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Understanding the molecular interactions of different radical scavengers with ribonucleotide reductase M2 (hRRM2) domain: opening the gates and gaining access

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Abstract

We employed a combination of molecular docking and dynamics to understand the interaction of three different radical scavengers (SB-HSC21, ABNM13 and trimidox) with ribonucleotide reductase M2 (hRRM2) domain. On the basis of the observed results, we can propose how these ligands interact with the enzyme, and cease the radical transfer step from the di-iron center to TYR176. All the ligands alter the electron density over TYR176, –OH group by forming an extremely stable H-bond with either –NHOH group, or with phenolic hydroxyl group of the ligands. This change in electronic density disrupts the water bridge between TYR176, –OH and the di-iron center, which stops the single electron transfer process from TYR176, –OH to iron. As a consequence the enzyme is inhibited. Another interesting observation that we are reporting is the two stage gate keeping mechanism of the RR active site tunnel. We describe these as the outer Gate-1 controlled by ARG330, and the inner Gate-2 controlled by SER263, PHE240, and PHE236. We also observed a dynamic conformational shift in these residues, the incoming ligands can go through, and interact with the underlying TYR176, –OH group. From the study we found the active—site of hRRM2 is extremely flexible and shows a significant induced fit.

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Acknowledgments

We thank University Grants Commission for providing necessary financial support for the current work. We also thank Mrs. Nibha Mishra and Dr. Venkatesan J for proofreading our manuscript.

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  1. Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Ranchi, 835 215, Jharkhand, India

    Arijit Basu & Barij N. Sinha

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  1. Arijit Basu
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  2. Barij N. Sinha
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Correspondence to Arijit Basu.

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Basu, A., Sinha, B.N. Understanding the molecular interactions of different radical scavengers with ribonucleotide reductase M2 (hRRM2) domain: opening the gates and gaining access. J Comput Aided Mol Des 26, 865–881 (2012). https://doi.org/10.1007/s10822-012-9581-y

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  • DOI: https://doi.org/10.1007/s10822-012-9581-y

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