Shape-based similarity searching in chemical databases

Wiley Interdisciplinary Reviews: Computational Molecular Science

Volumn 3, Issue 3, 2013, Pages 226-241

  Finn, Paul W ^a   Morris, Garrett M ^a  

^a INHIBOX LTD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPETITIVE PERFORMANCE; COMPUTATIONAL PERFORMANCE; EXPLICIT REPRESENTATION; INTENSIVE RESEARCH; PARTIAL SHAPE MATCHING; RELATIVE PERFORMANCE; SIMILARITY SEARCHING; STATISTICAL REPRESENTATIONS;

MOLECULAR RECOGNITION;

LIGANDS;

EID: 84876478580     PISSN: 17590876     EISSN: 17590884     Source Type: Journal    
DOI: 10.1002/wcms.1128     Document Type: Review

References (89)

1. Moser D, Wisniewska JM, Hahn S, Achenbach J, Buscato E, Klingler FM, Hofmann B, Steinhilber D, Proschak E. Dual-target virtual screening by pharmacophore elucidation and molecular shape filtering. ACS Med Chem Lett 2012, 3:155-158.
2. Harada T, Nakagawa Y, Ogura T, Yamada Y, Ohe T, Miyagawa H. Virtual screening for ligands of the insect molting hormone receptor. J Chem Inf Model 2011, 51:296-305.
3. Naylor E, Arredouani A, Vasudevan SR, Lewis AM, Parkesh R, Mizote A, Rosen D, Thomas JM, Izumi M, Ganesan A, et al. Identification of a chemical probe for NAADP by virtual screening. Nat Chem Biol 2009, 5:220-226.
4. Brown RJC, Brown RFC. Melting point and molecular symmetry. J Chem Edu 2000, 77:724.
5. Ishikawa M, Hashimoto Y. Improvement in aqueous solubility in small molecule drug discovery programs by disruption of molecular planarity and symmetry. J Med Chem 2011, 54:1539-1554.
6. Lovering F, Bikker J, Humblet C. Escape from flatland: increasing saturation as an approach to improving clinical success. J Med Chem 2009, 52:6752-6756.
7. Connolly ML. Solvent-accessible surfaces of proteins and nucleic acids. Science 1983, 221:709-713.
8. Connolly ML. Computation of molecular volume. J Am Chem Soc 1985, 107:1118-1124.
9. Masek BB, Merchant A, Matthew JB. Molecular shape comparison of angiotensin II receptor antagonists. J Med Chem 1993, 36:1230-1238.
10. Sastry GM, Dixon SL, Sherman W. Rapid shape-based ligand alignment and virtual screening method based on atom/feature-pair similarities and volume overlap scoring. J Chem Inf Model 2011, 51:2455-2466.
11. Good AC, Hodgkin EE, Richards WG. The utilization of Gaussian functions for the rapid evaluation of molecular similarity. J Chem Inf Comp Sci 1992, 32:188-191.
12. Good AC, Richards WG. Rapid evaluation of shape similarity using Gaussian functions. J Chem Inf Comput Sci 1993, 33:112-116.
13. Walker DP, Arteca GA, Mezey P. A complete shape characterization for molecular charge densities represented by Gaussian-type functions. J Comput Chem 1991, 12:220-230.
14. Grant JA, Pickup BT. Gaussian description of molecular shape. J Phys Chem 1995, 99:3503-3510.
15. ROCS. Santa Fe, NM: OpenEye Scientific Software Inc., 2005.
16. Rush TS III, Grant JA, Mosyak L, Nicholls A. A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. J Med Chem 2005, 48:1489-1495.
17. Haque IS, Pande VS. PAPER-accelerating parallel evaluations of ROCS. J Comput Chem 2010, 31:117-132.
18. Kazhdan M, Funkhouser T, Rusinkiewicz S. Rotation invariant spherical harmonic representation of 3D shape descriptors. In: Proceedings of the 1st Eurographics Symposium on Geometry Processing (SGP 2003). Aachen, Germany: Association for Computing Machinery; 2003.
19. Max NL, Getzoff ED. Spherical harmonic molecular surfaces. IEEE Comput Graph Appl 1988, 8:42-50.
20. Duncan BS, Olson AJ. Approximation and characterization of molecular surfaces. Biopolymers 1993, 33:219-229.
21. Ritchie DW, Kemp GJ. Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. J Comput Chem 1999, 20:383-395.
22. Ritchie DW, Kemp GJ. Protein docking using spherical polar Fourier correlations. Proteins 2000, 39:178-194.
23. Mavridis L, Hudson BD, Ritchie DW. Toward high throughput 3D virtual screening using spherical harmonic molecular surface representations. J Chem Inf Model 2007, 47:1787-1796.
24. Venkatraman V, Chakravarthy PR, Kihara D. Application of 3D Zernike descriptors to shape-based ligand similarity searching. J Cheminform 2009, 1:19.
25. Sael L, Li B, La D, Fang Y, Ramani K, Rustamov R, Kihara D. Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins 2008, 72:1259-1273.
26. Ballester PJ, Richards WG. Ultrafast shape recognition to search compound databases for similar molecular shapes. J Comput Chem 2007, 28:1711-1723.
27. Armstrong MS, Morris GM, Finn PW, Sharma R, Richards WG. Molecular similarity including chirality. J Mol Graph Model 2009, 28:368-370.
28. Zhou T, Lafleur K, Caflisch A. Complementing ultrafast shape recognition with an optical isomerism descriptor. J Mol Graph Model 2010, 29:443-449.
29. Armstrong MS, Morris GM, Finn PW, Sharma R, Moretti L, Cooper RI, Richards WG. ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics. J Comput Aided Mol Des 2010, 24:789-801.
30. Armstrong MS, Finn PW, Morris GM, Richards WG. Improving the accuracy of ultrafast ligand-based screening: incorporating lipophilicity into ElectroShape as an extra dimension. J Comput Aided Mol Des 2011, 25:785-790.
31. Masek BB, Merchant A, Matthew JB. Molecular skins: a new concept for quantitative shape matching of a protein with its small molecule mimics. Proteins 1993, 17:193-202.
32. Perkins TD, Mills JE, Dean PM. Molecular surface-volume and property matching to superpose flexible dissimilar molecules. J Comput Aided Mol Des 1995, 9:479-490.
33. Chau PL, Dean PM. Molecular recognition. 3D surface structure comparison by gnomonic projection. J Mol Graph 1987, 5:97-100.
34. Dean PMC PL. Molecular recognition: optimized searching through rotational 3-space for pattern matches on molecular surfaces. J Mol Graph 1987, 5:152-158.
35. Blaney F, Finn P, Phippen R, Wyatt M. Molecular surface comparison: application to drug design. J Mol Graph 1993, 11:99-105, 124.
36. Hofbauer C, Lohninger H, Aszodi A. SURFCOMP: a novel graph-based approach to molecular surface comparison. J Chem Inf Comput Sci 2004, 44:837-847.
37. Jain AN. Ligand-based structural hypotheses for virtual screening. J Med Chem 2004, 47:947-961.
38. Zauhar RJ, Moyna G, Tian L, Li Z, Welsh WJ. Shape signatures: a new approach to computer-aided ligand- and receptor-based drug design. J Med Chem 2003, 46:5674-5690.
39. Shape Signatures. Available at: http://shapesignatures.umdnj.edu. (Accessed October 28, 2012).
40. Vainio MJ, Puranen JS, Johnson MS. ShaEP: molecular overlay based on shape and electrostatic potential. J Chem Inf Model 2009, 49:492-502.
41. Cheeseright T, Mackey M, Rose S, Vinter A. Molecular field extrema as descriptors of biological activity: definition and validation. J Chem Inf Model 2006, 46:665-676.
42. Liu X, Jiang H, Li H. SHAFTS: a hybrid approach for 3D molecular similarity calculation. 1. Method and assessment of virtual screening. J Chem Inf Model 2011, 51:2372-2385.
43. Cramer RD, Clark RD, Patterson DE, Ferguson AM. Bioisosterism as a molecular diversity descriptor: steric fields of single 'topomeric' conformers. J Med Chem 1996, 39:3060-3069.
44. Cramer RD. Topomer CoMFA: a design methodology for rapid lead optimization. J Med Chem 2003, 46:374-388.
45. Ikeuchi K. Recognition of 3-D objects using the extended Gaussian image. In: International Joint Conference on Artificial Intelligence, 1981. Vancouver, Canada: University of British Columbia; 1981.
46. Ankerst M, Kastenmuller G, Kriegel HP, Seidl T. Nearest neighbor classification in 3D protein databases. Proc Int Conf Intell Syst Mol Biol 1999:34-43.
47. Osada R, Funkhouser T, Chazelle B, Dobkin D. Matching 3D models with shape distributions. In: Proceedings of the International Conference on Shape Modeling and Applications. Genova, Italy; 2001.
48. Xiang P, Hua CQ, Gang FX, Chuan ZB. Pose insensitive 3D retrieval by Poisson shape histogram. In: Seventh International Conference on Computational Science, ICCS. Beijing, China; 2007.
49. Bustos B, Keim D, Saupe D, Schreck T, Vranic D. An experimental effectiveness comparison of methods for 3D similarity search. Int J Digital Libr 2006, 6:39-54.
50. Tangelder JWH, Veltkamp RC. A survey of content based 3D shape retrieval methods. Multimed Tools Appl 2008, 39:441-471.
51. Hamza A, Wei NN, Zhan CG. Ligand-based virtual screening approach using a new scoring function. J Chem Inf Model 2012, 52:963-974.
52. Chen X, Lin Y, Liu M, Gilson MK. The Binding Database: data management and interface design. Bioinformatics 2002, 18:130-139.
53. Binding DB. The Binding Database. Available at: http://www.bindingdb.org. (Accessed October 28, 2012).
54. Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK, Binding DB. A Web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res 2007, 35:D198-D201.
55. Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem 2006, 49:6789-6801.
56. Young DMT, Venkatapathy R, Harten P. Are the chemical structures in your QSAR correct? QSAR Combin Sci 2008, 27:1337-1345.
57. Fourches D, Muratov E, Tropsha A. Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research. J Chem Inf Model 2010, 50:1189-1204.
58. Scior T, Bender A, Tresadern G, Medina-Franco JL, Martinez-Mayorga K, Langer T, Cuanalo-Contreras K, Agrafiotis DK. Recognizing pitfalls in virtual screening: a critical review. J Chem Inf Model 2012.
59. Ebejer JP, Morris GM, Deane CM. Freely available conformer generation methods: how good are they? J Chem Inf Model 2012, 52:1146-1158.
60. Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH. PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res 2009, 37:W623-W633.
61. Bolton EE, Chen J, Kim S, Han L, He S, Shi W, Simonyan V, Sun Y, Thiessen PA, Wang J, et al. PubChem3D: a new resource for scientists. J Cheminform 2011, 3:32.
62. Irwin JJ, Shoichet BK. ZINC-a free database of commercially available compounds for virtual screening. J Chem Inf Model 2005, 45:177-182.
63. Del Rio A, Barbosa AJ, Caporuscio F, Mangiatordi GF. CoCoCo: a free suite of multiconformational chemical databases for high-throughput virtual screening purposes. Mol Biosyst 2010, 6:2122-2128.
64. ChEMBL-DB. Available at: https://www.ebi.ac.uk/chembldb. (Accessed October 28, 2012).
65. Seiler KP, George GA, Happ MP, Bodycombe NE, Carrinski HA, Norton S, Brudz S, Sullivan JP, Muhlich J, Serrano M, et al. ChemBank: a small-molecule screening and cheminformatics resource database. Nucleic Acids Res 2008, 36:D351-D359.
66. Bolton EE, Kim S, Bryant SH. PubChem3D: diversity of shape. J Cheminform 2011, 3:9.
67. Nicholls A. What do we know and when do we know it? J Comput Aided Mol Des 2008, 22:239-255.
68. Truchon JF, Bayly CI. Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem. J Chem Inf Model 2007, 47:488-508.
69. Kirchmair J, Distinto S, Markt P, Schuster D, Spitzer GM, Liedl KR, Wolber G. How to optimize shape-based virtual screening: choosing the right query and including chemical information. J Chem Inf Model 2009, 49:678-692.
70. Good AC, Oprea TI. Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? J Comput Aided Mol Des 2008, 22:169-178.
71. Rohrer SG, Baumann K. Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data. J Chem Inf Model 2009, 49:169-184.
72. Nicholls A, McGaughey GB, Sheridan RP, Good AC, Warren G, Mathieu M, Muchmore SW, Brown SP, Grant JA, Haigh JA, et al. Molecular shape and medicinal chemistry: a perspective. J Med Chem 2010, 53:3862-3886.
73. Giganti D, Guillemain H, Spadoni JL, Nilges M, Zagury JF, Montes M. Comparative evaluation of 3D virtual ligand screening methods: impact of the molecular alignment on enrichment. J Chem Inf Model 2010, 50:992-1004.
74. Hu G, Kuang G, Xiao W, Li W, Liu G, Tang Y. Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening. J Chem Inf Model 2012.
75. Lopez-Ramos M, Perruccio F. HPPD: ligand- and target-based virtual screening on a herbicide target. J Chem Inf Model 2010, 50:801-814.
76. Thimm M, Goede A, Hougardy S, Preissner R. Comparison of 2D similarity and 3D superposition. Application to searching a conformational drug database. J Chem Inf Comput Sci 2004, 44:1816-1822.
77. McGaughey GB, Sheridan RP, Bayly CI, Culberson JC, Kreatsoulas C, Lindsley S, Maiorov V, Truchon JF, Cornell WD. Comparison of topological, shape, and docking methods in virtual screening. J Chem Inf Model 2007, 47:1504-1519.
78. Venkatraman V, Perez-Nueno VI, Mavridis L, Ritchie DW. Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods. J Chem Inf Model 2010, 50:2079-2093.
79. Tawa GJ, Baber JC, Humblet C. Computation of 3D queries for ROCS based virtual screens. J Comput Aided Mol Des 2009, 23:853-868.
80. Perez-Nueno VI, Ritchie DW. Using consensus-shape clustering to identify promiscuous ligands and protein targets and to choose the right query for shape-based virtual screening. J Chem Inf Model 2011, 51:1233-1248.
81. Sato T, Yuki H, Takaya D, Sasaki S, Tanaka A, Honma T. Application of support vector machine to three-dimensional shape-based virtual screening using comprehensive three-dimensional molecular shape overlay with known inhibitors. J Chem Inf Model 2012.
82. Ebalunode JO, Zheng W. Unconventional 2D shape similarity method affords comparable enrichment as a 3D shape method in virtual screening experiments. J Chem Inf Model 2009, 49:1313-1320.
83. Ripphausen P, Nisius B, Peltason L, Bajorath J. Quo vadis, virtual screening? A comprehensive survey of prospective applications. J Med Chem 2010, 53:8461-8467.
84. Ripphausen P, Wassermann AM, Bajorath J. REPROVIS-DB: a benchmark system for ligand-based virtual screening derived from reproducible prospective applications. J Chem Inf Model 2011, 51:2467-2473.
85. Wang Q, Birod K, Angioni C, Grosch S, Geppert T, Schneider P, Rupp M, Schneider G. Spherical harmonics coefficients for ligand-based virtual screening of cyclooxygenase inhibitors. PLoS One 2011, 6:e21554.
86. Lalonde JM, Elban MA, Courter JR, Sugawara A, Soeta T, Madani N, Princiotto AM, Kwon YD, Kwong PD, Schon A, et al. Design, synthesis and biological evaluation of small molecule inhibitors of CD4-gp120 binding based on virtual screening. Bioorg Med Chem 2011, 19:91-101.
87. Baell JB, Holloway GA. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem 2010, 53:2719-2740.
88. Ballester PJ, Westwood I, Laurieri N, Sim E, Richards WG. Prospective virtual screening with ultrafast shape recognition: the identification of novel inhibitors of arylamine N-acetyltransferases. J R Soc Interface 2010, 7:335-342.
89. Muchmore SW, Souers AJ, Akritopoulou-Zanze I. The use of three-dimensional shape and electrostatic similarity searching in the identification of a melanin-concentrating hormone receptor 1 antagonist. Chem Biol Drug Des 2006, 67:174-176.