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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

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Abstract

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 p16INK4a) suppresses the transcription of p16INK4a 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 p16INK4a. 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 p16INK4a 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 p16INK4a 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 p16INK4a.

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Acknowledgments

R. Krishna and P. Manivel thanks University Grant Commission (UGC), Government of India for providing financial assistance (F.No.37-313/2009 (SR)) to carry out the Research work. Kannan M. (No.F. 14-2(SC)/2009 (SA-III)) and Nishith Saurav Topno (No.F. 14-2(ST)/2010 (SA-III)) thank UGC for Rajiv Gandhi National Fellowship to pursue their PhD degree. J. Muthukumaran (No.09/559/(0076)/2011/EMR-I) thanks CSIR (Council of Scientific and Industrial Research) for Senior Research fellowship. R. Krishna also thanks Department of Biotechnology and Department of Information technology, Government of India, New Delhi for their financial support to Centre for Bioinformatics, Pondicherry University. We thank E. Malanco, P. Elavarasan and S. Manikandan, Senior technical assistants, Centre for Bioinformatics, Pondicherry University for their technical supports. Authors also extend their greetings and regards to Jayakanthan M. and Bhuvaenshwari S. for their timely help to carry out the research work.

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  1. Centre for Bioinformatics, School of Life sciences, Pondicherry University, Puducherry, 605014, India

    Kannan Muthu, Manivel Panneerselvam, Muthukumaran Jayaraman, Nishith Saurav Topno, Arindam Atanu Das & Krishna Ramadas

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  1. Kannan Muthu
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  2. Manivel Panneerselvam
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Correspondence to Krishna Ramadas.

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Muthu, K., Panneerselvam, M., Jayaraman, M. et al. 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. J Mol Model 18, 4865–4884 (2012). https://doi.org/10.1007/s00894-012-1489-x

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