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Theoretical study of binding affinity for diamidine with DNA

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Abstract

Diamidine molecules, which have been recognized as the powerful gene drug candidates over the past decades, can bind in the DNA minor groove, inhibit the duplication of morbid sequences, and fight against a number of human and animal diseases. In this paper, on the basis of the binding models of a series of diamidines with DNA, the important influencing factors for the binding affinity of diamidines with DNA were systematically analyzed. The obtained results demonstrated that the curvature, length, distal group, and heteroaromatic ring of diamidine are four important factors, which could influence their binding affinities. Specifically, the better the curvature of the diamidine fits DNA minor groove, the higher the binding affinity is; increasing the molecular length within a certain range can make the binding affinity higher; changing the distal group of diamidine from amidino to imidazole or pyrimidine is favorable for improving the corresponding binding affinity; and the introduction of central heteroaromatic rings of diamidine molecules influences their binding affinities. One diamidine (named as DB103d) with ideal DNA binding affinity validates the four important factors proposed in the present work. The results obtained in this work might be helpful for the design of new efficient diamidine-based drug candidates.

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Acknowledgments

The authors acknowledge financial support from the National Natural Science Foundation of China (No. 21001095).

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    Authors and Affiliations

    1. College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, 450001, Henan Province, People’s Republic of China

      Chen Song, Xuening Zhang, Fangfang Li, Yanyan Zhu, Chunmei Liu, Xue Li, Yue Li, Wenjing Zhang, Donghui Wei & Mingsheng Tang

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    1. Chen Song
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    2. Xuening Zhang
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    3. Fangfang Li
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    7. Yue Li
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    Correspondence to Yanyan Zhu, Wenjing Zhang or Mingsheng Tang.

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    Chen Song and Xuening Zhang have contributed equally to this work.

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    Song, C., Zhang, X., Li, F. et al. Theoretical study of binding affinity for diamidine with DNA. Struct Chem 27, 681–696 (2016). https://doi.org/10.1007/s11224-015-0610-z

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