Exploring the effect of D61G mutation on SHP2 cause gain of function activity by a molecular dynamics study

<p>Noonan syndrome (NS) is a common autosomal dominant congenital disorder which could cause the congenital cardiopathy and cancer predisposition. Previous studies reported that the knock-in mouse models of the mutant D61G of SHP2 exhibited the major features of NS, which demonstrated that the mutation D61G of SHP2 could cause NS. To explore the effect of D61G mutation on SHP2 and explain the high activity of the mutant, molecular dynamic simulations were performed on wild type (WT) of SHP2 and the mutated SHP2-D61G, respectively. The principal component analysis and dynamic cross-correlation mapping, associated with secondary structure, showed that the D61G mutation affected the motions of two regions (residues Asn 58-Thr 59 and Val 460-His 462) in SHP2 from β to turn. Moreover, the residue interaction networks analysis, the hydrogen bond occupancy analysis and the binding free energies were calculated to gain detailed insight into the influence of the mutant D61G on the two regions, revealing that the major differences between SHP2-WT and SHP2-D61G were the different interactions between Gly 61 and Gly 462, Gly 61 and Ala 461, Gln 506 and Ile 463, Gly 61 and Asn 58, Ile 463 and Thr 466, Gly 462 and Cys 459. Consequently, our findings here may provide knowledge to understand the increased activity of SHP2 caused by the mutant D61G.</p

Discovery of 1H-pyrazolo[3,4-<i>b</i>]pyrazine derivatives as selective allosteric inhibitor of protein tyrosine phosphatase SHP2 for the treatment of KRAS^G12C-mutant non-small cell lung cancer

The high expression or mutation of SHP2 can induce cancer, so targeting SHP2 has become a new strategy for cancer treatment. In this study, we used the previously reported SHP2 allosteric inhibitor IACS-13909 as a lead drug for structural derivation and modification, and synthesized three SHP2 inhibitors. Among them, 1H-pyrazolo[3,4-b]pyrazine derivative 4b was a highly selective SHP2 allosteric inhibitor, with an IC50 value of 3.2 nM, and its inhibitory activity was 17.75 times than that of the positive control IACS-13909. The cell proliferation experiment detected that compound 4b would markedly inhibit the proliferation of various cancer cells. Interestingly, compound 4b was highly sensitive to KRASG12C-mutant non-small cell lung cancer NCI-H358 cells, with an IC50 value of 0.58 μM and its antiproliferative activity was 4.79 times than that of IACS-13909. Furthermore, the combination therapy of compound 4b and KRASG12C inhibitor sotorasib would play a strong synergistic effect against NCI-H358 cells. The western blot experiment detected that compound 4b markedly downregulated the phosphorylation levels of ERK and AKT in NCI-H358 cells. Molecular docking study predicted that compound 4b bound to the allosteric site of SHP2 and formed H-bond interactions with key residues Thr108, Glu110, Arg111, and Phe113. In summary, this study aims to provide new ideas for the development of SHP2 allosteric inhibitors for the treatment of KRASG12C mutant non-small cell lung cancer. Communicated by Ramaswamy H. Sarma</p

Distribution of wait time and duration of radiotherapy for nasopharyngeal cancer patients from 2008 to 2011 by multivariate analysis using a random-intercept model (n = 3605).

†<p>CCRT, Concurrent chemoradiotherapy.</p>‡<p>RT, Radiotherapy.</p><p>CI, confidence interval.</p><p>Distribution of wait time and duration of radiotherapy for nasopharyngeal cancer patients from 2008 to 2011 by multivariate analysis using a random-intercept model (n = 3605).</p

An Approach to Optically Pure Bridging Chiral <i>p</i>-<i>tert</i>-Butylcalix[4]arenes through a Homologous Anionic Ortho-Fries Rearrangement

A novel efficient approach to optically pure bridging chiral calix[4]­arenes through a homologous anionic ortho-Fries rearrangement of inherently chiral calix[4]­arenes was presented for the first time. As a result, two pairs of <i>N</i>,<i>N</i>′-dimethylformamidyl-substituted bridging chiral <i>p</i>-<i>tert</i>-butylcalix­[4]­arene enantiomers were facilely obtained. Their absolute configurations were determined through ROESY analysis, ECD comparison, and X-ray crystallographic analysis

Distribution of wait time and duration of radiotherapy for nasopharyngeal cancer patients from 2008 to 2011 by univariate analysis (n = 3,605).

†<p>CCRT, Concurrent chemoradiotherapy.</p>‡<p>RT, Radiotherapy.</p><p>SD, standard deviation;</p><p>Distribution of wait time and duration of radiotherapy for nasopharyngeal cancer patients from 2008 to 2011 by univariate analysis (n = 3,605).</p

Additional file 7: of Isocitrate dehydrogenase 1–snail axis dysfunction significantly correlates with breast cancer prognosis and regulates cell invasion ability

Figure S3. IDH1 stable knockdown significantly promoted MDA-MB-231 cell motility. (a) The expression levels of IDH1 were examined in two IDH1 stable knockdown MDA-MB-231 cells (shIDH1#1 and shIDH1#2) through western blotting. (b) Invasion ability was assessed using the Transwell assay in MDA-MB-231 cells with IDH1 stable knockdown and a scrambled control. The cell images of the representative experiment are provided. (c) Values were quantified using Ascent software, as detailed. Data are reported as the number of invading cells relative to the control (means Âą standard deviation (SD)). (d) Expression levels of IDH1, snail, slug, twist, and actin were examined in shIDH1#1, shIDH1#2, and the scrambled control through western blotting. (TIFF 3572 kb

Additional file 9: of Isocitrate dehydrogenase 1–snail axis dysfunction significantly correlates with breast cancer prognosis and regulates cell invasion ability

Figure S5. IDH1 knockdown accelerated MCF7 cell proliferation and migration ability. (a) the expression levels of IDH1 were examined in MCF7 cells with siIDH1#1, siIDH1#2, and control transfection through western blotting. (b) A wound healing assay was employed to examine MCF7 cells transfected with siIDH1#1, siIDH1#2, and the scrambled control. (c) The expression levels of IDH1, snail, slug, twist and actin were examined in siIDH1#1, siIDH1#2, and the scrambled control through western blotting. (d) The proliferation assay was performed in MCF-7 cells transfected with the scrambled control, siIDH1#1 and siIDH1#2, respectively. (TIFF 4527 kb

Additional file 10: of Isocitrate dehydrogenase 1–snail axis dysfunction significantly correlates with breast cancer prognosis and regulates cell invasion ability

Figure S6. Gene set enrichment analysis for differential expression of genes in MDA-MB-231 cells transfected with si-IDH1 compared with those transfected with scramble control. (a) Differential expression of genes (upregulated or downregulated twofold change) was identified using a microarray approach. These gene sets were significantly enriched in metastasis-associated terms from the Kyoto Encyclopedia of Genes and Genomes. (b) Schematic putative signaling pathway illustrating IDH1-modulated cancer cell invasion. (TIFF 1728 kb

Additional file 8: of Isocitrate dehydrogenase 1–snail axis dysfunction significantly correlates with breast cancer prognosis and regulates cell invasion ability

Figure S4. IDH1 knockdown significantly accelerated HS578T and BT549 cell motility. (a), (d) Invasion ability was assessed using the Transwell assay in HS578T and BT549 cells with si-IDH1 and scramble control. The cell images of a representative experiment are shown. (b), (e) Values quantified using Ascent software are shown. Data are reported as the number of colonies relative to the control (means Âą standard deviation (SD)). (c), (f) Expression levels of EMT-related markers were examined in HS578T and BT549 cells transfected with si-IDH1 and scramble control by western blotting. (TIFF 4403 kb

Additional file 3: of Isocitrate dehydrogenase 1–snail axis dysfunction significantly correlates with breast cancer prognosis and regulates cell invasion ability

Table S3. Correlation of IDH1 expression with molecular markers in patients with breast cancer. (DOCX 16 kb