Journal: Oncotarget

Article Title: Tomentodione M sensitizes multidrug resistant cancer cells by decreasing P-glycoprotein via inhibition of p38 MAPK signaling

doi: 10.18632/oncotarget.21949

Figure Lengend Snippet: (A) Chemical structure and molecular weight of Tomentodione M (TTM). (B) QRT-PCR analysis of MDR1 , MRP1 and BCRP mRNA levels relative to GAPDH in parental and multi-drug resistant (MDR) MCF-7 and K562 cancer cells. Note: The relative mRNA levels are expressed as fold-changes relative to control group, which is arbitrarily represented as 1. The data are representative of at least 6 replicates. (C) Representative western blot showing P-gp protein levels in MCF-7/MDR and K562/MDR cells relative to their corresponding parental cells. GAPDH was used as loading control. (D-F) MTT and CCK-8 assays showing cell viability of multidrug resistant cell lines (MCF-7/MDR and K562/MDR) and their corresponding parental cell lines (MCF-7 and K562), as well as non-tumor cell line (MCF-10A) treated with 0-100 μM TTM for 48 hr. Inhibition of cell proliferation by different concentrations of TTM were calculated based on the ratio of absorbance in treatment and control samples. The absorbance was evaluated at a test wavelength of 570 nm, and a reference wavelength of 630 nm in MTT assays. The absorbance at 450 nm was used in CCK-8 assays. Note: Values represent mean ± SEM from three independent experiments. *** denotes P < 0.001 compared to control.

Article Snippet: The MDR1 plasmid was purchased from Genscript (Nanjing, China).

Techniques: Molecular Weight, Quantitative RT-PCR, Control, Western Blot, CCK-8 Assay, Inhibition

Journal: Nature

Article Title: Targeting G1–S-checkpoint-compromised cancers with cyclin A/B RxL inhibitors

doi: 10.1038/s41586-025-09433-w

Figure Lengend Snippet: a , Overlay of cyclin A/Cdk2 complexes shown in surface representation with bound ligands at the RxL binding site, including a macrocycle (yellow, PDB: 1URC) and p27Kip1 (purple, PDB: 1JSU). b , Computational model of a lariat decapeptide macrocycle bound at the RxL binding site, based on the bound structures of p27Kip1 (purple) and lariat macrocycle (yellow), as a ligand alignment template for binding prediction. c , Structures of CIRc-001, CIRc-004, CIRc-014, CIRc-018, CIRc-019 and CIRc-028. Two published cyclin A2 co-crystal structures with ligand bound at the RxL binding site, including the macrocycle, Ace-Arg-Lys-Leu-Phe-Gly (PDB code: 1URC) and the p27Kip1 peptide (PDB code: 1JSU), were used to generate a reference binding mode for our lariat macrocycles (Extended Data Fig. 1a above ). All modelling studies were performed using the Schrodinger software suite (version 2023-3). The crystal structures were first prepared using the Protein Preparation Workflow with default settings, and the cyclin A/Cdk2 complexes were subsequently aligned by using the protein structure alignment module. The bound ligands, aligned at the RxL binding motif, were combined to produce a template for novel ligand alignment. Specifically, the template model (Extended Data Fig. 1b above ) is a lariat decapeptide (Lys-Pro-Ser-Ala-Cys-Arg-Lys-Leu-Phe-Gly) that contains the N-terminal hexapeptide segment of p27Kip1 (Lys25-Pro26-Ser27-Ala28-Cys29-Arg30, PDB: 1JSU) and the lariat cyclic pentapeptide (Lys502-Leu503-Phe504-Gly505, PDB: 1URC). To generate binding models of novel peptidic macrocycles, the 3D coordinates were generated by LigPrep and projected onto the template model by performing the maximum common substructure alignment for macrocycles in the ligand alignment module in Maestro (version 13.7.125) with cyclin A crystal structure (PDB: 1URC) specified as the receptor. The aligned ligand was further refined in the binding site by running Glide (ver. 10.0) SP docking with the “refine only” option in a docking grid based on the lariat-bound cyclin A crystal structure (PDB: 1URC). The docking grid was generated using the template model with default parameters. d , Detailed representation of modelled hydrogen bonds of CIRc-004 to Ile281, Trp217 and Gln 254 on cyclin A. e , Binding kinetic parameters determined in a WaveDelta instrument (Malvern Pananalytical) to Cyclin/Cdk complexes immobilized by amine coupling on a 4PCP chip (Malvern Pananalytical). Dissociation constant (K D ; in nM), association rate (k a ; in M −1 sec −1 ) and dissociation rate (k d ; in sec −1 ). f , Compounds physicochemical properties including Molecular Weight (MW), calculated water/oil partition (cLogP), kinetic solubility measured in 5% DMSO at pH 7.4 (mM), measured distribution coefficient between water and octanol (LogD) and MDCK cell apical to basolateral permeability (MDCK Papp; x10-6 cm/sec). g , Hypothesized model: In RB1 -deficient cancers (e.g. SCLC) where E2F1 activity is dysregulated, targeting the cyclin A-E2F1 interaction hyperactivates E2F1, which could selectively impair tumour growth. Figure was created with BioRender. h . Waterfall plot of GI50s for four SCLC and the non-transformed WI-38 fibroblast cell lines for compounds listed in Fig. .

Article Snippet: MDCK monolayer cell permeability, kinetic solubility ( K sol ), and logD experimental values were generated by Quintara Discovery using standard experimental conditions.

Techniques: Binding Assay, Software, Generated, Molecular Weight, Solubility, Permeability, Activity Assay, Transformation Assay