Brian Feng Johannes Hermann. NIH Sarah Boyce Andrea McReynolds Patsy Babbitt/S. Brown Kristin Coan Niu Huang Mike Keiser Jerome Hert
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1 Brian Feng Johannes Hermann Bryan Roth Alan Graves Yu Chen Paul Ensberger NIH Veena Thomas Kerim Babaoglu Frank Raushel Sarah Boyce Andrea McReynolds Patsy Babbitt/S. Brown Kristin Coan Niu Huang Mike Keiser Jerome Hert
2 What is the information content of a molecule? DHFR GART TS
3 A curious pharmacological fact Similar ligands can recognize dissimilar proteins: Antifolates GPCR Dihydrofolate reductase Thymidylate synthetase Glycinamide ribonucleotide formyltransferase Opioids (Methadone) μ receptor (GPCR) NMDA receptor (Ion Channel) Serotonin and serotonergics 5-HT 1-2,4-7 receptors (GPCR) Ion Channel 5-HT 3 receptor (Ion Channel) How are targets related when judged by their ligands?
4 Hundreds of Ligand Sets Annotated by Target compare sets by calculating all pair-wise similarities DHFR TS Encode each molecule by bitstring fingerprints (e.g., Daylight) Score pair-wise similarity by Tanimoto coefficients Compare all pairs between in each set Σ = raw set score
5 Comparing sets to thymidylate synthase ligands TS DHFR Thrombin Raw Score Mike Keiser
6 Calculating score significance: Z-scores and expectation values (a la BLAST) Standard deviations Raw score means Extreme value distribution Expectation values Product of set sizes Mike Keiser
7 For any ligand set, which other is most similar? Query Rank Size Similar Activity Classes E-value # identical Max Tc 1 50 Androgen 0* Aromatase Inhibitor Antiglucocorticoid Cytochrom P450 Inhibitor Estrogen Antiestrogen α-Steroid reductase inhibitor Antiandrogen Androgen 5 HT1F Agonist β1 Adrenergic Agonist α-hydroxylase Inhibitor HT1F Agonist HT1D Agonist HT1B Agonist HT1 Agonist Dopamine (D4) Antagonist HT1A Antagonist Adrenergic (beta1) Agonist Adrenergic (beta) Agonist Adrenergic (beta1) Blocker Adrenoceptor (beta3) Agonist Adrenergic (beta) Blocker Adrenergic, Ophthalmic Adrenergic (alpha1) Blocker
8 Mapping all sets (threshold graph, E-value < 1) Most ligand sets unrelated Related ligand sets form archipelagos Archipelagos biologically sensible. Phosphodiesterases Antifolates Beta-Lactam Antibiotics 5-HT 1 & 2 5-HT 3 & 4 Node Annotated ligand set (e.g., TS inhibitor) Edge A comparison between two sets Mike Keiser
9 Anything unexpected? Testable? Size Activity Class E-value Max TC Antimuscarinic Muscarinic M3 Antagonist Opioid Agonist NMDA Receptor Antagonist Muscarinic (M1) Agonist Cyclooxygenase Inhibitor Antihistaminic O O N + Mike Keiser, Mark Van Zostrow
10 Methadone is a 1μM M3 antagonist Radioligand displacement from M3 receptors by methadone Response to carbachol agonist in the presence of methadone (Ca++ mobilization) Bryan Roth, Paul Ensberger
11 Anything unexpected? Testable? Screen PubChem compounds for similarities to MDDR classes Off-target predictions for Emetine & loperamide (and 28 others) Query Rank Size Activity Class E-value Max TC Emetine Adrenergic (α2) Blocker Dipeptidyl Aminopeptidase IV Inhibitor Dopamine (D1) Antagonist Substance P Antagonist Dopamine (D3) Antagonist Neurokinin NK3 Antagonist Loperamide Neurokinin NK2 Antagonist Substance P Antagonist Neurokinin NK3 Antagonist Adrenergic (α1) Blocker Protein Kinase C Inhibitor Muscarinic M3 Antagonist Mike Keiser
12 Testing off-target predictions for loperamide & emetine Loperamide antagonizes NK2 receptors (Kd ~ 1uM) Keiser et al., Nat. Biotech, 2007 Emetine antagonizes α2 adrenergic receptors (Kd ~0.5 um) Bryan Roth, Blaine Armbruster
13 SEA is sea.docking.org
14 Relating targets via ligand chemistry Sets of ligands may be compared A model of random background leads to quantitative expectation values Most targets unrelated by ligand set Those that are form archipelagos Archipelagos biologically sensible. New links articulated through the agents used to test biological events drugs & reagents
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