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Promiscuous patterns and perils in PubChem and the MLSCN

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Jeremy Yang
Jeremy Yang
FormationTechnologie
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Promiscuous patterns and perils in PubChem and the MLSCN Jeremy J Yang Cristian Bologa Tudor Oprea Division of Biocomputing Dept of Biochem. & Mol. Biology NM Mol. Libraries Screening Center University of New Mexico
Goals ,[object Object],[object Object],[object Object],[object Object]
Background ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],10 6 10 0
Promiscuity defined ,[object Object],[object Object],[object Object],[object Object],Bioactivity for multiple targets, i.e. “frequent-hitter”, non-selective binder Multi-target bioactivity for involved scaffold Scaffold may be a determinant or simply an informatic device. Scaffold promiscuity [working definition]
Real vs phony promiscuity ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
PubChem: cathedral or bazaar? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],(a) National Cathedral, Washington, DC (b) Santa Fe Flea Market, Santa Fe, NM a b ref: “The Cathedral and the Bazaar”, Eric Raymond, 1997.
PubChem and MLSCN* ,[object Object],[object Object],[object Object],[object Object],*MLSCN = Molecular Libraries Screening Center Network, to be MLPCN, Molecular Libraries Program Center Network
PubChem and MLSMR ,[object Object],[object Object],[object Object],[object Object],Plot c/o Victor Panchenco, BioFocusDPI
MLSMR and MLSCN actives ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],94,148 104,078 93,616 104,610 532 10,462 (Some MLSCN compounds – esp secondary assays – from other sources such as commercial vendors.)‏ *June 2008
Selected published pre-filtering expert knowledge* ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],*generalizable domain knowledge
Selected pre-filtering semi-public expertise ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
MLSMR filtering protocols ,[object Object],[object Object],[object Object],[object Object],[object Object]
MLSMR re-filtered... ,[object Object],[object Object],[object Object],*search failed via PC GUI
MLSMR re-filtered... Example rejects:
Pre-filtering at UNM Java servlet using ChemAxon/JChem
Activity multiplicity – all assays compounds active in any assay peril? 103894 MLSCN compounds 724 MLSCN assays
Activity multiplicity – screening assays compounds active in any screening assay peril 89954 MLSCN compounds 268 MLSCN assays
Top 100 hier-scaffolds*, active PubChem MLSMR Example scaffold #1 *Wilkins, J. Med Chem 2005
Top active hier-scaffolds: example #1 Scaffold: 33 rd most common 510 active compounds 34 assays c1c2c([nH]c(=O)cn2)ncn1 Top 12 compounds Top 12 of 510 compounds CID, #assays active
Top active hier-scaffolds: example #1 #compounds vs #assays in which they are active
Top active hier-scaffolds: example #1 All from NCGC
Other promiscuous scaffolds COMPOUNDS:total/tested/active ASSAYS:tested/active SAMPLES:tested/active
Other promiscuous scaffolds COMPOUNDS:total/tested/active ASSAYS:tested/active SAMPLES:tested/active
Other promiscuous scaffolds COMPOUNDS:total/tested/active ASSAYS:tested/active SAMPLES:tested/active
Activity mining with PubChem GUI Lots of great functionality, but not everything...
Activity mining with command line Automation is good...
Example scaffold #2 62 nd most common 523 active compounds 208 assays c1ccc(cc1)NC(=O)c2ccco2 Top active hier-scaffolds: example #2 Top 12 of 523 compounds CID, #assays active
Top active hier-scaffolds: example #2 #compounds vs #assays in which they are active
Top active hier-scaffolds: example #2 #compounds vs #assays in which they are active
Top active hier-scaffolds: example #3 Example scaffold #4 1307 th most common 27 active compounds 140 assays c1nc-2c(=O)[nH]c(=O)nc2[nH]n1 toxoflavin
Top active hier-scaffolds: example #3 #compounds vs #assays in which they are active
Digression: PubChem bug... substructure search for CID 66541 143 hits substructure search for C2(C1=NC=NNC1=NC(N2)=O)=O 143 hits substructure search for c1nc-2c(=O)[nH]c(=O)nc2[nH]n1 0 hits Ergo: aromatic structural queries not allowed?
Top active hier-scaffolds: example #3
More example scaffolds and histograms of #compounds vs. #assays in which compounds are active
Scaffold promiscuity vs. SEA* ,[object Object],SEA (Similarity Ensemble Approach): For given query molecule, are there bioactive similars and for what targets? *Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotech 25 (2), 197-206 (2007). http://shoichetlab.compbio.ucsf.edu/~keiser/sea/
Possibilities ,[object Object],[object Object],[object Object],[object Object],[object Object]
Possibilities ,[object Object],*"Is There a General Model for Bioactivity?", T.I. Oprea, O. Ursu, C.G. Bologa, and L.A. Sklar, The 8th International Conference on Chemical Structures, June, 2008, Noordwijkerhout, The Netherlands (http://www.int-conf-chem-structures.org/pdf/B-6.pdf).
Data mining methodology notes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],PUG = NCBI PubChem Power User Gateway (http)‏ Entrez = NCBI Entrez eUtils API OE = OpenEye OEChem All code Perl or Python *June 2008
Now for some general comments... 10 6 10 0
Probability – in HTS game etc. In other words: Quantity vs. Quality E not striking out = 1 – E striking out E success = 1 – (1 - E hit ) N where E hit = probability of hit per try N = number of tries
Probability, more hard lessons *&quot;Method and Apparatus for Designing Molecules with Desired Properties by Evolving Successive Populations,&quot; David Weininger, U.S. patent US5434796, 1995. De novo molecular design Case study: Grok and Grope*, 1992, Weininger, Blaney, Dixon GA -> virtual library, docking fitness, lots of cpu cycles But you need to recognize a good hit, including all aspects of fitness (ADMET, synthesis, etc.). <- approximation from memory ,[object Object],[object Object],[object Object]
Probability, more quantity vs quality “ Quantitative high-throughput screening: A titration-based approach that efficiently identifies biological activities in large chemical libraries”, Inglese et al., PNAS, 103, 2006, 11473-11478.
Probability and prejudice Lucky CEOs, coaches, and fund managers, Kahneman's 2002 Nobel prize for economics-psychology, good stories vs. Occam's razor, confirmation bias, pathological pattern-recognizers are we.
Statistics and signficance “ The Trouble with QSAR (or How I Learned To Stop Worrying and Embrace Fallacy)”, Stephen R. Johnson, J. Chem. Inf. Model., 48 (1), 25 -26, 2008.
Conclusions ,[object Object],[object Object],[object Object]
Conclusions ,[object Object],[object Object],[object Object]
Conclusions (from Chris Lipinski*)‏ ,[object Object],[object Object],[object Object],[object Object],*Chris Lipinski, Nanosyn Open House talk, Feb 16, 2008.
Acknowledgements, thanks ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],OpenEye Software c/o: ,[object Object]
Scaffolds and chemotypes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],*Ertl, et al., Quest for the Rings
HierScaffolds: - scaffolds are one or several rings connected by linkers - compounds can be related by any of their scaffolds

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Promiscuous patterns and perils in PubChem and the MLSCN

  • 1. Promiscuous patterns and perils in PubChem and the MLSCN Jeremy J Yang Cristian Bologa Tudor Oprea Division of Biocomputing Dept of Biochem. & Mol. Biology NM Mol. Libraries Screening Center University of New Mexico
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  • 15. Pre-filtering at UNM Java servlet using ChemAxon/JChem
  • 16. Activity multiplicity – all assays compounds active in any assay peril? 103894 MLSCN compounds 724 MLSCN assays
  • 17. Activity multiplicity – screening assays compounds active in any screening assay peril 89954 MLSCN compounds 268 MLSCN assays
  • 18. Top 100 hier-scaffolds*, active PubChem MLSMR Example scaffold #1 *Wilkins, J. Med Chem 2005
  • 19. Top active hier-scaffolds: example #1 Scaffold: 33 rd most common 510 active compounds 34 assays c1c2c([nH]c(=O)cn2)ncn1 Top 12 compounds Top 12 of 510 compounds CID, #assays active
  • 20. Top active hier-scaffolds: example #1 #compounds vs #assays in which they are active
  • 21. Top active hier-scaffolds: example #1 All from NCGC
  • 22. Other promiscuous scaffolds COMPOUNDS:total/tested/active ASSAYS:tested/active SAMPLES:tested/active
  • 23. Other promiscuous scaffolds COMPOUNDS:total/tested/active ASSAYS:tested/active SAMPLES:tested/active
  • 24. Other promiscuous scaffolds COMPOUNDS:total/tested/active ASSAYS:tested/active SAMPLES:tested/active
  • 25. Activity mining with PubChem GUI Lots of great functionality, but not everything...
  • 26. Activity mining with command line Automation is good...
  • 27. Example scaffold #2 62 nd most common 523 active compounds 208 assays c1ccc(cc1)NC(=O)c2ccco2 Top active hier-scaffolds: example #2 Top 12 of 523 compounds CID, #assays active
  • 28. Top active hier-scaffolds: example #2 #compounds vs #assays in which they are active
  • 29. Top active hier-scaffolds: example #2 #compounds vs #assays in which they are active
  • 30. Top active hier-scaffolds: example #3 Example scaffold #4 1307 th most common 27 active compounds 140 assays c1nc-2c(=O)[nH]c(=O)nc2[nH]n1 toxoflavin
  • 31. Top active hier-scaffolds: example #3 #compounds vs #assays in which they are active
  • 32. Digression: PubChem bug... substructure search for CID 66541 143 hits substructure search for C2(C1=NC=NNC1=NC(N2)=O)=O 143 hits substructure search for c1nc-2c(=O)[nH]c(=O)nc2[nH]n1 0 hits Ergo: aromatic structural queries not allowed?
  • 34. More example scaffolds and histograms of #compounds vs. #assays in which compounds are active
  • 35.
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  • 37.
  • 38.
  • 39. Now for some general comments... 10 6 10 0
  • 40. Probability – in HTS game etc. In other words: Quantity vs. Quality E not striking out = 1 – E striking out E success = 1 – (1 - E hit ) N where E hit = probability of hit per try N = number of tries
  • 41.
  • 42. Probability, more quantity vs quality “ Quantitative high-throughput screening: A titration-based approach that efficiently identifies biological activities in large chemical libraries”, Inglese et al., PNAS, 103, 2006, 11473-11478.
  • 43. Probability and prejudice Lucky CEOs, coaches, and fund managers, Kahneman's 2002 Nobel prize for economics-psychology, good stories vs. Occam's razor, confirmation bias, pathological pattern-recognizers are we.
  • 44. Statistics and signficance “ The Trouble with QSAR (or How I Learned To Stop Worrying and Embrace Fallacy)”, Stephen R. Johnson, J. Chem. Inf. Model., 48 (1), 25 -26, 2008.
  • 45.
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  • 50. HierScaffolds: - scaffolds are one or several rings connected by linkers - compounds can be related by any of their scaffolds