Structural insights into interacting mechanism of ID1 protein with an antagonist ID1/3-PA7 and agonist ETS-1 in treatment of ovarian cancer: molecular docking and dynamics studies.
Among the many abnormally expressed proteins in ovarian cancer, the prominent cancer in women, ID1 (inhibitors of DNA binding protein 1) is a potential one among other several targets. Interaction of ID1 with ETS-1 (transcriptional activator of p16(INK4a)) suppresses the transcription of p16(INK4a) and causes abnormal cell proliferation. A peptide aptamer (ID1/3-PA7) has been designed to prevent this interaction and thereby leading to the transcription of p16(INK4a). However, the structural basis behind the molecular interaction of ID1 with ETS-1 (agonist) and ID1/3-PA7 (antagonist) is poorly understood. In order to understand this structural recognition and their interaction mechanism, in silico methods were used. From this interaction analysis, the residues of ETS-1 involved in interaction with the p16(INK4a) promoter were found to be targeted by ID1. Subsequently, ETS-1 binding residues of ID1 were found to be targeted by its aptamer- ID1/3-PA7. These results suggest that both ETS-1 and ID1/3-PA7 binds at the same region harbored by the residues-H97, D100, R103, D104, L107, A144, C145, D149, D150 and C154 of ID1. All these observations correlate with the experimental reports, suggesting that the identified residues might play a crucial role in promulgating the oncogenic effects of ID1. In silico alanine scanning mutagenesis also confirms the role of identified hot spot residues in p16(INK4a) regulation. Finally, the molecular dynamic simulation studies reveal the prolonged stability of the aforementioned interacting complexes. The obtained results throw light on the structure and residues of ID1 involved in transcriptional regulation of p16(INK4a).
Centre for Bioinformatics, School of Life sciences, Pondicherry University, Puducherry 605014, India.
Kannan
K
Muthu
Manivel
M
Panneerselvam
Muthukumaran
M
Jayaraman
Nishith Saurav
NS
Topno
Arindam Atanu
AA
Das
Krishna
K
Ramadas
D052158:Aptamers, Peptide / Q000378:metabolism* / Q000494:pharmacology; D001665:Binding Sites; D049109:Cell Proliferation; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000235:genetics / Q000378:metabolism*; D015195:Drug Design; D005260:Female; D006801:Humans; D051798:Inhibitor of Differentiation Protein 1 / Q000819:agonists / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D010051:Ovarian Neoplasms / Q000188:drug therapy; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D050784:Proto-Oncogene Protein c-ets-1 / Q000737:chemistry / Q000378:metabolism*; D014158:Transcription, Genetic
D052158:Aptamers, Peptide; D019941:Cyclin-Dependent Kinase Inhibitor p16; C494041:ETS1 protein, human; C497453:ID1 protein, human; D051798:Inhibitor of Differentiation Protein 1; D050784:Proto-Oncogene Protein c-ets-1