Computational methodologies for compound database searching that utilize experimental protein-ligand interaction information

Chemical Biology and Drug Design

Volumn 76, Issue 3, 2010, Pages 191-200

  Tan, Lu ^a   Batista, Jose ^a,b   Bajorath, Jürgen ^a  

^a UNIVERSITY OF BONN   (Germany)

^b JADO Technologies GmbH   (Germany)

Author keywords

fingerprints; interacting fragments; ligand and structure based virtual screening; pharmacophores; protein ligand interactions; similarity searching; X ray structures

Indexed keywords

LIGAND; PROTEIN;

DATA BASE; DRUG PROTEIN BINDING; DRUG SCREENING; LIGAND BINDING; MOLECULAR DOCKING; PHARMACOPHORE; PRIORITY JOURNAL; REVIEW;

BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DRUG DISCOVERY; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 77955262882     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2010.01007.x     Document Type: Review

References (49)

1. Vogt M., Bajorath J. (2009) Data mining approaches for compound selection and iterative screening. In : Balakin K.V., editor. Pharmaceutical Data Mining: Approaches and Applications for Drug Discovery. Hoboken, NJ, USA : John Wiley & Sons p. 115 143.
2. Willett P. (2006) Similarity-based virtual screening using 2D fingerprints. Drug Discov Today 11 : 1046 1053.
3. Stahura F.L., Bajorath J. (2005) New methodologies for ligand-based virtual screening. Curr Pharm Des 11 : 1189 1202.
4. Eckert H., Bajorath J. (2007) Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches. Drug Discov Today 12 : 225 233.
5. Bajorath J. (2002) Integration of virtual and high-throughput screening. Nat Rev Drug Discov 1 : 882 894.
6. Jain A.N. (2004) Virtual screening in lead discovery and optimization. Curr Opin Drug Discov Devel 7 : 396 403.
7. Kitchen D.B., Decornez H., Furr J.R., Bajorath J. (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3 : 935 949.
8. Shoichet B.K. (2004) Virtual screening of chemical libraries. Nature 432 : 862 865.
9. Klebe G. (2006) Virtual ligand screening: strategies, perspectives and limitations. Drug Discov Today 11 : 580 594.
10. Halperin I., Ma B., Wolfson H., Nussinov R. (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins: Struct, Funct, Bioinf 47 : 409 443.
11. Johnson M.A., Maggiora G.M. (1990) Concepts and Applications of Molecular Similarity. New York, USA : John Wiley & Sons.
12. Wei D., Zhang R., Du Q., Gao W., Li Y., Gao H., Wang S., Zhang X., Li A., Sirois S., Chou K. (2006) Anti-SARS drug screening by molecular docking. Amino Acids 31 : 73 80.
13. Barreiro G., Guimarães C.R.W., Tubert-Brohman I., Lyons T.M., Tirado-Rives J., Jorgensen W.L. (2007) Search for non-nucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring. J Chem Inf Model 47 : 2416 2428.
14. Tikhonova I.G., Sum C.S., Neumann S., Engel S., Raaka B.M., Costanzi S., Gershengorn M.C. (2008) Discovery of novel agonists and antagonists of the free fatty acid receptor 1 (FFAR1) using virtual screening. J Med Chem 51 : 625 633.
15. Lin T., Melgar M.M., Kurth D., Swamidass S.J., Purdon J., Tseng T., Gago G., Baldi P., Gramajo H., Tsai S. (2006) Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. Proc Natl Acad Sci USA 103 : 3072 3077.
16. Bissantz C., Schalon C., Guba W., Stahl M. (2005) Focused library design in GPCR projects on the example of 5-HT(2c) agonists: comparison of structure-based virtual screening with ligand-based search methods. Proteins: Struct, Funct, Bioinf 61 : 938 952.
17. Vidal D., Thormann M., Pons M. (2006) A novel search engine for virtual screening of very large databases. J Chem Inf Model 46 : 836 843.
18. Tan L., Geppert H., Sisay M.T., Gütschow M., Bajorath J. (2008) Integrating structure- and ligand-based virtual screening: comparison of individual, parallel, and fused molecular docking and similarity search calculations on multiple targets. ChemMedChem 3 : 1566 1571.
19. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. (2000) The protein data bank. Nucleic Acids Res 28 : 235 242.
20. Wolber G., Langer T. (2005) LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J Chem Inf Model 45 : 160 169.
21. Mason J.S., Morize I., Menard P.R., Cheney D.L., Hulme C., Labaudiniere R.F. (1999) New 4-point pharmacophore method for molecular similarity and diversity applications: overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures. J Med Chem 42 : 3251 3264.
22. Baroni M., Cruciani G., Sciabola S., Perruccio F., Mason J.S. (2007) A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): theory and application. J Chem Inf Model 47 : 279 294.
23. Weill N., Rognan D. (2009) Development and validation of a novel protein-ligand fingerprint to mine chemogenomic space: application to G protein-coupled receptors and their ligands. J Chem Inf Model 49 : 1049 1062.
24. Sato T., Honma T., Yokoyama S. (2010) Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening. J Chem Inf Model 50 : 170 185.
25. Deng Z., Chuaqui C., Singh J. (2004) Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J Med Chem 47 : 337 344.
26. Chuaqui C., Deng Z., Singh J. (2005) Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening. J Med Chem 48 : 121 133.
27. Deng Z., Chuaqui C., Singh J. (2006) Knowledge-based design of target-focused libraries using protein-ligand interaction constraints. J Med Chem 49 : 490 500.
28. Nandigam R.K., Kim S., Singh J., Chuaqui C. (2009) Position specific interaction dependent scoring technique for virtual screening based on weighted protein-ligand interaction fingerprint profiles. J Chem Inf Model 49 : 1185 1192.
29. Kelly M.D., Mancera R.L. (2004) Expanded interaction fingerprint method for analyzing ligand binding modes in docking and structure-based drug design. J Chem Inf Comput Sci 44 : 1942 1951.
30. Marcou G., Rognan D. (2007) Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J Chem Inf Model 47 : 195 207.
31. Venhorst J., Núñez S., Terpstra J.W., Kruse C.G. (2008) Assessment of scaffold hopping efficiency by use of molecular interaction fingerprints. J Med Chem 51 : 3222 3229.
32. Mpamhanga C.P., Chen B., McLay I.M., Willett P. (2006) Knowledge-based interaction fingerprint scoring: a simple method for improving the effectiveness of fast scoring functions. J Chem Inf Model 46 : 686 698.
33. Pérez-Nueno V.I., Rabal O., Borrell J.I., Teixidó J. (2009) APIF: a new interaction fingerprint based on atom pairs and its application to virtual screening. J Chem Inf Model 49 : 1245 1260.
34. Crisman T.J., Sisay M.T., Bajorath J. (2008) Ligand-target interaction-based weighing of substructures for virtual screening. J Chem Inf Model 48 : 1955 1964.
35. Tan L., Lounkine E., Bajorath J. (2008) Similarity searching using fingerprints of molecular fragments involved in protein-ligand interactions. J Chem Inf Model 48 : 2308 2312.
36. Tan L., Bajorath J. (2009) Utilizing target-ligand interaction information in fingerprint searching for ligands of related targets. Chem Biol Drug Des 74 : 25 32.
37. Tan L., Vogt M., Bajorath J. (2009) Three-dimensional protein-ligand interaction scaling of two-dimensional fingerprints. Chem Biol Drug Des 74 : 449 456.
38. Batista J., Tan L., Bajorath J. (2010) Atom-centered interacting fragments and similarity search applications. J Chem Inf Model 50 : 79 86.
39. Kroemer R.T., Vulpetti A., McDonald J.J., Rohrer D.C., Trosset J., Giordanetto F., Cotesta S., McMartin C., Kihlén M., Stouten P.F.W. (2004) Assessment of docking poses: interactions-based accuracy classification (IBAC) versus crystal structure deviations. J Chem Inf Comput Sci 44 : 871 881.
40. Naumann T., Matter H. (2002) Structural classification of protein kinases using 3D molecular interaction field analysis of their ligand binding sites: target family landscapes. J Med Chem 45 : 2366 2378.
41. Extended Connectivity Fingerprint (ECFP). San Diego, CA, USA : Scitegic Pipeline Pilot, Accelrys Inc.
42. Durant J.L., Leland B.A., Henry D.R., Nourse J.G. (2002) Reoptimization of MDL keys for use in drug discovery. J Chem Inf Comput Sci 42 : 1273 1280.
43. Wang Y., Bajorath J. (2010) Advanced fingerprint methods for similarity searching: balancing molecular complexity effects. Comb Chem High Throughput Screen 13 : 220 228.
44. Chen J., Holliday J., Bradshaw J. (2009) A machine learning approach to weighting schemes in the data fusion of similarity coefficients. J Chem Inf Model 49 : 185 194.
45. Holliday J.D., Salim N., Whittle M., Willett P. (2003) Analysis and display of the size dependence of chemical similarity coefficients. J Chem Inf Comput Sci 43 : 819 828.
46. Xue L., Stahura F.L., Godden J.W., Bajorath J. (2001) Fingerprint scaling increases the probability of identifying molecules with similar activity in virtual screening calculations. J Chem Inf Comput Sci 41 : 746 753.
47. Xue L., Godden J.W., Stahura F.L., Bajorath J. (2003) Profile scaling increases the similarity search performance of molecular fingerprints containing numerical descriptors and structural keys. J Chem Inf Comput Sci 43 : 1218 1225.
48. Hu Y., Lounkine E., Bajorath J. (2009) Filtering and counting of extended connectivity fingerprint features maximizes compound recall and the structural diversity of hits. Chem Biol Drug Des 74 : 92 98.
49. Tan L., Batista J., Bajorath J. (2010) Rationalization of the performance and target dependence of similarity searching incorporating protein-ligand interaction information. J Chem Inf Model in press.