Journal: Nature Communications

Article Title: Leveraging the multivalent p53 peptide-MdmX interaction to guide the improvement of small molecule inhibitors

doi: 10.1038/s41467-022-28721-x

Figure Lengend Snippet: a Alignment of the amino acid sequence of N-MdmX with that of N-Mdm2. Non-identical residues on N-MdmX are shown in red. b A cartoon model representing N-MdmX and N-Mdm2 structures, based on their crystal structures in complex with p53p. c Each ligand-binding pocket on N-MdmX or N-Mdm2 is composed of three subsites, i.e., the F19 p53p , W23 p53p , and L26 p53p subsites, with reference to the three key binding residues of p53p. d The amino acid sequence of the p53p peptide. Three key residues, i.e., F19 p53p , W23 p53p and L26 p53p , are in red. e The structure of p53p with three key residues highlighted. f Nutlin-3a can be docked tightly into the three subsites on N-Mdm2, mimicking p53p.

Article Snippet: The p53p ΔF19 gene was synthesized by GenScript (Wuxi, China) and sub-cloned to the pET28-MdmX plasmid.

Techniques: Sequencing, Ligand Binding Assay, Binding Assay

Journal: Nature Communications

Article Title: Leveraging the multivalent p53 peptide-MdmX interaction to guide the improvement of small molecule inhibitors

doi: 10.1038/s41467-022-28721-x

Figure Lengend Snippet: a The structures of the N-MdmX/nutlin-3a complexes superimposed on those of the N-MdmX/p53p complexes. Green stick: nutlin-3a ; purple stick: F19 p53p , W23 p53p , and L26 p53p . b Major side-chain conformational deviations occurred at the residues in the F19 p53p subsite and L26 p53p subsite of N-MdmX in complex with nutlin-3a and p53p. c – f Fast backbone dynamics ( ps–ns ) of N-MdmX in complex with nutlin-3a ( c , d ) or p53p ( e , f ). The order parameter ( S 2 ) and timescale of motion (τ e ) of N-MdmX in both complexes are plotted against the backbone amide residue. The secondary structure is shown on the top of the graph. R, S, and H denote the flexible region, β-sheet and α-helix, respectively. Regions with enhanced dynamics are shaded in gray. The data are represented as mean values ± SD and error bars for each parameter represent the propagated uncertainty determined from Monte Carlo simulations. Source data for ( c – f ) are provided as a Source Data file.

Article Snippet: The p53p ΔF19 gene was synthesized by GenScript (Wuxi, China) and sub-cloned to the pET28-MdmX plasmid.

Techniques: Residue

Journal: Nature Communications

Article Title: Leveraging the multivalent p53 peptide-MdmX interaction to guide the improvement of small molecule inhibitors

doi: 10.1038/s41467-022-28721-x

Figure Lengend Snippet: a A representative crystal structure of N-Mdm2 in complex with nutlin-3a (red line). b The structure N-MdmX/nutlin-3a complexes (in purple) are superimposed on those of the N-Mdm2/nutline-3a complexes (in yellow). c Comparison of major side-chain configurations between the F19 p53p subsites of N-MdmX and N-Mdm2. d A 2Fo-Fc map contoured at 1.5 σ of a section of the H72 side chain on N-Mdm2 revealing two configurations. e , f Comparison of major side chain configurations in the W23 p53p and L26 p53p subsites, respectively, between N-MdmX and N-Mdm2.

Article Snippet: The p53p ΔF19 gene was synthesized by GenScript (Wuxi, China) and sub-cloned to the pET28-MdmX plasmid.

Techniques: Comparison

Journal: Nature Communications

Article Title: Leveraging the multivalent p53 peptide-MdmX interaction to guide the improvement of small molecule inhibitors

doi: 10.1038/s41467-022-28721-x

Figure Lengend Snippet: a Affinity comparison of p53p F19 with p53p and p53p ΔF19 . n = 3 independent experiments and the data are represented as mean values ± SD. Source data are provided as a Source Data file. b The crystal structure of N-MdmX in complex with p53p F19 (purple) is superimposed on that of N-MdmX in complex with p53p (green). c A p53p ΔF19 -MdmX fusion protein was constructed for screening pharmacophores that could specifically target the F19 p53p subsite on N-MdmX. d , e Four benzodiazepine analogs ( d ) and their pharmacophores ( e ).

Article Snippet: The p53p ΔF19 gene was synthesized by GenScript (Wuxi, China) and sub-cloned to the pET28-MdmX plasmid.

Techniques: Comparison, Construct

Journal: Nature Communications

Article Title: Leveraging the multivalent p53 peptide-MdmX interaction to guide the improvement of small molecule inhibitors

doi: 10.1038/s41467-022-28721-x

Figure Lengend Snippet: a The perturbation of the 15 N- 1 H HSQC resonances of the W23 p53p side chain by four benzodiazepine compounds are compared. Protein and ligand ratios: black, 1:0; green, 1:0.5; blue, 1:1; yellow, 1:1.5 and red, 1:2. b , c The perturbation of the 15 N– 1 H HSQC resonances of the W23 p53p side chain by five pharmacophores are compared. The protein and ligand ratios: black, 1:0; green, 1:0.5; blue, 1:1; yellow, 1:1.5; red, 1:2, orange, 1:3 and purple, 1:5.

Article Snippet: The p53p ΔF19 gene was synthesized by GenScript (Wuxi, China) and sub-cloned to the pET28-MdmX plasmid.

Techniques:

Journal: Nature Communications

Article Title: Leveraging the multivalent p53 peptide-MdmX interaction to guide the improvement of small molecule inhibitors

doi: 10.1038/s41467-022-28721-x

Figure Lengend Snippet: a The structure and activity relationships of p53p and nutlin analogs are compared based on Fg1 and Fg5. n = 3 independent experiments and the data are represented as mean values ± SD. Source data are provided as a Source Data file. b Molecular structures of nutlin analogs H202 and H203. c , d Structure models of N-MdmX interacting with H202 and H203, evaluated by molecular docking.

Article Snippet: The p53p ΔF19 gene was synthesized by GenScript (Wuxi, China) and sub-cloned to the pET28-MdmX plasmid.

Techniques: Activity Assay

Journal: Scientific reports

Article Title: Integrating bioinformatics and ferroptosis to reveal the protective mechanism of Astragaloside IV on chronic heart failure rats.

doi: 10.1038/s41598-024-72011-z

Figure Lengend Snippet: Fig. 3. PPI network of common targets and network of core targets. (a) PPI network of common targets. (b) First screening of common targets. (c) Second screening of core targets. (d) Screening of key target p53 through topological analysis.

Article Snippet: Phospho-p53 (p-p53) antibody (Cat#82530) came from Cell Signaling Technology (USA).

Techniques:

Journal: Scientific reports

Article Title: Integrating bioinformatics and ferroptosis to reveal the protective mechanism of Astragaloside IV on chronic heart failure rats.

doi: 10.1038/s41598-024-72011-z

Figure Lengend Snippet: Fig. 5. Molecular docking model of p53 with AS-IV. (a) Molecular docking model without surface of receptor. (b) Molecular docking model showing surface of receptor.

Article Snippet: Phospho-p53 (p-p53) antibody (Cat#82530) came from Cell Signaling Technology (USA).

Techniques:

Journal: Scientific reports

Article Title: Integrating bioinformatics and ferroptosis to reveal the protective mechanism of Astragaloside IV on chronic heart failure rats.

doi: 10.1038/s41598-024-72011-z

Figure Lengend Snippet: Fig. 6. MD simulation analysis of p53-AS-IV complex. (a) RMSD curve of p53, AS-IV and p53-AS-IV complex. (b) RMSF curve of p53’s amino acid chains. (c) Rg curve of p53. (d) SASA curve of p53. (e) H-bonds of p53-AS-IV complex.

Article Snippet: Phospho-p53 (p-p53) antibody (Cat#82530) came from Cell Signaling Technology (USA).

Techniques:

Journal: Scientific reports

Article Title: Integrating bioinformatics and ferroptosis to reveal the protective mechanism of Astragaloside IV on chronic heart failure rats.

doi: 10.1038/s41598-024-72011-z

Figure Lengend Snippet: Fig. 11. AS-IV regulated the expression of p53/SLC7A11/GPX4 signaling pathway. (a) The mRNA expression of p53/SLC7A11/GPX4 signaling pathway (n = 3). (b) The representative Western Blotting bands of p53/ SLC7A11/GPX4 signaling pathway. The original blots/gels were presented in Supplementary Figure. (c) The protein expression of p53/SLC7A11/GPX4 signaling pathway (n = 3). **P < 0.01, *P < 0.05 vs. Sham group; ##P < 0.01, #P < 0.05 vs. Model group.

Article Snippet: Phospho-p53 (p-p53) antibody (Cat#82530) came from Cell Signaling Technology (USA).

Techniques: Expressing, Western Blot

Journal: Heliyon

Article Title: Synergistic effect of perampanel with temozolomide on glioblastoma cells in vivo

doi: 10.1016/j.heliyon.2025.e43167

Figure Lengend Snippet: Fig. 3. U-87MG (a) and 0125-DGC (b) cell lines were treated with 10 μM perampanel, 10 μM temozolomide, or 10 μM temozolomide with 10 μM perampanel. Whole cell lysates were analyzed by immunoblotting using the indicated primary antibodies. Protein expression levels of phosphorylated-p53 (p-p53), Fas receptor (FAS-R), cleaved caspase-8, anti-B-cell lymphoma 2-associated X protein (BAX) and cleaved caspase-3 in both U-87MG and 0125-DGC cells were most enhanced after administration of the combination therapy of temozolomide and perampanel. P: perampanel, T: temozolomide, T + P: temozolomide and perampanel.

Article Snippet: Anti-phosphorylated-p53 (p-p53) antibody (#9284; Cell Signaling Technology, Danvers, MA, USA), anti-B-cell lymphoma 2-associated X protein (Bax) antibody (sc-20067; Santa Cruz Biotechnology, Dallas, TX, USA), anti-Fas receptor (Fas-R) antibody (sc-8009; Santa Cruz Biotechnology), anti-caspase-3 antibody (sc-56070; Santa Cruz Biotechnology), and anti-caspase-8 antibody (sc-56053; Santa Cruz Biotechnology) were used as primary antibodies.

Techniques: Western Blot, Expressing