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Molecules 2013, 18(4), 3760-3778; doi:10.3390/molecules18043760
Article

Comparing the Suitability of Autodock, Gold and Glide for the Docking and Predicting the Possible Targets of Ru(II)-Based Complexes as Anticancer Agents

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Received: 19 February 2013; in revised form: 7 March 2013 / Accepted: 18 March 2013 / Published: 25 March 2013
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Abstract: In cancer chemotherapy, metal-based complexes have been recognized as the most promising means of inhibiting cancer growth due to the successful application of cis-platin and its derivatives above many of the existing organic anticancer agents. The limitations in their rational design can be traced to the complexity of the mechanism of their operations, lack of proper knowledge of their targets and lack of force fields in docking packages to appropriately define the metal centre of the organometallic complexes. In this paper, some of the promising anticancer complexes of Ru(II) such as the rapta-based complexes formulated as [Ru(η6-p-cymene)L2(pta)] and those with unusual ligands are considered. CatB and kinases which have been experimentally confirmed as possible targets of the complexes are also predicted by the three methods as one of the most targeted receptors while TopII and HDAC7 are predicted by two and one of the methods as best targets. The interesting features of the binding of the complexes show that some of the complexes preferentially target specific macromolecules than the others, which is an indication of their specificity and possibility of their therapeutic combination without severe side effects that may come from competition for the same target. Also, introduction of unusual ligands is found to significantly improve the activities of most of the complexes studied. Strong correlations are observed for the predicted binding sites and the orientation of the complexes within the binding site by the three methods of docking. However there are disparities in the ranking of the complexes by the three method of docking, especially that of Glide.
Keywords: docking; meta-based complexes; binding site interaction; unusual ligands; cancer receptors docking; meta-based complexes; binding site interaction; unusual ligands; cancer receptors
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Adeniyi, A.A.; Ajibade, P.A. Comparing the Suitability of Autodock, Gold and Glide for the Docking and Predicting the Possible Targets of Ru(II)-Based Complexes as Anticancer Agents. Molecules 2013, 18, 3760-3778.

AMA Style

Adeniyi AA, Ajibade PA. Comparing the Suitability of Autodock, Gold and Glide for the Docking and Predicting the Possible Targets of Ru(II)-Based Complexes as Anticancer Agents. Molecules. 2013; 18(4):3760-3778.

Chicago/Turabian Style

Adeniyi, Adebayo A.; Ajibade, Peter A. 2013. "Comparing the Suitability of Autodock, Gold and Glide for the Docking and Predicting the Possible Targets of Ru(II)-Based Complexes as Anticancer Agents." Molecules 18, no. 4: 3760-3778.



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