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Finding Ligand Binding Sites on a Proteome-wide Scale and its Implications

Finding Ligand Binding Sites on a Proteome-wide Scale and its Implications. Philip E. Bourne University of California San Diego pbourne@ucsd.edu http://www.sdsc.edu/pb/Talks/. HUPO San Diego Feb. 2009. The truth is we know very little about how the major drugs we take work

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Finding Ligand Binding Sites on a Proteome-wide Scale and its Implications

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  1. Finding Ligand Binding Sites on a Proteome-wide Scale and its Implications Philip E. Bourne University of California San Diego pbourne@ucsd.edu http://www.sdsc.edu/pb/Talks/ HUPO San Diego Feb. 2009

  2. The truth is we know very little about how the major drugs we take work We know even less about what side effects they might have Drug discovery seems to be approached in a very consistent and conventional way The cost of bringing a drug to market is huge ~$800M The cost of failure is even higher e.g. Vioxx - $4.85Bn Motivation

  3. The truth is we know very little about how the major drugs we take work – receptors are unknown We know even less about what side effects they might have - receptors are unknown Drug discovery seems to be approached in a very consistent and conventional way The cost of bringing a drug to market is huge ~$800M – drug reuse is a big business The cost of failure is even higher e.g. Vioxx - $4.85Bn - fail early and cheaply Motivation

  4. What if… • We can characterize a protein-ligand binding site from a 3D structure (primary site) and search for that site on a proteome wide scale? • We could perhaps find alternative binding sites (off-targets) for existing pharmaceuticals and NCEs? • We could use it for lead optimization and possible ADME/Tox prediction

  5. What Do Off-targets Tell Us? One of three things: Nothing A possible explanation for a side-effect of a drug A possible repositioning of a drug to treat a completely different condition Today I will give you examples of both 2 and 3 and illustrate the complexity of the problem

  6. Agenda Computational Methodology Side Effects - The Tamoxifen Story Repositioning an Existing Drug - The TB Story Salvaging $800M – The Torcetrapib Story

  7. Need to Start with a 3D Drug-Receptor Complex - The PDB Contains Many Examples

  8. A Reverse Engineering Approach to Drug Discovery Across Gene Families Characterize ligand binding site of primary target (Geometric Potential) Identify off-targets by ligand binding site similarity (Sequence order independent profile-profile alignment) Extract known drugs or inhibitors of the primary and/or off-targets Search for similar small molecules … Dock molecules to both primary and off-targets Statistics analysis of docking score correlations Computational Methodology

  9. Characterization of the Ligand Binding Site - The Geometric Potential • Conceptually similar to hydrophobicity or electrostatic potential that is dependant on both global and local environments • Initially assign Ca atom with a value that is the distance to the environmental boundary • Update the value with those of surrounding Ca atoms dependent on distances and orientation – atoms within a 10A radius define i Computational Methodology Xie and Bourne 2007 BMC Bioinformatics, 8(Suppl 4):S9

  10. Discrimination Power of the Geometric Potential • Geometric potential can distinguish binding and non-binding sites 100 0 Geometric Potential Scale Computational Methodology Xie and Bourne 2007 BMC Bioinformatics, 8(Suppl 4):S9

  11. Local Sequence-order Independent Alignment with Maximum-Weight Sub-Graph Algorithm Structure A Structure B L E R V K D L L E R V K D L • Build an associated graph from the graph representations of two structures being compared. Each of the nodes is assigned with a weight from the similarity matrix • The maximum-weight clique corresponds to the optimum alignment of the two structures Xie and Bourne 2008 PNAS, 105(14) 5441

  12. Nothing in Biology {including Drug Discovery} Makes Sense Except in the Light of Evolution Theodosius Dobzhansky (1900-1975)

  13. Similarity Matrix of Alignment • Chemical Similarity • Amino acid grouping: (LVIMC), (AGSTP), (FYW), and (EDNQKRH) • Amino acid chemical similarity matrix • Evolutionary Correlation • Amino acid substitution matrix such as BLOSUM45 • Similarity score between two sequence profiles fa, fb are the 20 amino acid target frequencies of profile a and b, respectively Sa, Sb are the PSSM of profile a and b, respectively Xie and Bourne 2008 PNAS, 105(14) 5441 Computational Methodology

  14. Agenda Computational Methodology Repositioning an Existing Drug - The TB Story Side Effects - The Tamoxifen Story Salvaging $800M – The Torcetrapib Story

  15. Found.. Evolutionary linkage between: NAD-binding Rossmann fold S-adenosylmethionine (SAM)-binding domain of SAM-dependent methyltransferases Catechol-O-methyl transferase (COMT) is SAM-dependent methyltransferase Entacapone and tolcapone are used as COMT inhibitors in Parkinson’s disease treatment Hypothesis: Further investigation of NAD-binding proteins may uncover a potential new drug target for entacapone and tolcapone Repositioning an Existing Drug - The TB Story Repositioning an Existing Drug - The TB Story

  16. Functional Site Similarity between COMT and ENR Entacapone and tolcapone docked onto 215 NAD-binding proteins from different species M.tuberculosisEnoyl-acyl carrier protein reductaseENR (InhA) discovered as potential new drug target ENR is the primary target of many existing anti-TB drugs but all are very toxic ENR catalyses the final, rate-determining step in the fatty acid elongation cycle Alignment of the COMT and ENR binding sites revealed similarities ... Repositioning an Existing Drug - The TB Story

  17. Summary of the TB Story Entacapone and tolcapone shown to have potential for repositioning Direct mechanism of action avoids M. tuberculosis resistance mechanisms Possess excellent safety profiles with few side effects – already on the market In vivo support Assay of direct binding of entacapone and tolcapone to ENR reveals promising leads with no chemical relationship to existing drugs Repositioning an Existing Drug - The TB Story PLoS Comp Biol Under Review

  18. Agenda Computational Methodology Repositioning an Existing Drug - The TB Story Side Effects - The Tamoxifen Story Salvaging $800M – The Torcetrapib Story

  19. Selective Estrogen Receptor Modulators (SERM) • One of the largest classes of drugs • Breast cancer, osteoporosis, birth control etc. • Amine and benzine moiety Side Effects - The Tamoxifen Story PLoS Comp. Biol., 2007 3(11) e217

  20. Adverse Effects of SERMs cardiac abnormalities loss of calcium homeostatis thromboembolic disorders ????? ocular toxicities Side Effects - The Tamoxifen Story PLoS Comp. Biol., 3(11) e217

  21. Structure and Function of SERCASacroplasmic Reticulum (SR) Ca2+ ion channel ATPase • Regulating cytosolic calcium levels in cardiac and skeletal muscle • Cytosolic and transmembrane domains • Predicted SERM binding site locates in the TM, inhibiting Ca2+ uptake Side Effects - The Tamoxifen Story PLoS Comp. Biol., 3(11) e217

  22. The Challenge • Design modified SERMs that bind as strongly to estrogen receptors but do not have strong binding to SERCA, yet maintain other characteristics of the activity profile Side Effects - The Tamoxifen Story PLoS Comp. Biol., 3(11) e217

  23. Agenda Computational Methodology Repositioning an Existing Drug - The TB Story Side Effects - The Tamoxifen Story Salvaging $800M – The Torcetrapib Story

  24. The Torcetrapib Story PLoS Comp Biol Under Minor Revision

  25. Cholesteryl Ester Transfer Protein (CETP) collects triglycerides from very low density or low density lipoproteins (VLDL or LDL) and exchanges them for cholesteryl esters from high density lipoproteins (and vice versa) A long tunnel with two major binding sites. Docking studies suggest that it possible that torcetrapib binds to both of them. The torcetrapib binding site is unknown. Docking studies show that both sites can bind to torcetrapib with the docking score around -8.0. CETP inhibitor X CETP LDL HDL Bad Cholesterol Good Cholesterol The Torcetrapib Story PLoS Comp Biol Under Minor Revision

  26. JTT705 Torcetrapib Anacetrapib JTT705 VDR – RXR FA + RAS FABP ? PPARα PPARδ ? ? PPARγ High blood pressure + JNK/IKK pathway JNK/NF-KB pathway Anti-inflammatory function Immune response to infection PLoS Comp Biol Under Minor Revision

  27. Summary • We have established a protocol to look for off-targets for existing therapeutics and NCEs • Understanding these in the context of pathways would seem to be the next step towards a new understanding • Lots of other opportunities to examine existing drugs

  28. Bioinformatics Final Examples.. • Donepezil for treating Alzheimer’s shows positive effects against other neurological disorders • Orlistat used to treat obesity has proven effective against certain cancer types • Ritonavir used to treat AIDS effective against TB • Nelfinavir used to treat AIDS effective against different types of cancers

  29. Acknowledgements Lei Xie Li Xie Jian Wang Sarah Kinnings

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