Virtual screening using covalent docking to find activators for G245S mutant p53

Abstract

TP53 is the most mutated gene in all cancers. The mutant protein also accumulates in cells. The high frequency of p53 mutations makes the protein a promising target for anti-cancer therapy. Only a few molecules have been found, using in vitro screening, to reactivate the mutant protein. APR-246 is currently the most successful mutant p53 activator, which reactivates the transcriptional activity of p53 by covalently binding to C124 of the protein. We have recently created in silico models of G245S-mp53 in its apo and DNA-bound forms. In this paper we further report on our in silico screening for potential activators of G245S-mp53. We filtered the ZINC15 database (13 million compounds) to only include drug-like molecules with moderate to standard reactivity. Our filtered database of 130,000 compounds was screened using the DOCKTITE protocol in the Molecular Operating Environment software. We performed covalent docking at C124 of G245S-mp53 to identify potential activators of the mutant protein. The docked compounds were ranked using a consensus scoring approach. We also used ADMET Predictor™ to predict pharmacokinetics and the possible toxicities of the compounds. Our screening procedure has identified compounds, mostly thiosemicarbazones and halo-carbonyls, with the best potential as G245S-mp53 activators, which are described in this work. Based on its binding scores and ADMET risk score, compound 2 is likely to have the best potential as a G245S-mp53 activator compared to the other top hits.

Fig 1

Plots of the DBI, pSF and SSR/SST clustering metrics for the equilibrated (A) apo and (B) DNA-bound G245S-mp53. The pSF values were normalized to fit on the graph.

Fig 2. The top ten hits from our covalent docking virtual screening.

The hits are ranked based on their DSX score. The reactive moiety of molecules is tagged by ‘Ta’, which marks the thiol group of C124 of G245S-mp53 in case of a true hit. Mwt = molecular weight of the compound.

Fig 3. Compound 2 covalently bound to G245S-mp53.

(A) The protein’s molecular surface is shown in grey. Loop L1, where compound 2 is covalently bound, is colored as an orange ribbon. Helix H2 and loop L3, which interact with the DNA are colored red and green, respectively. The mutated S245 in loop L3 is shown as green spheres. Compound 2 is represented by its molecular surface and is colored based on its electrostatic potential. (B) The ligand interaction scheme of compound 2 with the minimized G245S-mp53.