Citation: Shi-Ming Peng, Yu Zhou, Niu Huang. Improving the accuracy of pose prediction in molecular docking via structural filtering and conformational clustering[J]. Chinese Chemical Letters, ;2013, 24(11): 1001-1004. shu

Improving the accuracy of pose prediction in molecular docking via structural filtering and conformational clustering

Shi-Ming Peng ^a,c ,
Yu Zhou ^b,c ,
Niu Huang ^c,,

1.
a College of Biological Sciences, China Agricultural University, Beijing 100193, China;
2.
b College of Life Sciences, Beijing Normal University, Beijing 100875, China;
3.
c National Institute of Biological Sciences, Beijing 102206, China

Corresponding author: Niu Huang,
Received Date: 7 March 2013
Available Online: 27 May 2013

Structure-based virtual screening (molecular docking) is now one of the most pragmatic techniques to leverage target structure for ligand discovery. Accurate binding pose prediction is critical to molecular docking. Here, we describe a general strategy to improve the accuracy of docking pose prediction by implementing the structural descriptor-based filtering and KGS-penalty function-based conformational clustering in an unbiased manner. We assessed our method against 150 high-quality protein-ligand complex structures. Surprisingly, such simple components are sufficient to improve the accuracy of docking pose prediction. The success rate of predicting near-native docking pose increased from 53% of the targets to 78%. We expect that our strategymay have general usage in improving currently available molecular docking programs.
- Molecular docking,
- Pose prediction,
- Structural descriptor,
- Conformational clustering
1. [1]
  [1] X. Barril, R.E. Hubbard, S.D. Morley, Virtual screening in structure-based drug discovery, Mini Rev. Med. Chem. 4 (2004) 779-791.
2. [2]
  [2] H. Xu, Z. Jin, S. Liu, et al., Design, synthesis characterization and in vitro biological activity of a series of 3-aryl-6-(bromoarylmethyl)-7H-thiazolo[3,2-b]-1, 2, 4-triazin-7-one derivatives as the novel acetylcholinesterase inhibitors, Chin. Chem. Lett. 23 (2012) 765-768.
3. [3]
  [3] F. Zeng, S. Peng, L. Li, et al., HAT off: structure-based identification of druglike inhibitors of p300 histone acetyltransferase, Acta Pharm. Sin. 48 (2013) 700-708.
4. [4]
  [4] X.H. Ma, F. Zhu, X. Liu, et al., Virtual screening methods as tools for drug lead discovery from large chemical libraries, Curr. Med. Chem. 19 (2012) 5562-5571.
5. [5]
  [5] B.K. Shoichet, Virtual screening of chemical libraries, Nature 432 (2004) 862-865.
6. [6]
  [6] N. Huang, C. Kalyanaraman, K. Bernacki, M.P. Jacobson, Molecular mechanics methods for predicting protein-ligand binding, Phys. Chem. Chem. Phys. 8 (2006) 5166-5177.
7. [7]
  [7] R. Cao, M. Liu, M. Yin, et al., Discovery of novel tubulin inhibitors via structurebased hierarchical virtual screening, J. Chem. Inf. Model. 52 (2012) 2730-2740.
8. [8]
  [8] N. Huang, C. Kalyanaraman, J.J. Irwin, M.P. Jacobson, Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening, J. Chem. Inf. Model. 46 (2006) 243-253.
9. [9]
  [9] M.G. Lerner, K.L. Meagher, H.A. Carlson, Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design, J. Comput. Aided Mol. Des. 22 (2008) 727-736.
10. [10]
  [10] D.M. Lorber, B.K. Shoichet, Hierarchical docking of databases of multiple ligand conformations, Curr. Top. Med. Chem. 5 (2005) 739-749.
11. [11]
  [11] L.A. Kelley, S.P. Gardner, M.J. Sutcliffe, An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies, Protein Eng. 9 (1996) 1063-1065.
12. [12]
  [12] J.H. Hsieh, S. Yin, S. Liu, et al., Combined application of cheminformatics-and physical force field-based scoring functions improves binding affinity prediction for CSAR data sets, J. Chem. Inf. Model. 51 (2011) 2027-2035.
13. [13]
  [13] J.H. Hsieh, S. Yin, X.S. Wang, et al., Cheminformatics meets molecular mechanics: a combined application of knowledge-based pose scoring and physical force fieldbased hit scoring functions improves the accuracy of structure-based virtual screening, J. Chem. Inf. Model. 52 (2012) 16-28.
14. [14]
  [14] M.D. Eldridge, C.W. Murray, T.R. Auton, G.V. Paolini, R.P. Mee, Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes, J. Comput. Aided Mol. Des. 11 (1997) 425-445.
15. [15]
  [15] C.A. Sotriffer, P. Sanschagrin, H. Matter, G. Klebe, SFCscore: scoring functions for affinity prediction of protein-ligand complexes, Proteins 73 (2008) 395-419.
16. [16]
  [16] J.B. Dunbar Jr., R.D. Smith, C.Y. Yang, et al., CSAR benchmark exercise of 2010: selection of the protein-ligand complexes, J. Chem. Inf. Model. 51 (2011) 2036-2046.
17. [17]
  [17] N. Huang, B.K. Shoichet, J.J. Irwin, Benchmarking sets for molecular docking, J. Med. Chem. 49 (2006) 6789-6801.
18. [18]
  [18] J.J. Irwin, B.K. Shoichet, ZINC-a free database of commercially available compounds for virtual screening, J. Chem. Inf. Model. 45 (2005) 177-182.
19. [19]
  [19] C.S. Rapp, C. Schonbrun, M.P. Jacobson, C. Kalyanaraman, N. Huang, Automated site preparation in physics-based rescoring of receptor ligand complexes, Proteins 77 (2009) 52-61.
20. [20]
  [20] E.F. Pettersen, T.D.Goddard, C.C.Huang, et al.,UCSF Chimera-a visualizationsystem for exploratory research and analysis, J. Comput. Chem. 25 (2004) 1605-1612.
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沈阳化工大学材料科学与工程学院沈阳 110142