Journal: Chinese Medicine

Article Title: In silico approach in reveal traditional medicine plants pharmacological material basis

doi: 10.1186/s13020-018-0190-0

Figure Lengend Snippet: Common druggable targets/protein databases overview

Article Snippet: HPRD (Human Protein Reference Database) , Johns Hopkins University and the Institute of Bioinformatics, USA , http://www.hprd.org , HPRD is a database of curated proteomic information pertaining to human proteins. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data , [ ] .

Techniques: Binding Assay, Functional Assay, Generated, Sequencing, Gene Expression, Protein-Protein interactions, High Throughput Screening Assay, Transduction, Ligand Binding Assay

Journal: Nature chemical biology

Article Title: Diabetes reversal by inhibition of the low molecular weight tyrosine phosphatase

doi: 10.1038/nchembio.2344

Figure Lengend Snippet: (a) Surface representation of human LMPTP-A showing phosphate (P) non-covalently bound in the active-site. Residues are colored according to magnitude of shift in the HSQC 15 N- 1 H spectrum upon Compd. 18 titration (red>orange>green). Gray residues had negligible shifts or could not be assigned. (b) Crystal structure of bovine LMPTP W49Y/N50E bound to orthovanadate and Compd. 18 (cyan and blue sticks; Q=quinoline; Pip=piperidine; BN=benzonitrile; L=linker), with selected side-chains (yellow=carbon; red=oxygen; blue=nitrogen; pink=vanadium) and H-bonds/ionic interactions (dashed green/gray lines) shown. (c) Inhibition of phosphatase activity of LMPTP-A/mutants by Compd. 18 using 0.4 mM OMFP substrate. Mean±SD % activity is shown. Data is representative of 3 independent experiments. (d) Compd. 18 modeled into the crystal structure of phosphate-bound human LMPTP, based on an overlay with the bovine ternary complex crystal structure (RMSD=0.33 Å). Selected residues are colored by NMR shift as in (a) . Dashed red line depicts predicted clash between apical oxygen (“A”) of phosphate and Q. (e–f) Structural rationale for SAR data, with atoms at 66% of their true radii. (e) “Side” view of pocket, rotated ~90° about a horizontal axis. The molecular surface has been sliced through the active-site to reveal the tight fit of Q in the pocket. Atoms with a formal charge (±) are labeled. BN is highly polarized, as indicated (δ±); arrows labeled “S” indicate solvent exposure of ring substitutions. (f) “Top” view looking down at the active-site pocket filled by Q. Arrow above atom N1 locates the “saddle-point” at pocket exit.

Article Snippet: cDNAs encoding mouse and human LMPTP-A (protein reference sequences NP_067305.2 and NP_004291.1) and bovine LMPTP (protein reference sequence NP_776403.1) were codon-optimized for E. coli , synthesized, and cloned into the pGEX-4T vector using BamHI/EcoRI by Genscript.

Techniques: Titration, Inhibition, Activity Assay, Labeling, Solvent