Journal: Genes & Cancer

Article Title: Suberoylanilide hydroxamic acid (SAHA) reverses chemoresistance in head and neck cancer cells by targeting cancer stem cells via the downregulation of nanog

doi:

Figure Lengend Snippet: A-B: CAL27-CisR and its parental cell line CAL27 (A) or UD-SCC-2-CisR and its parental cell line UD-SCC-2 (B) were treated with different concentrations of SAHA and cell proliferation was assessed byMTT assay. C-D: CAL27-CisR (C) or UD-SCC-2-CisR (D) cells were treated with SAHA or cisplatin (CDDP) alone or in combination at 0.25, 0.5, 1, 1.5 and 2 times their respective IC 50 doses and cell proliferation was assessed by MTT assay. Results were analyzed according to Chou-Talalay method and the combination index (CI) values calculated by CompuSyn software. E-F: CAL27-CisR (E) or UD-SCC-2-CisR (F) cells were treated with SAHA and survivin expression was examined by Western blotting. G-H: CAL27-CisR (G) and UD-SCC-2-CisR (H) cells were treated with SAHA (3 μM and 4 μM) and tumor cell apoptosis was analyzed by annexin V staining.

Article Snippet: IC 50 values for SAHA and cisplatin for tumor cell proliferation inhibition was calculated using GraphPad Prism software (GraphPad Sofware, Inc., San Diego, CA) and combination index (CI) was calculated using CompuSyn software (ComboSyn, Inc., Paramus, NJ).

Techniques: MTT Assay, Software, Expressing, Western Blot, Staining

Journal: Journal of Medicinal Chemistry

Article Title: Identification of Novel Human 15-Lipoxygenase-2 (h15-LOX-2) Inhibitors Using a Virtual Screening Approach

doi: 10.1021/acs.jmedchem.4c01884

Figure Lengend Snippet: Schematic representation of the virtual screening (VS) protocol used in this study to select novel potential h15-LOX-2 inhibitors from the ZINC-Curated database. (A) Representation of the sequence of selection filters applied to the ZINC-Curated database in each VS step. (B) Schematic representation of the steps to generate the shape-based model that was used as the first filter in the VS protocol: 1. Alignment of low energy conformation structures of two known h15-LOX-2 inhibitors ( LIT-04 and LIT-05 ), using LigandScout’s alignment algorithm, and 2. Shape-based model generation using ROCS. The molecular shape surface is represented in gray. The figure was prepared by using LigandScout and ROCS.

Article Snippet: Babel , v.2.2.3 (Open Babel Development Team) was used to generate molecular fingerprints; FILTER module of OMEGA − v. v.2.5.1.5/v.4.1.2.0 (Openeye Scientific Sofware Inc., Santa Fe, NM) was used to filter the compounds database for drug-like properties and to check the presence of PAINS substructures in the structures of the identified inhibitors; GOLD , v.5.2 ( CCDC , T he Cambridge Crystallographic Data Center, Cambridge, U.K.) was used for docking; GraphPad Prism v.9/v.10 (GraphPad Software, Boston, MA) was used for experimental data analysis; LigandScout , v.4.4.7 (Inte:Ligand GmbH, Maria Enzersdorf, Austria) was used for protein–ligand interaction recognition; MoKa , v.2.6 (Molecular Discovery Ltd.., Borehamwood, U.K.) was used to attribute protonation states based on in silico predictions of p K a values; OMEGA − v.2.5.1.5 (Openeye Scientific Sofware Inc.., Santa Fe, NM) was used for conformers generation; Open Babel , v.2.3.1 (Open Babel Development Team) was used to generate 3D structures of compounds; PyMOL v.2.5.0 (Schrödinger Inc.., New York, NY) was used for protein’s structures visualization; QUACPAC v.2.0.0.3 (Openeye Scientific Sofware Inc., Santa Fe, NM) was used to generate tautomers and to attribute protonation states; ROCS , v.3.3.0.3/v.3.4.3.0 (Openeye Scientific Sofware Inc.., Santa Fe, NM) was used to perform shape-based screening; SwissADME , (University of Lausanne, Lausanne, Switzerland) was used for physicochemical properties and drug-likeness predictions; SYBYL-X v.2.1.1 (Certara Inc.., PA) was used for protein’s structure preparation for docking procedures and for protein’s solvent-accessible area calculations.

Techniques: Sequencing, Selection