A modification-centric assessment tool for the performance of chemoproteomic probes.

Chemoproteomics has emerged as a key technology to expand the functional space in complex proteomes for probing fundamental biology and for discovering new small-molecule-based therapies. Here we report a modification-centric computational tool termed pChem to provide a streamlined pipeline for unbiased performance assessment of chemoproteomic probes. The pipeline starts with an experimental setting for isotopically coding probe-derived modifications that can be automatically recognized by pChem, with masses accurately calculated and sites precisely localized. pChem exports on-demand reports by scoring the profiling efficiency, modification homogeneity and proteome-wide residue selectivity of a tested probe. The performance and robustness of pChem were benchmarked by applying it to eighteen bioorthogonal probes. These analyses reveal that the formation of unexpected probe-derived modifications can be driven by endogenous reactive metabolites (for example, bioactive aldehydes and glutathione). pChem is a powerful and user-friendly tool that aims to facilitate the development of probes for the ever-growing field of chemoproteomics.

Tubulin inhibitors: pharmacophore modeling, virtual screening and molecular docking.

AIM: To construct a quantitative pharmacophore model of tubulin inhibitors and to discovery new leads with potent antitumor activities. METHODS: Ligand-based pharmacophore modeling was used to identify the chemical features responsible for inhibiting tubulin polymerization. A set of 26 training compounds was used to generate hypothetical pharmacophores using the HypoGen algorithm. The structures were further validated using the test set, Fischer randomization method, leave-one-out method and a decoy set, and the best model was chosen to screen the Specs database. Hit compounds were subjected to molecular docking study using a Molecular Operating Environment (MOE) software and to biological evaluation in vitro. RESULTS: Hypo1 was demonstrated to be the best pharmacophore model that exhibited the highest correlation coefficient (0.9582), largest cost difference (70.905) and lowest RMSD value (0.6977). Hypo1 consisted of one hydrogen-bond acceptor, a hydrogen-bond donor, a hydrophobic feature, a ring aromatic feature and three excluded volumes. Hypo1 was validated with four different methods and had a goodness-of-hit score of 0.81. When Hypo1 was used in virtual screening of the Specs database, 952 drug-like compounds were revealed. After docking into the colchicine-binding site of tubulin, 5 drug-like compounds with the required interaction with the critical amino acid residues and the binding free energies < -4 kcal/mol were selected as representative leads. Compounds 1 and 3 exhibited inhibitory activity against MCF-7 human breast cancer cells in vitro. CONCLUSION: Hypo1 is a quantitative pharmacophore model for tubulin inhibitors, which not only provides a better understanding of their interaction with tubulin, but also assists in discovering new potential leads with antitumor activities.

[Gene Polymorphism of Inflammation-related Cytokines Correlates with the Susceptibility to DLBCL].

OBJECTIVE: To investigate the relationship of gene polymorphisms of inflammattion related cytokines with incidence of diffuse large B-cell lymphoma(DLBCL) in Gansu Han population. METHODS: The gene polymorphism of inflammation-related cytokines were detected by high-resolution melting(HRM) curve. RESULTS: The homozygous CC genotype carrying IL-1RA rs4251961 gene locus was related with the risk of DLBCL in comparison with homozygous TT, the OR was 0.83 of homozygous CC, 95% CI=0.697-0.997,P<0.05), while the C allele of IL-1RA rs4251961 gene locus significantly correlated with the high incidence of diffuse large B-cell lymphoma compared with T allele(OR=8.83, 95% CI=1.909-40.813,P<0.01). CONCLUSION: The minor allele C of IL-1RA rs4251961 gene locus significantly relates with the susceptibility to DLBCL.

Expression and correlation of sodium/iodide symporter and thyroid stimulating hormone receptor in human thyroid carcinoma.

AIMS: To investigate the expression of sodium/iodide symporter (NIS) and thyroid stimulating hormone receptor (TSHR) in human thyroid cancer. PATIENTS AND METHODS: NIS and TSHR mRNA levels quantified by real-time PCR as well as NIS and TSHR proteins evaluated by immunohistochemistry were examined in surgical specimens including 38 benign nodules, 32 thyroid carcinomas and 36 normal thyroid samples. RESULTS: NIS and TSHR mRNA levels in thyroid carcinomas were significantly lower than in benign nodules and normal thyroid samples (P <0.001). Interestingly, we found that NIS and TSHR mRNA expression in benign nodules had similar levels to those in normal thyroid tissues. However, NIS and TSHR protein expression in benign nodules and thyroid carcinomas was stronger than in normal thyroid samples (P <0.05) but mainly located in cytoplasm. In addition, there was a significant positive correlation between NIS and TSHR in benign nodules and normal thyroid samples (r = 0.551 and 0.667, respectively, P = 0.001 and 0.000, respectively) but there was no such correlation in thyroid carcinomas (r = 0.222, P = 0.376). CONCLUSIONS: In thyroid carcinomas, NIS and TSHR mRNA levels were lower but the proteins were overexpressed. The NIS protein mainly locates in the cytoplasm, which therefore lacks the ability of transporting and absorbing iodine in patients with thyroid carcinoma. In addition, there was no correlation between NIS and TSHR in thyroid cancer, which may explain why, even after TSH stimulation, 10-20% of these malignant tumors are unable to concentrate enough radioiodine for effective therapy.