Slide 1

Biology Oriented SynthesisA New Approach to Drug DesignRuoying Gong

Department of ChemistryMarch 12, 20091What Is A Drug?Drug is any substance used in the treatment, prevention, or diagnosis of disease

The earliest drugs were natural products

Currently, more drugs are synthesized or semi-synthesized

2Collins Essential English Dictionary 2nd Edition, HarperCollins Publishers, 20062Drug DiscoveryTrial and error testingRandom screening

Rational drug designStructural information of a drug receptorInformation of a ligand

3Twyman, R., The Human Genome, 2002Greer, J., et. al. J Med Chem. 1994, 37, 103510543Rational Drug Design Process4Genomics/ProteomicsPotential Ligand ClassCrystal StructureCloning/Protein ExpressionDomain Architecture PredictionBioinformaticsHigh Throughput ScreenBreinbauer, R., et. al. Angew. Chem. Int. Ed. 2002, 41, 2878 - 2890X-ray crystallographyNMR spectroscopyModelingDocking200,000 compound/week4Rational Drug Design Process5Potential Ligand ClassSynthesize Library of Similar CompoundsBreinbauer, R., et. al. Angew. Chem. Int. Ed. 2002, 41, 2878 - 2890HitsLeadDrugStructure-activity relationshipBioavailabilityFormulationBiological testsPharmacological testsClinical tests5Drawback of Rational Drug DesignTime consumingCostlyLimited understanding of drug receptorsLabour intensiveLow hit rate generated6 6New Approach to Drug DesignNovel approach Biology oriented synthesis

Created by Waldmann groupMax Planck Institute, Germany

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7Drug and Drug ReceptorKnowledge of 3D structure of protein can assist in the design of drug scaffold8

ProteinLigand binding siteCatalytic core8Protein Structure

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Petsko, G. A. et. Al. Protein Structure and Function New Science Press Ltd., 2004 9Similar 3D structure,function, andprimary structureProtein 1Protein 3Protein 2Protein Classification10Protein family10Proteins In the Same FamilySimilar mechanismSimilar primary structure Similar 3D structureSimilar amino acid residues11

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Process of Ligand Discovery12TargetProteinModel Protein

12Waldmann ApproachCompare proteins with their 3D structure

Use a natural inhibitor as guiding structure for compound library development

1313Protein Domain and FoldProtein DomainTertiary structure folded independently as functional units

Protein foldConformational arrangement of protein secondary structures into tertiary structure14Alberts, B. et. al. The Shape and Structure of Proteins. New York and London: Garland Science, 2002

14Protein Structure Architecture15Proteins(100,000 450,000)Domains(4,000 50,000)Folds(800 1,000)SCOP databank: Murzin, A. G., Brenner, S. E., J. Mol. Biol. 1995, 247, 536 - 54015Superfold and SupersiteSuperfold: highly populated folds

Supersite: common ligand binding sites within a superfold16Alberts, B. et. al. The Shape and Structure of Proteins. New York and London: Garland Science, 2002

16Classification Comparison Protein FamilySimilar primary structureSimilar ligand binding site Protein FoldNot related to primary structureSimilar ligand binding site17

17Biology Oriented SynthesisBiologyProtein Structure Similarity Clustering (PSSC)

ChemistryCompound library synthesized according to guiding structure of natural inhibitor 18Koch, M. A. et al Drug Discovery Today. 2005, 10, 471 - 48318Grouping Proteins TogetherProtein Structure Similarity Clustering (PSSC)3D similarity of ligand binding sites

Ignore the amino acid sequence identity

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19Computation Tools UsedStructural Classification of Proteins (SCOP)

Dali/Fold Classification Based on Structure-Structure Alignment of Proteins (FSSP) Database

Combinatorial Extension (CE) superimposition algorithm 2020Protein Clustering Process211Protein of Interest2Structural AlignmentDali/FSSP3Interesting casesSequence identity (SI) < 20%4Superimposition of Catalytic CoresRoot mean square deviation (RMSD) < 5Grishin, N.V., et al J. Struct. Biol. 2001, 134, 167 - 18521

1.Protein of Interest - Cdc25APhosphatase familyRhodanese foldCatalytic site contains Cys-430, Glu-431Regulates progression of cell divisionA potential antitumor drug target

22Koch, M. A., Wittenberg, L. O., et. al. PNAS 2004, 101, 16721 - 16726222.Structure Alignment23Cdc25AAChE11HSD1,223

3.Acetylcholinesterase (AChE)/-hydrogenase family/-hydrogenase foldCatalytic site contains Ser-200Terminate synaptic transmission Target protein in the treatment of myasthenia gravis, glaucoma, and Alzheimers disease24Koch, M. A., Wittenberg, L. O., et. al. PNAS 2004, 101, 16721 - 16726244.Superimposition

25Super-siteCdc25AAChEKoch, M. A., Wittenberg, L. O., et. al. PNAS 2004, 101, 16721 - 16726Cys-430 (Cdc25A)Ser-200 (AChE)252.Structure Alignment26Cdc25AAChE11HSD1,211HSD1,226

3. Isoenzymes 11HSD1,2Tyrosine-dependent oxidoreductase familyRossmann foldTyrosine residue located at catalytic site27Koch, M. A., Wittenberg, L. O., et. al. PNAS 2004, 101, 16721 - 167262711HSD1Reduces cortisone to the active hormone cortisolPotential target for treatment of obesity, the metabolic syndrome, and type 2 diabetes

28Koch, M. A., Wittenberg, L. O., et. al. PNAS 2004, 101, 16721 - 16726

2811HSD2Catalyzes the oxidation of cortisol into the inactive cortisoneInhibition causes sodium retention resulting in hypertension

29Koch, M. A., Wittenberg, L. O., et. al. PNAS 2004, 101, 16721 - 16726

.294.Superimposition

30Cdc25A11HSD111HSD2Super-siteKoch, M. A., Wittenberg, L. O., et. al. PNAS 2004, 101, 16721 - 16726Cys-430 (Cdc25A)Tyr-183 (11HSD1)Tyr-232 (11HSD2)

30Structure Alignment31Cdc25AAChE11HSD1,211HSD1,231Superimposition

32Cdc25A11HSD1AChESuper-siteKoch, M. A., Wittenberg, L. O., et. al. PNAS 2004, 101, 16721 - 16726Cys-430 (Cdc25A)Tyr-183 (11HSD1)Ser-200 (AChE)

32Cluster Member ComparisonCdc25AAChE11HSD1,2Protein familyPhosphatase/-hydrogenaseHydroxysteroiddehydrogenaseSequence identity-17%6%RMSD-2.64.933AChE11HSD1,2Sequence identity-6%RMSD-3.933Compound Library Discovery34

34Dysidiolide: Natural Inhibitor of Cdc25A35Dysidiolide, IC50=9.4MNatural inhibitor of Cdc25A

-hydroxybutenolideBrohm, D., et. al. Angew. Chem. Int. Ed. 2002, 41, 307 - 311 35Dysidiolide: Natural Inhibitor of Cdc25A36-hydroxybutenolideBrohm, D., et. al. Angew. Chem. Int. Ed. 2002, 41, 307 - 311

,-Unsaturated lactone

36Representative Synthesis37

37-Hydroxybutenolides Synthesis38

Koch, M. A., Wittenberg, L. O., et. al. PNAS 2004, 101, 16721 - 1672638,-Unsaturated Lactones Synthesis39

Koch, M. A., Wittenberg, L. O., et. al. PNAS 2004, 101, 16721 - 1672639Results147 compounds synthesized

Contains -hydroxybutenolide or ,-unsaturated lactone

Inhibitors with these structures have never been reported

40Cdc25AAChE11HSD111HSD2Hits (rate) 42(28.5%)3 (2%)3(2%)4(2%)40Best Compounds 41

Cdc25A, IC50=0.35MAChE, IC50>20M11HSD1, IC50=14M11HSD2, IC50=2.4M

Natural inhibitor of Cdc25ADysidiolide, IC50=9.4M

Cdc25A, IC50=45MAChE, IC50>20M11HSD1, IC50=10M11HSD2, IC50=95M

Cdc25A, IC50=1.8MAChE, IC50>20M11HSD1, IC50=19M11HSD2, IC50=11M

Cdc25A, IC50>100MAChE, IC50>20M11HSD1, IC50=19M11HSD2, IC50=5.3M

Koch, M. A., Wittenberg, L. O., et. al. PNAS 2004, 101, 16721 - 1672641Take Home MessagePSSC group proteins together regardless of primary structure identity

High hit rate achieved from small library sizeCompound library was designed to mimic the structure of natural products (NPs)4242Second ApproachStructure of NP dictates the way it binds to proteins

Structural classification of natural products (SCONP)

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Natural inhibitor of Cdc25ADysidiolide, IC50=9.4M43Structural Classification of Natural Products (SCONP)MethodChose compounds in the Dictionary of Natural Products containing ring structuresCreate scaffold map

Properties of SCONPStructural relationships between different NP classes

Tool for NP derived compound library development

4444Computational Simulation to Generate SCONPDeglycosylation prior to running simulation

Neglect stereochemistry

Reduce structural complexity of multi-ring systems

Choose heterocyclic substructures as parent scaffolds4545

46N-HeterocyclesO-HeterocyclesCarbocyclesScaffolds of Natural productsWaldmann, H., et. al. PNAS. 2005, 102, 17272-1727746Implications of SCONPParent scaffold represents a substructure of a respective offspring scaffold

Two to four-ring-containing NPs are the most common scaffolds

Scaffolds include the structural information of how NPs bind to proteins

474711HSD1Potential target for treatment of obesity, the metabolic syndrome, and type 2 diabetesInhibition of isoenzyme 11HSD2 causes sodium retention resulting in hypertension

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48Glycyrrhetinic Acid49

Glycyrrhetinic Acid (GA)Natural inhibitor of Cdc25A49Glycyrrhetinic Acid50

Glycyrrhetinic Acid (GA)Natural inhibitor of Cdc25A50Glycyrrhetinic Acid51

Glycyrrhetinic Acid (GA)Natural inhibitor of Cdc25A51

Scaffolds of Natural Products52Waldmann, H., et. al. PNAS. 2005, 102, 17272-17277Carbocycles52Scaffolds of Natural Products53Waldmann, H., et. al. PNAS. 2005, 102, 17272-17277

DysidiolideNatural inhibitor of Cdc25A

Glycyrrhetinic Acid (GA)Natural inhibitor of Cdc25A?53Compound Library Synthesis54Waldmann, H., et. al. PNAS. 2005, 102, 17272-17277

54Library General Structure55

Waldmann, H., et. al. PNAS. 2005, 102, 17272-1727755Results162 members synthesized with the simple bicycle ring scaffold

28 compounds selectively inhibit 11HSD1

Inhibitors with this bicycle ring scaffold have never been reported56

11HSD111HSD2Hits (rate)30(18.5%)3(2%)56Best Compounds57

11HSD1, IC50=0.31M11HSD2, IC50=6.6M

11HSD1, IC50=0.74M11HSD2, IC50>30M

11HSD1, IC50=0.35M11HSD2, IC50>30M

Waldmann, H., et. al. PNAS. 2005, 102, 17272-17277Glycyrrhetinic Acid (GA)Natural inhibitor of Cdc25A57Combined With PSSC and SCONP58PSSC

Natural inhibitor

BiologyOriented Synthesis(BIOS)

Compound LibraryBiologyChemistry

TargetNren-Mller, et. al. PNAS. 2006, 103, 10606-10611

58ConclusionPSSC classifies proteins together by 3D similarity of ligand binding siteSCONP is a guiding tool for NP derived compound library developmentSmall compound libraries synthesized generate high hit rates for proteins from different familiesThe chemical and biological approaches of BIOS were useful for the synthesis of drug-like compounds5959

AcknowledgementDr. Robert BenDr. Mathieu LeclereRoger TamJennifer ChaytorElisabeth von MoosPawel CzechuraJohn TrantWendy CampbellSandra FerreiraTaline BoghossianJackie Tokarew60