Identification of High Affinity Non-Peptidic Small Molecule Inhibitors of MDM2-p53 Interactions through Structure-Based Virtual Screening Strategies

  • Bandaru, Srinivas (Institute of Genetics and Hospital for Genetic Diseases, Osmania University) ;
  • Ponnala, Deepika (Institute of Genetics and Hospital for Genetic Diseases, Osmania University) ;
  • Lakkaraju, Chandana (Institute of Genetics and Hospital for Genetic Diseases, Osmania University) ;
  • Bhukya, Chaitanya Kumar (Institute of Genetics and Hospital for Genetic Diseases, Osmania University) ;
  • Shaheen, Uzma (Institute of Genetics and Hospital for Genetic Diseases, Osmania University) ;
  • Nayarisseri, Anuraj (In silico Research Laboratory, Eminent Biosciences)
  • Published : 2015.05.18


Background: Approaches in disruption of MDM2-p53 interactions have now emerged as an important therapeutic strategy in resurrecting wild type p53 functional status. The present study highlights virtual screening strategies in identification of high affinity small molecule non-peptidic inhibitors. Nutlin3A and RG7112 belonging to compound class of Cis-imidazoline, MI219 of Spiro-oxindole class and Benzodiazepine derived TDP 665759 served as query small molecules for similarity search with a threshold of 95%. The query molecules and the similar molecules corresponding to each query were docked at the transactivation binding cleft of MDM2 protein. Aided by MolDock algorithm, high affinity compound against MDM2 was retrieved. Patch Dock supervised Protein-Protein interactions were established between MDM2 and ligand (query and similar) bound and free states of p53. Compounds with PubCid 68870345, 77819398, 71132874, and 11952782 respectively structurally similar to Nutlin3A, RG7112, Mi219 and TDP 665759 demonstrated higher affinity to MDM2 in comparison to their parent compounds. Evident from the protein-protein interaction studies, all the similar compounds except for 77819398 (similar to RG 7112) showed appreciable inhibitory potential. Of particular relevance, compound 68870345 akin to Nutlin 3A had highest inhibitory potential that respectively showed 1.3, 1.2, 1.16 and 1.26 folds higher inhibitory potential than Nutilin 3A, MI 219, RG 7112 and TDP 1665759. Compound 68870345 was further mapped for structure based pharamacophoric features. In the study, we report Cis-imidazoline derivative compound; Pubcid: 68870345 to have highest inhibitory potential in blocking MDM2-p53 interactions hitherto discovered.


MDM2-p53 interactions;virtual screening;molecular docking


  1. Ahmad S, Gromiha M, Fawareh H, Sarai A (2004). ASAView: database and tool for solvent accessibility representation in proteins. BMC bioinformatics, 5, 51.
  2. Bandaru S, Marri VK, Kasera P, et al (2014). Structure based virtual screening of ligands to identify cysteinyl leukotriene receptor 1 antagonist. Bioinformat, 10, 652.
  3. Basse MJ, Betzi S, Bourgeas R, et al (2013). 2P2Idb: a structural database dedicated to orthosteric modulation of protein-protein interactions. Nucleic Acids Res, 41, 824-27.
  4. Chen J, Marechal V, Levine AJ (1993). Mapping of the p53 and mdm-2 interaction domains. Mol Cell Biol, 13, 4107-14.
  5. Cheng F, Li W, Zhou Y, et al (2012). admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J Chem Inf Model, 52, 3099-105.
  6. DeLeo AB, Jay G, Appella E, Dubois GC, et al (1979). Detection of a transformation-related antigen in chemically induced sarcomas and other transformed cells of the mouse. Proc Natl Acad Sci U S A, 76, 2420-4.
  7. Feki A, Irminger-Finger I (2004). Mutational spectrum of p53 mutations in primary breast and ovarian tumors. Crit Rev Oncol Hematol, 52, 103-16.
  8. Freedman DA, Levine AJ (1998). Nuclear export is required for degradation of endogenous p53 by MDM2 and human papillomavirus E6. Mol Cell Biol, 18, 7288-93.
  9. Fridman JS, Lowe SW (2003). Control of apoptosis by p53. Oncogene, 22, 9030-40.
  10. Haupt Y, Maya R, Kazaz A, Oren M (1997). MDM2 promotes the rapid degradation of p53. Nature, 387, 296-9.
  11. Lane DP, Crawford LV (1979). T antigen is bound to a host protein in SV40-transformed cells. Nature, 278, 261-3.
  12. Linzer DI, Levine AJ (1979). Characterization of a 54K dalton cellular SV40 tumor antigen present in SV40-transformed cells and uninfected embryonal carcinoma cells. Cell, 17, 43-52.
  13. Liu J, Zheng Y, Lei D, et al (2011). MDM2 309T> G polymorphism and risk of squamous cell carcinomas of head and neck: a meta-analysis. Asian Pac J Cancer Prev, 12, 1899-03.
  14. Maunz A, Gutlein M, Rautenberg M, et al (2013). Lazar: a modular predictive toxicology framework. Front Pharmacol, 4, 38.
  15. Momand J, Jung D, Wilczynski S, Niland J (1998). The MDM2 gene amplification database. Nucleic Acids Res, 26, 3453-9.
  16. Momand J, Zambetti GP, Olson DC, George D, Levine AJ (1992). The mdm-2 oncogene product forms a complex with the p53 protein and inhibits p53- mediated transactivation. Cell, 69, 1237-45.
  17. Nelder JA, Mead R (1965). A simplex method for function minimization. Comput J, 7, 308-13.
  18. Oliner JD, Kinzler KW, Meltzer PS, et al (1992). Amplification of a gene encoding a p53-associated protein in human sarcomas. Nature, 358, 80-3.
  19. Patton JT, Mayo LD, Singhi AD, et al (2006). Levels of HdmX expression dictate the sensitivity of normal and transformed cells to Nutlin- 3. Cancer Res, 66, 3169-76.
  20. Ray-Coquard I, Blay JY, Italiano A, et al (2012). Effect of the MDM2 antagonist RG7112 on the P53 pathway in patients with MDM2-amplified, well-differentiated or dedifferentiated liposarcoma: an exploratory proof-of-mechanism study. Lancet Oncol, 13, 1133-40.
  21. Reichmann D, Phillip Y, Carmi A, Schreiber G (2008). On the contribution of water-mediated interactions to protein-complex stability. Biochem, 47, 1051-60.
  22. Sarek G, Kurki S, Enback J, et al (2007). Reactivation of the p53 pathway as a treatment modality for KSHVinduced lymphomas. J Clin Invest, 117, 1019-28.
  23. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005). PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res, 33, 363-67.
  24. Shangary S, Qin D, McEachern D, et al (2008). Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition. Proc Natl Acad Sci USA, 105, 3933-8.
  25. Srivatanakul P, Sriplung H (2004). Epidemiology of liver cancer: an overview. Asian Pac J Cancer Prev, 5, 118-25
  26. Stakleff KS, Sloan T, Blanco D, et al (2012). Resveratrol exerts differential effects in vitro and in vivo against ovarian cancer cells. Asian Pac J Cancer Prev, 13, 1333-40.
  27. Teodoro JG, Evans SK, GreenMR (2007). Inhibition of tumor angiogenesis by p53: a new role for the guardian of the genome. J Mol Med, 85, 1175-86.
  28. Thomsen R, Christensen MH (2006). MolDock: a new technique for high-accuracy molecular docking. J Med Chem, 49, 3315-21.
  29. Chanda Sinha, Anuradha Nischal, Srinivas Bandaru, et al (2015). An In silico Approach for Identification of Novel Inhibitors as a Potential Therapeutics Targeting HIV-1 Viral Infectivity Factor. Current Topics Med Chem, 15, 65-72.
  30. Tian, X, Tian Y, Ma P, et al (2013). Association between MDM2 SNP309 T>G and risk of gastric cancer: a meta-analysis. Asian Pac J Cancer Prev, 14, 1925-9.
  31. Tovar C, Rosinski J, Filipovic Z, et al (2006). Small-molecule MDM2 antagonists reveal aberrant p53 signaling in cancer: implications for therapy. Proc Natl Acad Sci U S A, 103, 1888-93.
  32. Vassilev LT, Vu BT, Graves B, et al (2004). In vivo activation of the p53 pathway by small molecule antagonists of MDM2. Science, 303, 844-8.
  33. Vassilev LT,Vu BT,Graves B, et al (2004). In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science, 303, 844-8.
  34. Vousden KH, Lu X (2002). Live or let die: the cell's response to p53. Nat Rev Cancer, 2, 594-604.
  35. Wu X, Bayle JH, Olson D, Levine AJ (1993). The p53-mdm-2 autoregulatory feedback loop. Genes Dev, 7, 1126-32.
  36. Xu T, Xu ZC, Zou Q, Yu B et al (2012). P53 Arg72Pro polymorphism and bladder cancer risk--meta-analysis evidence for a link in Asians but not Caucasians. Asian Pac J Cancer Prev, 13, 2349-54.
  37. Yang JM, Chen CC (2004). Gemdock: A generic evolutionary method for molecular docking. Proteins, 55, 288-304.
  38. Yang ZH, Zhou CL, Zhu H et al (2014). A functional SNP in the MDM2 promoter mediates E2F1 affinity to modulate cyclin D1 expression in tumor cell proliferation. Asian Pac J Cancer Prev, 15, 3817.