raloxifene (Marketed as Evista by Eli Lilly and Company) and Bazedoxifene [Marketed as Duavee (conjugated estrogens / bazedoxifene) by Pfizer] as novel inhibitors of IL-6/GP130 protein-protein interactions using multiple ligand simultaneous docking and drug repositioning approaches. Multiple drug scaffolds were simultaneously docked into binding hot spots of GP130 D1 domain by multiple ligand simultaneous docking to compete with the key interacting residues of IL-6, followed by tethering to generate virtual hit compounds. Similarity searches of virtual hits on drug databases identified Raloxifene and Bazedoxifene as potential inhibitors of IL-6/GP130 interaction. Both Raloxifene and Bazedoxifene are known as selective estrogen receptor modulators and we identified their novel function as GP130 inhibitors. Raloxifene and Bazedoxifene inhibited IL-6 mediated induction of STAT3 phosphorylation in cancer cells, which confirm their ability to inhibit IL-6/GP130 signaling. In contrast, Raloxifene and Bazedoxifene did not inhibit the induction of STAT1 phosphorylation by IFN-γ in cancer cells indicating their selectivity. Raloxifene and Bazedoxifene also inhibited STAT3 phosphorylation and resulted in apoptosis in cancer cells expressing elevated IL-6 levels. In addition, addition of excess IL-6 reversed the expression level of STAT3 phosphorylation which was decreased by Raloxifene or Bazedoxifene supporting that both FDA-approved drugs act through IL-6/GP130 signaling. Compared with an original GP130 inhibitor MDL-A whose IC50 values were 108-216 µM in cancer cell lines, Raloxifene and Bazedoxifene were found more potent in inhibiting cell viability which the IC50 values for Raloxifene and Bazedoxifene were 6.9-8.9 µM and 3.4-4.4 µM respectively in the same cancer cell lines expressing elevated IL-6 levels. Furthermore, both Raloxifene and Bazedoxifene significantly suppressed the tumor growth of human RH30 sarcoma cells in mouse xenograft model in vivo. These findings suggest that FDA-approved drugs Raloxifene and Bazedoxifene may serve as novel GP130-targeting therapeutic drugs in IL-6 dependent cancers. Citation Format: Hui Xiao, Yang Bian, Chengguang Zhao, Li Lin, David Jou, Huameng Li, Chenglong Li, Jiayuh Lin. GP130 as a novel therapeutic target in il-6-dependent cancers. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4598. doi:10.1158/1538-7445.AM2014-4598

Souring control in fluid samples of oil industry using a multiple ligand simultaneous docking (MLSD) strategy

We have used docking techniques in order to propose potential inhibitors to the enzymes adenosine phosphosulfate reductase and adenosine triphosphate sulfurylase that are responsible, among other deleterious effects, for causing souring of oil and gas reservoirs. Three candidates selected through molecular docking revealed new and improved polar and hydrophobic interactions with the above-mentioned enzymes. Microbiological laboratory assays performed subsequently corroborated the results of computer modelling that the three compounds can efficiently control the biogenic sulfide production.

Drug Design Targeting Protein–Protein Interactions (PPIs) Using Multiple Ligand Simultaneous Docking (MLSD) and Drug Repositioning: Discovery of Raloxifene and Bazedoxifene as Novel Inhibitors of IL-6/GP130 Interface

The IL-6/GP130/STAT3 pathway is critical for the progression of multiple types of cancers. We report here the discovery of raloxifene and bazedoxifene as novel inhibitors of IL-6/GP130 protein-protein interactions (PPIs) using multiple ligand simultaneous docking (MLSD) and drug repositioning approaches. Multiple drug scaffolds were simultaneously docked into hot spots of GP130 D1 domain by MLSD to compete with the key interacting residues of IL-6, followed by tethering to generate virtual hit compounds. Similarity searches of virtual hits on drug databases identified raloxifene and bazedoxifene as potential inhibitors of IL-6/GP130 interaction. In cancer cell assays both compounds bind to GP130 and demonstrated selective inhibition of IL-6 induced STAT3 phosphorylation and were significantly more potent than the previously reported natural product inhibitor MDL-A. The identified drugs represent a new class of lead compounds with piperidine, benzothiophene, and indole scaffolds to inhibit IL-6 induced homodimerization of GP130. Besides potential direct usage for clinic trials, the two compounds can also serve as lead compounds for optimization to speed the development of drugs selectively targeting the IL-6/GP130/STAT3 cancer signaling pathway.

Abstract 4772: Novel drug discovery approach targeting STAT3 for breast cancer therapy using MLSD and drug repositioning

Abstract Constitutive activation of Signal Transducers and Activators of Transcription 3 (STAT3) signaling is frequently detected in human cancer, including breast cancer, and has emerged as a viable molecular target for breast cancer treatment. Novel therapeutic approaches are needed for breast cancer if significant improvements in survival are to occur. To date, few STAT3 inhibitors are available for the therapy of breast cancer. Conventional high throughput screening and virtual docking drug discovery approaches identified many hits, but only a few of them may be developed into drugs. To accelerate STAT3 drug development, we used a novel drug discovery approach with multiple ligand simultaneous docking (MLSD) which we have developed and drug repositioning to search against FDA approved drug and experimental drug database in DrugBank. Using this new method, we identified the FDA-approved drug celecoxib (a COX-2 inhibitor) with a novel function to target STAT3 [Predictive STAT3 binding dissociation constant (Kd)= 8.6 μM]. In addition, a novel celecoxib analog (8A) was developed exhibiting stronger STAT3 binding (Predicted Kd= 0.12 μM, 71-fold stronger than celecoxib). Although 8A has stronger STAT3 binding, it has weaker COX-2 binding (521-fold weaker than celecoxib), suggesting its selectivity on STAT3 versus COX-2. Minimal COX-2 inhibition by 8A may reduce cardiovascular and gastrointestinal risks associated with COX-2 inhibitors. The ability of 8A to inhibit STAT3 was tested through a combination of Western Blot, MTT cell viability assay, and Immunofluorescence Standing. 8A inhibited the P-STAT3 stimulated by IL-6 but not the induction of STAT1, STAT2, STAT4, STAT5, and STAT6 phosphorylation stimulated by IFN-γ, IFN-γ, and IL-4. 8A also inhibited the induction of STAT3 nuclear localization by IL-6, which could prevent STAT3 function as a transcription factor. 8A inhibited STAT3 phosphorylation and resulted in the induction apoptosis on breast cancer cells as evidenced by caspase-3 cleavage. Further, 8A has a lower IC50 than celecoxib and was more potent than celecoxib to inhibit STAT3 phosphorylation and induce apoptosis in breast cancer cells, which confirmed the stronger STAT3 binding energy than celecoxib. In summary, our study is the first report using MLSD and drug repositioning to develop drug-like STAT3 inhibitors. This novel method has a potential to significantly speed up the STAT3 drug development for the therapy of breast cancer and possibly other types of human cancer which express constitutive STAT3 signaling. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4772. doi:1538-7445.AM2012-4772

Abstract A223: Novel drug development approach targeting STAT3 for sarcoma therapy using MLSD and drug reposition.

Abstract Constitutive activation of Signal Transducers and Activators of Transcription 3 (STAT3) signaling is frequently detected in human cancer including rhabdomyosarcoma, osteosarcoma, and Ewing's sarcoma and has emerged as a viable molecular target for sarcoma treatment. Rhabdomyosarcoma is the most common soft tissue sarcoma in pediatric patients{Niu, 1999 #1867}. Osteosarcoma is the most commonly diagnosed primary malignant tumor of bone, which mainly affects adolescents and young adults. Ewing's sarcoma is the second most common primary bone malignancy in pediatric patients. Novel therapeutic approaches are needed for these childhood sarcomas if significant improvements in survival are to occur. To date, however, no known STAT3 inhibitors are available for the therapy of childhood sarcomas yet. Conventional high throughput screening and virtual docking drug discovery approaches identified many hits, but only a few of them may be developed into drugs. To accelerate STAT3 drug development, we used a novel drug discovery approach with multiple ligand simultaneous docking (MLSD), which we have developed and drug repositioning to search against FDA approved drug and experimental drug database in DrugBank. Using this new method, we identified the FDA-approved drug celecoxib (a COX-2 inhibitor) with a novel function to target STAT3 [Predictive STAT3 binding dissociation constant (Kd)=8.6μM]. In addition, a novel celecoxib analog (8A) was developed exhibiting stronger STAT3 binding (Predicted Kd=0.12 M; 71-fold stronger than celecoxib). Although 8A has stronger STAT3 binding, it has weaker COX-2 binding (521-fold weaker than celecoxib), suggesting its selectivity on STAT3 versus COX-2. Minimal COX-2 inhibition of 8A may reduce cardiovascular and gastrointestinal risks associated with COX-2 inhibitors. The ability of 8A to inhibit STAT3 was tested. 8A inhibited the P-STAT3 stimulated by IL-6 but not the induction of STAT1 phosphorylation by IFN-γ. 8A also inhibited the induction of STAT3 nuclear localization by IL-6, which could prevent STAT3 functions as a transcription factor. 8A inhibited STAT3 phosphorylation and resulted in the induction apoptosis on sarcoma cells as evidenced by caspase-3 cleavage. Further, 8A was more potent than celecoxib to inhibit STAT3 phosphorylation and induce apoptosis in sarcoma cells, which confirmed the stronger STAT3 binding energy than celecoxib. In summary, our study is the first report using MLSD and drug repositioning to develop drug-like STAT3 inhibitors. This novel method has a potential to significantly speed up the STAT3 drug development for the therapy of childhood sarcoma and possibly other types of human cancer express constitutive STAT3 signaling. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A223.

Fragment-Based Drug Design and Drug Repositioning Using Multiple Ligand Simultaneous Docking (MLSD): Identifying Celecoxib and Template Compounds as Novel Inhibitors of Signal Transducer and Activator of Transcription 3 (STAT3)

We describe a novel method of drug discovery using MLSD and drug repositioning, with cancer target STAT3 being used as a test case. Multiple drug scaffolds were simultaneously docked into hot spots of STAT3 by MLSD, followed by tethering to generate virtual template compounds. Similarity search of virtual hits on drug database identified celecoxib as a novel inhibitor of STAT3. Furthermore, we designed two novel lead inhibitors based on one of the lead templates and celecoxib.

Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of protein

Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein-ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl-xL complex with ABT-737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single-ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X-ray crystallographic maps, and aiding fragment-based drug design, respectively.