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CSAR scoring challenge reveals the need for new concepts in estimating protein-ligand binding affinity.
MedLine Citation:
PMID:  21612285     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
The dG prediction accuracy by the Lead Finder docking software on the CSAR test set was characterized by R<sup>2</sup>=0.62 and RMSD=1.93 kcal/mol, and the method of preparation of the full-atom structures of the test set did not significantly affect the resulting accuracy of predictions. The dG prediction accuracy by the Lead Finder docking software on the CSAR test set was characterized by R<sup>2</sup>=0.62 and RMSD=1.93 kcal/mol, and the method of preparation of the full-atom structures of the test set did not significantly affect the resulting accuracy of predictions. The primary factors determining the correlation between the predicted and experimental values were the Van der Waals interactions and solvation effects. Those two factors alone accounted for R2=0.50. The other factors that affected the accuracy of predictions, listed in the order of decreasing importance, were the change of ligand's internal energy upon binding with protein, the electrostatic interactions and the hydrogen bonds. It appears that those latter factors contributed to the independence of the prediction results from the method of full-atom structure preparation. Then, we turned our attention to the other factors that could potentially improve the scoring function in order to raise the accuracy of the dG prediction. It turned out that the ligand-centric factors, including Mw, cLogP, PSA etc. or protein-centric factors, such as the functional class of protein, did not improve the prediction accuracy. Following that, we explored if the weak molecular interactions such as X-H...Ar, X-H...Hal, CO...Hal, C-H...X, stacking and -cationic interactions (where X is N or O), that are generally of interest to the medicinal chemists despite their lack of proper molecular mechanical parameterization, could improve dG prediction. Our analysis revealed that out of these new interactions only CO…Hal is statistically significant for dG predictions using Lead FInder scoring function. Accounting for the CO…Hal interaction resulted in the reduction of the RMSD from 2.19 to 0.69 kcal/mol for the corresponding structures. The other weak interaction factors were not statistically significant and therefore irrelevant to the accuracy of dG prediction. On the basis of our findings from our participation in the CSAR scoring challenge we conclude that a significant increase of accuracy predictions necessitates breakthrough scoring approaches. We anticipate that the explicit accounting for water molecules, protein flexibility and a more thermodynamically accurate method of dG calculation rather than single point energy calculation may lead to such breakthroughs.
Authors:
Fedor Novikov; Alexey Zeifman; Oleg Stroganov; Viktor Stroylov; Val Kulkov; Ghermes Chilov
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2011-5-25
Journal Detail:
Title:  Journal of chemical information and modeling     Volume:  -     ISSN:  1549-960X     ISO Abbreviation:  -     Publication Date:  2011 May 
Date Detail:
Created Date:  2011-5-26     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101230060     Medline TA:  J Chem Inf Model     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
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