Comparing structural fingerprints using a literature-based similarity benchmark

Journal of Cheminformatics

Volumn 8, Issue 1, 2016, Pages

  O'Boyle, Noel M ^a   Sayle, Roger A ^a  

^a NextMove Software Ltd   (United Kingdom)

Author keywords

Molecular fingerprints; Similarity benchmark; Similarity searching; Structural similarity

Indexed keywords

EID: 84976870121     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/s13321-016-0148-0     Document Type: Article

References (54)

1. Johnson MA, Maggiora GM (1990) Concepts and applications of molecular similarity. Wiley, New York
2. Maggiora GM (2006) On outliers and activity cliffs - why QSAR often disappoints. J Chem Inf Model 46:1535. doi: 10.1021/ci060117s
3. Willett P (2014) The calculation of molecular structural similarity: principles and practice. Mol Inform 33:403-413. doi: 10.1002/minf.201400024
4. Muegge I, Mukherjee P (2016) An overview of molecular fingerprint similarity search in virtual screening. Expert Opin Drug Discov 11:137-148. doi: 10.1517/17460441.2016.1117070
5. Stumpfe D, Bajorath J (2011) Similarity searching. Wiley Interdiscip Rev Comput Mol Sci 1:260-282. doi: 10.1002/wcms.23
6. Cereto-Massagué A, Ojeda MJ, Valls C et al (2015) Molecular fingerprint similarity search in virtual screening. Methods 71:58-63. doi: 10.1016/j.ymeth.2014.08.005
7. McGaughey GB, Sheridan RP, Bayly CI et al (2007) Comparison of topological, shape, and docking methods in virtual screening. J Chem Inf Model 47:1504-1519. doi: 10.1021/ci700052x
8. Venkatraman V, Pérez-Nueno VI, Mavridis L, Ritchie DW (2010) Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods. J Chem Inf Model 50:2079-2093. doi: 10.1021/ci100263p
9. Riniker S, Landrum GA (2013) Open-source platform to benchmark fingerprints for ligand-based virtual screening. J Cheminf 5:26. doi: 10.1186/1758-2946-5-26
10. Tiikkainen P, Markt P, Wolber G et al (2009) Critical comparison of virtual screening methods against the MUV data set. J Chem Inf Model 49:2168-2178. doi: 10.1021/ci900249b
11. Heikamp K, Bajorath J (2011) Large-scale similarity search profiling of ChEMBL compound data sets. J Chem Inf Model 51:1831-1839. doi: 10.1021/ci200199u
12. Patterson DE, Cramer RD, Ferguson AM et al (1996) Neighborhood behavior: a useful concept for validation of "molecular diversity" descriptors. J Med Chem 39:3049-3059. doi: 10.1021/jm960290n
13. Horvath D, Jeandenans C (2003) Neighborhood behavior of in silico structural spaces with respect to in vitro activity spaces - a novel understanding of the molecular similarity principle in the context of multiple receptor binding profiles. J Chem Inf Comput Sci 43:680-690. doi: 10.1021/ci025634z
14. Papadatos G, Cooper AWJ, Kadirkamanathan V et al (2009) Analysis of neighborhood behavior in lead optimization and array design. J Chem Inf Model 49:195-208. doi: 10.1021/ci800302g
15. Steffen A, Kogej T, Tyrchan C, Engkvist O (2009) Comparison of molecular fingerprint methods on the basis of biological profile data. J Chem Inf Model 49:338-347. doi: 10.1021/ci800326z
16. Hert J, Willett P, Wilton DJ et al (2004) Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Org Biomol Chem 2:3256-3266. doi: 10.1039/B409865J
17. Bender A, Jenkins JL, Scheiber J et al (2009) How similar are similarity searching methods? a principal component analysis of molecular descriptor space. J Chem Inf Model 49:108-119. doi: 10.1021/ci800249s
18. Sastry M, Lowrie JF, Dixon SL, Sherman W (2010) Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments. J Chem Inf Model 50:771-784. doi: 10.1021/ci100062n
19. Briem H, Lessel UF (2000) In vitro and in silico affinity fingerprints: finding similarities beyond structural classes. Perspect Drug Discov Des 20:231-244. doi: 10.1023/A:1008793325522
20. Duan J, Dixon SL, Lowrie JF, Sherman W (2010) Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods. J Mol Graph Model 29:157-170. doi: 10.1016/j.jmgm.2010.05.008
21. Franco P, Porta N, Holliday JD, Willett P (2014) The use of 2D fingerprint methods to support the assessment of structural similarity in orphan drug legislation. J Cheminf 6:5. doi: 10.1186/1758-2946-6-5
22. Maggiora G, Vogt M, Stumpfe D, Bajorath J (2014) Molecular similarity in medicinal chemistry. J Med Chem 57:3186-3204. doi: 10.1021/jm401411z
23. Bento AP, Gaulton A, Hersey A et al (2014) The ChEMBL bioactivity database: an update. Nucleic Acids Res 42:D1083-D1090. doi: 10.1093/nar/gkt1031
24. Riniker S, Landrum G (2016) Code repository for benchmarking platform. https://github.com/rdkit/benchmarking-platform. Accessed 15 Jan 2016
25. RDKit (2016) Cheminformatics and machine learning software. http://rdkit.org/. Accessed 15 Jan 2016
26. Nilakantan R, Bauman N, Dixon JS, Venkataraghavan R (1987) Topological torsion: a new molecular descriptor for SAR applications. Comparison with other descriptors. J Chem Inf Model 27:82-85. doi: 10.1021/ci00054a008
27. Carhart RE, Smith DH, Venkataraghavan R (1985) Atom pairs as molecular features in structure-activity studies: definition and applications. J Chem Inf Comput Sci 25:64-73. doi: 10.1021/ci00046a002
28. Gedeck P, Rohde B, Bartels C (2006) QSAR - how good is it in practice? comparison of descriptor sets on an unbiased cross section of corporate data sets. J Chem Inf Model 46:1924-1936. doi: 10.1021/ci050413p
29. Rogers D, Hahn M (2010) Extended-connectivity fingerprints. J Chem Inf Model 50:742-754. doi: 10.1021/ci100050t1 comment on PubPeer
30. Ertl P, Patiny L, Sander T et al (2015) Wikipedia chemical structure explorer: substructure and similarity searching of molecules from Wikipedia. J Cheminf 7:10. doi: 10.1186/s13321-015-0061-y
31. Wikipedia structure search (2016) http://www.cheminfo.org/wikipedia/. Accessed 15 Jan 2016
32. Jones E, Oliphant T, Peterson P (2001) others. SciPy, Open source scientific tools for Python
33. Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6:65-70
34. Huang N, Shoichet BK, Irwin JJ (2006) Benchmarking sets for molecular docking. J Med Chem 49:6789-6801. doi: 10.1021/jm0608356
35. Rohrer SG, Baumann K (2009) Maximum unbiased validation (MUV) data sets for virtual screening based on PubChem bioactivity data. J Chem Inf Model 49:169-184. doi: 10.1021/ci8002649
36. Truchon J-F, Bayly CI (2007) Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem. J Chem Inf Model 47:488-508. doi: 10.1021/ci600426e
37. Sheridan RP (2008) Alternative global goodness metrics and sensitivity analysis: heuristics to check the robustness of conclusions from studies comparing virtual screening methods. J Chem Inf Model 48:426-433. doi: 10.1021/ci700380x
38. Peprah K, Zhu XY, Eyunni SVK et al (2012) Multi-receptor drug design: Haloperidol as a scaffold for the design and synthesis of atypical antipsychotic agents. Bioorg Med Chem 20:1291-1297. doi: 10.1016/j.bmc.2011.12.019
39. Maurya SK, Gollapalli DR, Kirubakaran S et al (2009) Triazole inhibitors of Cryptosporidium parvum inosine 5′-monophosphate dehydrogenase. J Med Chem 52:4623-4630. doi: 10.1021/jm900410u
40. Sard H, Kumaran G, Morency C et al (2005) SAR of psilocybin analogs: discovery of a selective 5-HT2C agonist. Bioorg Med Chem Lett 15:4555-4559. doi: 10.1016/j.bmcl.2005.06.104
41. Meng H, Liu Y, Zhai Y, Lai L (2013) Optimization of 5-hydroxytryptamines as dual function inhibitors targeting phospholipase A2 and leukotriene A4 hydrolase. Eur J Med Chem 59:160-167. doi: 10.1016/j.ejmech.2012.10.057
42. DeFalco J, Steiger D, Dourado M et al (2010) 5-Benzyloxytryptamine as an antagonist of TRPM8. Bioorg Med Chem Lett 20:7076-7079. doi: 10.1016/j.bmcl.2010.09.099
43. Matzen L, van Amsterdam C, Rautenberg W et al (2000) 5-HT reuptake inhibitors with 5-HT1B/1D antagonistic activity: a new approach toward efficient antidepressants. J Med Chem 43:1149-1157. doi: 10.1021/jm9811054
44. Conway RJ, Valant C, Christopoulos A et al (2012) Synthesis and SAR study of 4-arylpiperidines and 4-aryl-1,2,3,6-tetrahydropyridines as 5-HT2C agonists. Bioorg Med Chem Lett 22:2560-2564. doi: 10.1016/j.bmcl.2012.01.122
45. Palmer AM, Münch G, Brehm C et al (2008) 5-Substituted 1H-pyrrolo[3,2-b]pyridines as inhibitors of gastric acid secretion. Bioorg Med Chem 16:1511-1530. doi: 10.1016/j.bmc.2007.10.017
46. Palmer AM, Grobbel B, Brehm C et al (2007) Preparation of tetrahydroimidazo[2,1-a]isoquinolines and their use as inhibitors of gastric acid secretion. Bioorg Med Chem 15:7647-7660. doi: 10.1016/j.bmc.2007.08.065
47. Kaminski JJ, Wallmark B, Briving C, Andersson BM (1991) Antiulcer agents. 5. Inhibition of gastric H+/K+-ATPase by substituted imidazo[1,2-a]pyridines and related analogs and its implication in modeling the high affinity potassium ion binding site of the gastric proton pump enzyme. J Med Chem 34:533-541. doi: 10.1021/jm00106a008
48. Panchal T, Bailey N, Bamford M et al (2009) Evaluation of basic, heterocyclic ring systems as templates for use as potassium competitive acid blockers (pCABs). Bioorg Med Chem Lett 19:6813-6817. doi: 10.1016/j.bmcl.2009.07.002
49. DeMarinis RM, Shah DH, Hall RF et al (1982) α-adrenergic agents. 2. Synthesis and α1-agonist activity of 2-aminotetralins. J Med Chem 25:136-141. doi: 10.1021/jm00344a009
50. Grunewald GL, Bartlett WJ, Reitz TJ et al (1986) Conformationally defined adrenergic agents. 9. Binding requirements of phenolic phenylethylamines in the benzonorbornene skeleton at the active site of phenylethanolamine N-methyltransferase. J Med Chem 29:1972-1982. doi: 10.1021/jm00160a029
51. Ye Q, Grunewald GL (1989) Conformationally defined adrenergic agents. 15. Conformationally restricted and conformationally defined tyramine analogs as inhibitors of phenylethanolamine N-methyltransferase. J Med Chem 32:478-486. doi: 10.1021/jm00122a032
52. Burn P, Crooks PA, Heatley F et al (1982) Synthesis and dopaminergic properties of some exo- and endo-2-aminobenzonorbornenes designed as rigid analogs of dopamine. J Med Chem 25:363-368. doi: 10.1021/jm00346a007
53. Nasr RJ, Swamidass SJ, Baldi PF (2009) Large scale study of multiple-molecule queries. J Cheminf 1:7. doi: 10.1186/1758-2946-1-7
54. Whittle M, Gillet VJ, Willett P, Loesel J (2006) Analysis of data fusion methods in virtual screening: similarity and group fusion. J Chem Inf Model 46:2206-2219. doi: 10.1021/ci0496144