Protein Ligand Interactions Docking

Protein Ligand Interactions Docking Andrea Schafferhans December 2013

Similar proteins have similar interaction partners (?) 2

Evidence: Analysing target relationships Nodes: proteins Edges: similar binding (within factor 103) Paolini,G.V. et al. (2006) Global mapping of pharmacological space. Nature biotechnology, 24, 805-15. 3

Evidence (2): Analysing target relationships Paolini,G.V. et al. (2006) Global mapping of pharmacological space. Nature biotechnology, 24, 805-15. 4

Applications Function prediction Drug development Target Class approach Side effects Polypharmacology / Network pharmacology Hopkins,A.L. (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol, 4, 682-690. 5

Interactions with (small) molecules Protein (structure) recap Binding sites Physical chemistry recap Binding site analysis Docking 4. Protein-Ligand-Wechselwirkungen als Grundlage der Arzneisto Abb. 4.1 Wie e liegt das Vitam detasche seine Oberfläche des stellt. Vom Pro gebung der Bin besseren Über und hinter der des Proteins au Image Source: Wirkstoffdesign: Entwurf und Wirkung von Arzneistoffen by Gerhard Klebe lein mit seinem Bild von Schlüssel und Schloss einen solch großen Einfluss auf die Wirkstoffforschung ausgeübt hat! Emil Fischer wäre sicher glücklich und stolz gewesen, hätte er die Ergebnisse der Röntgenstrukturanalysen von Protein-Ligand-Komplexen sehen kön- Isomeres und chemisch verwa der 6 andere Proteine diskrimin Beispiele dafür sind die Ver schnitt 23.3), Enzyme für me gen, z. B. die Cytochrome (Ab

Protein structure Image Source: Wikipedia 7

Amino acids 8

Binding Site Image from : Waszkowycz B, Clark DE., Gancia E. Outstanding challenges in protein ligand docking WIREs Comput Mol Sci 2011, 1: 229-259 9

Binding site Interactions C44 C34 C35 C43 C45 T19 3(H) C33 Glu 217(H) C42 C36 C46 C32 O14 C41 O13 C31 C22 C15 C11 Ile 174(H) C23 C21 C13 N12 C10 3.28 C24 C26 C7C C9 N C7B Gly 219(H) N8 CA C7A C7 O OE2 O O1A Glu 192(H) OE1 N5 2.93 CA O6 Trp 215(H) N Glu 97A(H) B Gly 216(H) 3.20 O C4 C3 CB Asn 98(H) C 2.88 C 3.02 O1B CG O C C6 C CD C25 O9 2.71 C2 Ser 214(H) C1 CA CA OG OG N N N CB CB Trp 60D(H) Cys 191(H) CA Ser 195(H) C O Tyr 60A(H) His 57(H) Val 213(H) Image: Ligplot of thrombin complex 10

What is a binding site? Function Binding other proteins (e.g. signal transduction) Binding substrates (enzymes) Binding Co-Factors (e.g. Heme) Form Cavity in the protein CAVE: induced fit / conformational selection Pragmatic Around all HETATM records in PDB (CAVE: e.g. metals ) 11

Binding site characteristics Usually a pocket or cleft in the protein Less hydrophobic than the interior of a protein Specific through complementarity of Form Electrostatic interactions Hydrogen bonds Hydrophobic interactions Henrich S, Salo-Ahen OM, Huang B, et al.: Computational approaches to identifying and characterizing protein binding sites for ligand design. Journal of Molecular Recognition 2010, 23:209-219 12

Finding binding sites geometrically Observation: Binding sites usually are the largest pockets e.g. 83% of enzyme active sites found in the largest pocket (Laskowski RA, et al. Protein clefts in molecular recognition and function. Protein Sci. 1996; 5:2438-2452.) 13

POCKET Fill the protein with a grid (3 Å spacing) Mark grid points as protein (within 3 Å of an atom ) or solvent Go along grid and mark solvent points that lie between protein points for potential pocket Find largest clusters of pocket points Levitt D, Banaszak L. POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graph 1992, 10:229-234. 14

LIGSITE Differences to POCKET More efficient searching for neighbour atoms Cubic diagonals also used for finding pockets è less dependent on orientation Grid points scored by the number of times they are found (between 0 and 7) è adjustable buriedness Smaller and adjustable grid spacing (best: 0.5 to 0.75 Å) Hendlich M, et al.: LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Mod. 1997, 15:359-363 15

Finding binding sites energetically Binding sites interact with the bound molecules è Find location of favourable interaction energies 16

Chemical equilibrium Protein + Ligand Protein-Ligand-Complex Ligand ]! [ Protein ] [ Kd = [ P " L " Complex ]!G = RT ln K!G " 5.7 kj mol # lg K!G =!H " T!S 17

Strength of interactions Interactions in gas phase Molecules ΔG [kj/mol] CH 4 CH 4-2 C 2 H 6 C 2 H 6-10 H 2 O H 2 O -22 NH 3 NH 3-18 Na + H 2 O -90 NH + 4 CH 3 COO - <-400 Source: Wirkstoffdesign: Entwurf und Wirkung von Arzneistoffen by Gerhard Klebe 18

Coulomb Potential Image Source: Wikipedia 19

Lenard Jones Potential Image Source: Cambridge MedChem Consulting (http://bit.ly/v6efod) 20

Typical interactions Hydrogen bonds Ionic interactions / salt bridges Metal complexes Kation - π Image Source: Wikipedia 21

Protein-Ligand-Wechselwirkungen Contributions4.of one H bond als Grundlage der Arzneistoffwirkung H N O O F O NH2 HN O H N HN H O 4.1 HHNN F H Pro300 Leu300 O NN O 4.2 OO NH NH 7,8 kj/mol 6,9 kj/mol 0,9 kj/mol O HHNN H Pro300 Leu300 OO G: H: -T S: H NN OO NH NH OO G: H: -T S: -0,8 kj/mol 5,1 kj/mol -5,9 kj/mol Source: Wirkstoffdesign: Entwurf und Wirkung von Arzneistoffen by Gerhard Klebe zur NH-Funktion von L Abb.Image 4.9 Fidarestat 4.1 (links) bildet mit seiner Carboxamidgruppe eine Wasserstoffbrücke 22 Durch den Austausch von Leucin gegen Prolin (rot) kann die H-Brücke nicht mehr gebildet werden. Dies führt zu ei lust von 7,8 kj/mol, der im Wesentlichen durch einen enthalpischen Preis ( H: 6,9 kj/mol) bezahlt wird. Sorbinil fehlt die Carboxamidgruppe. Der Austausch Leucin Prolin lässt die freie Bindungsenthalpie G praktisch unve

verteilt. Bei der Aufnahme eines Liganden kann sich diese Verteilung ändern. Je nach der Gesamtbilanz kann dadurch die Entropie zunehmen oder abnehmen. Das Gleiche gilt für die Rotation von Seitenketten, hauptsächlich von Methylgruppen. Ändert sich deren Rotationsverhalten, so beeinflusst dies ebenfalls die Gesamtentropie des Ligandenbindungsvorgangs. Entropy Ligand in Lösung gebundene H2O-Moleküle - ------- Rezeptor -------- Naturgemäß taucht bei der Disk Ligand-Wechselwirkungen die Fra Beitrag einer bestimmten Wassers dungsaffinität nun tatsächlich ist. sich die Frage beantworten, wen gand-komplexe miteinander ver Ligand-Rezeptor Komplex --------- freie Rotation locker assoziierte H2O-Moleküle.............. im Lösungsmittel frei bewegliche H2O-Moleküle Image Source: Wirkstoffdesign: Entwurf und Wirkung von Arzneistoffen by Gerhard Klebe Abb. 4.7 Illustration thermodynamischer Beiträge zur freien Bindungsenthalpie G. Vor der Bindung kann wegen. Er verfügt über eine bestimmte Translations- und Rotationsentropie. Darüber23hinaus ist der Ligand nimmt unterschiedliche Konformationen ein. Protein und Ligand sind solvatisiert, wobei H-Brücken zu Wass gangen werden. Einige Wassermoleküle befinden sich in losem Kontakt mit dem Protein oder dem Ligande

Finding binding sites energetically Binding sites interact with the bound molecules è Find location of favourable interaction energies 24

GRID Calculates interaction energies of probe molecules Uses three terms: Lennard-Jones (attraction + repulsion) electrostatic directional hydrogen bond Goodford, P.J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1985 28:849-857 25

GRID application Cluster energy minima è binding site BUT: Hard to cluster Computationally intensive Good for visual binding site characterisation Picture from: Henrich S, Salo-Ahen OM, Huang B, et al. JMR 2010, 23:209-19. 26

Q-SiteFinder GRID methyl probe (0.9 Å grid) Cluster: adjacent grid points that meet energy criterion Success: > 70% first predicted binding site > 90% first three 68% average precision (precision: overlap between ligand and predicted binding site) Laurie AT, Jackson RM: Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005, 21:1908-16 27

i-site Variation of Q-Site: Better probe distribution (more dense grid) Two energy limits low value for cluster seeds higher value for extension è filtering out meaningful clusters AMBER force field Morita M, Nakamura S, Shimizu K: Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures. Proteins 2008, 73:468-479 28

Challenges in binding site identification Protein flexibility can hide binding sites Use multiple experimental conformations Use molecular dynamics to generate conformations Dimerisation has to be considered Carefully look at PDB unit cell Carefully look at information about the protein 29

Analysing protein ligand interactions Properties to search: Ionic interactions / salt bridges Hydrogen bonds Metal coordination Cation-Pi interactions Pi stacking Hydrophobic interactions Clashes http://www.chemcomp.com/journal/ ligintdia.htm 30

Characterising (empty) binding sites Properties to characterise: Geometry Amino acid composition Solvation Hydrophobicity Electrostatics Interactions with functional groups 31

Hydrophobicity Measured by logp (partitioning between water and octanol) Map atom / residue based contributions Calculate interaction energies of hydrophobic probes (e.g. GRID) 32

Electrostatics Map electrostatic potential onto surface (e.g. using DelPhi, see http://structure.usc.edu/ howto/delphi-surfacepymol.html) CAVE: dependence on protonation! 33

Functional groups Superstar Analyse the spatial distribution of functional groups in CSD è density maps Break the protein into fragments found in CSD Map the observed distribution of interaction partners onto the protein Verdonk ML, Cole JC, Taylor R: SuperStar: a knowledge-based approach for identifying interaction sites in proteins. Journal of molecular biology 1999, 289:1093-108. 34

Binding site comparison Align structures in 3D Analyse differences and similarities of Amino acid composition Local conformation Pocket size Presence of interaction partners Straightforward in case of Sequence similarity or Structural similarity 35

RELIBASE 36

RELIBASE Stores binding sites from PDB structures Allows superposition of related binding sites Computes differences between binding sites Hendlich M, Bergner A, Günther J, Klebe G: Relibase: Design and Development of a Database for Comprehensive Analysis of Protein-Ligand Interactions. Journal of Molecular Biology 2003, 326:607-620. http://relibase.ccdc.cam.ac.uk 37

Similar but not homologous binding sites camp-dependent protein kinase (1cdk) with adenyl-imido-triphosphate trypanothione reductase (1aog) with flavine-adenine-dinucleotide 38

Similar but not homologous binding sites Graphics from www.ebi.ac.uk/pdbsum/ 39

Similar but not homologous binding sites Graphics from Schmitt S, Kuhn D, Klebe G. Journal of molecular biology 2002, 323:387-406 40