The development of a knowledge base for basic active structures: an example case of dopamine agonists

<p>Abstract</p> <p>Background</p> <p>Chemical compounds affecting a bioactivity can usually be classified into several groups, each of which shares a characteristic substructure. We call these substructures "basic active structures" or BASs. The extraction of BASs is challenging when the database of compounds contains a variety of skeletons. Data mining technology, associated with the work of chemists, has enabled the systematic elaboration of BASs.</p> <p>Results</p> <p>This paper presents a BAS knowledge base, BASiC, which currently covers 46 activities and is available on the Internet. We use the dopamine agonists D1, D2, and Dauto as examples and illustrate the process of BAS extraction. The resulting BASs were reasonably interpreted after proposing a few template structures.</p> <p>Conclusions</p> <p>The knowledge base is useful for drug design. Proposed BASs and their supporting structures in the knowledge base will facilitate the development of new template structures for other activities, and will be useful in the design of new lead compounds via reasonable interpretations of active structures.</p

Antitumor effect of the tyrosine kinase inhibitor nilotinib on gastrointestinal stromal tumor (GIST) and imatinib-resistant GIST cells.

Despite the benefits of imatinib for treating gastrointestinal stromal tumors (GIST), the prognosis for high risk GIST and imatinib-resistant (IR) GIST remains poor. The mechanisms of imatinib resistance have not yet been fully clarified. The aim of the study was to establish imatinib-resistant cell lines and investigate nilotinib, a second generation tyrosine kinase inhibitor (TKI), in preclinical models of GIST and imatinib-resistant GIST. For a model of imatinib-resistant GIST, we generated resistant cells from GK1C and GK3C cell lines by exposing them to imatinib for 6 months. The parent cell lines GK1C and GK3C showed imatinib sensitivity with IC50 of 4.59±0.97 µM and 11.15±1.48 µM, respectively. The imatinib-resistant cell lines GK1C-IR and GK3C-IR showed imatinib resistance with IC50 values of 11.74±0.17 µM (P<0.001) and 41.37±1.07 µM (P<0.001), respectively. The phosphorylation status of key cell signaling pathways, receptor tyrosine kinase KIT (CD117), platelet-derived growth factor receptor alpha (PDGFRA) and downstream signaling kinases: serine-threonine kinase Akt (AKT) and extracellular signal-regulated kinase 1/2 (ERK1/2) or the non-receptor tyrosine kinase: proto-oncogene tyrosine-protein kinase Src (SRC), was analyzed in established cell lines and ERK1/2 phosphorylation was found to be increased compared to the parental cells. Nilotinib demonstrated significant antitumor efficacy against GIST xenograft lines and imatinib-resistant GIST cell lines. Thus, nilotinib may have clinical potential for patients with GIST or imatinib-resistant GIST

Nilotinib antitumor activity in GIST xenograft models.

<p>(A) Immunohistochemistry staining for KIT in xenograft lines established from human GISTs: GK1X, GK2X and GK3X. (B) Tumor tissue fragments (∼5 mm³) were transplanted s.c. into the backs of BALB/cSlc-<i>nu/nu</i> mice that were randomized into 3 groups (n = 6–8). Doses of 40 mg/kg/day of imatinib, nilotinib or pure water (control) were administered by oral gavage daily for 28 days. Tumor size was measured every two to three days. (C) Tumor growth inhibition (TGI) on the day of evaluation was calculated as the ratio of tumor volume on the evaluation day to that on day 1.</p

Antitumor activity of nilotinib on GIST and imatinib-resistant GIST cells.

<p>Cells were maintained in supplemented medium for 12 h, and then incubated with nilotinib (0∼100 µM) for 72 h. Cell viability was determined by comparing treated cells with the untreated control. Data are means of triplicates from a representative experiment.</p

Quantitative phosphorylation analysis.

<p>Parental (GK1C and GK3C; red histograms) or imatinib-resistant GIST cell lines (GK1C-IR and GK3C-IR, blue histograms) were fixed and stained with anti phospho-KIT (Tyr719), anti phospho-PDGFRA (Tyr754), anti phospho-SRC (Tyr416), anti phospho-AKT (Ser473) and anti phospho-ERK1/2 (Thr202/Tyr204). Finally, cells were detected with Alexa Fluor 488 donkey anti-rabbit IgG antibody (Isotype control was reacted only with the secondary antibody). The MFI (mean of fluorescence intensity) values were calculated by FlowJo. GK1C: p-KIT = 3.21, p-PDGFRA = 10.3, p-SRC = 7.19, p-AKT = 20.3, p-ERK1/2 = 37.8. GK1C-IR: p-KIT = 3.30, p-PDGFRA = 12.8, p-SRC = 9.35, p-AKT = 20.5, p-ERK1/2 = 94.4. GK3C: p-KIT = 2.65, p-PDGFRA = 7.29, p-SRC = 5.35, p-AKT = 19.5, p-ERK1/2 = 32.2. GK3C-IR: p-KIT = 3.89, p-PDGFRA = 9.82, p-SRC = 8.31, p-AKT = 21.3, p-ERK1/2 = 115.</p

Establishment of imatinib-resistant GIST cell lines.

<p>(A, B) Immunohistochemical assay of KIT expression in GK1C-IR and GK3C-IR as determined by staining with DAB (magnification, 400x). (C, D) GK1C and GK1C-IR cells, GK3C and GK3C-IR cells, 2.5×10³ cells (per well) were seeded into 96-well microplates in triplicate 12 h before treatment, and then exposed to different concentrations (0∼100 µM) of imatinib for 72 h. The percentage of cellular proliferation was gauged using the WST-8 method. Imatinib-resistant (IR) cells showed resistance to imatinib with IC₅₀ of 11.74±0.17 µM (<i>p<0.001</i>) or 41.37±1.07 µM (<i>p<0.001</i>). Data are presented as means ± SD and evaluated using Student's <i>t</i> test.</p