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