Virtual screening for drug discovery. Markus Lill Purdue University

Transcription

1 Virtual screening for drug discovery Markus Lill Purdue University

2 Lecture material

3 I.1 Drug discovery Cl N Disease

4 I.1 Drug discovery Discovery (3-5 years) Target Discovery Assay Development Screening it to Lead

5 I.1 Drug discovery Start compounds A hit is a compound with robust activity in a primary screen against macromolecular target. A lead is a representative of a compound series with sufficient potential (as measured by potency, selectivity, pharmacokinetics, physicochemical properties, absence of toxicity and novelty) to progress to a full drug development program. 1 drug molecule

6 I.1 Drug discovery Discovery (3-5 years) Development (5-10 years) Launch Target Discovery Assay Screening it to Lead Lead Studies Clinical Studies Development ptimization Preclinical Registration Market

7 I.2 Rational drug design Emil Fischer (1894): Lock & Key principle Ligand Receptor Progesterone

8 I.2 Rational drug design Daniel Koshland (1958): Induced-fit theory Ligand Receptor Progesterone (K i = 3.5 nm) (R,S)-5-(3-Chlorophenyl)-1,2- dihydro-2,2,4-trimethyl- 5-chromeno[3,4-f]quinoline (K i = 0.43 nm) N Cl

9 I.2 Rational drug design dihedrals ijkl ijkl d ijkl angles ijk ijk a ijk bonds ij ij b ij j i j i ij ij ij ij ij j i N n k k r r k r B r A r q q cos 1 4 ),, V( r r

10 I.2 Rational drug design Structure-based drug design (direct design) Structure of macromolecular target is used Molecular complementarity: ptimal match of 3D recognition elements optimal activity Ligand-based drug design (indirect design) Structure of macromolecular target not available or not used Molecular similarity: similar structure similar activity dissimilar structure dissimilar activity Cl 24nM Cl 30nM??? N 65nM

11 I.3 Protein-ligand interactions Complementarity between protein and ligand: steric (size and topology) physico-chemical properties

12 I.3 Protein-ligand interactions Complementarity between protein and ligand steric (size and topology) Streptavidin with bound biotin (pdb-code: 1mk5) Lecture2_1.pse

13 I.3.1 Steric complementarity Why is steric complementarity relevant for strong protein-ligand interactions: van der Waals/London dispersive forces: Electron density fluctuation in molecular orbits results in temporarily formed dipole. _ + Electron repulsio This dipole induces dipole moment in nearby atoms. _ + _ + Dispersion The dipole moments favorably interact. V ( r) A r 12 B 6 r

14 I.3.1 Steric complementarity Why is steric complementarity relevant for strong protein-ligand interactions: ligand size to large (at least partially) energy cost of induced protein fit (if possible at all) other interactions (i.e. hydrogen-bond interactions, electrostatic interactions, polarization) are stronger between spatially close atoms (see following slides)

15 I.3 Protein-ligand interactions Complementarity between protein and ligand steric electrostatic (size and topology) charged groups polar groups _ F + _ N _ formal charge partial charge

16 I.3.2 Electrostatic interactions Electronegativity: The power of an atom in a molecule to attract electrons to itself. (Linus Pauling) 2.20 C 2.55 N 3.04 P S 2.58 F 3.98 Cl 3.16 Br 2.96 I _ + + F _ The larger the difference in electronegativity, the more polar is the bond. The atom having the higher electronegativity is the negative end of the dipole.

17 I.3.2 Electrostatic interactions Electrostatic interactions are long ranging V r V ( r) q 4πε 0 r + + Partial charges are almost alternating in sign

18 I.3.3 ydrogen bonding Characteristics: 1. Strong electrostatic dipole-dipole interactions 2. Also, covalent bonding features: Interatomic distances shorter than sum of van der Waals radii Strength of hydrogen bond shortness the Y distance Directionality ( Selectivity) Strength of hydrogen bond linearity of the X Y angle X LP Y LP 120 < < 180 linearity of the Y-LP angle < 45 Limited number of interaction partners Strength of hydrogen bond amount of electronic charge transferred

19 I.3.3 ydrogen bonding For organic molecules: Significant strength of hydrogen-bond between a hydrogen atom attached to an electronegative atom and an electronegative atom. Usually the electronegative atom is or N (S) Strength (neutral hydrogen bond): 4-5 kcal/mol Compare with: Covalent: ~ kcal/mol Van der Waals attraction: ~ kcal/mol

20 I.3.3 ydrogen bonding ptimal length of hydrogen bond Distance between heavy atoms [Å]: Donor - N- S- Acceptor ~ 2.7 ~ 2.9 ~ 3.4 N ~ 2.8 ~ 3.0 ~ 3.5 S ~ 3.5 ~ 3.7 ~ 4.3

21 I.3.3 ydrogen bonding Amino acids with hydrogen-bonding character: + 2 N N 2 N Arg [R] N 2 N Gln [Q] N N Ser [S] _ R N 2 N Asn [N] Glu [E] N N N Thr [T] N _ N Asp [D] + N 3 N N is [] N N Trp [W] Lys [K] N S N Cys [C] S Met [M] N Tyr [Y] N

22 I.3.3 ydrogen bonding Lecture3_1.pse ydrogen bonding plays an important role in determining the three-dimensional structures of proteins (e.g. -helix, -sheet), DNA and is critical for ligand binding to proteins (selectivity). Lecture3_2.pse -helix CDK2 kinase: Lecture3_3.pse -sheet

23 I.3.3 ydrogen bonding Example for favorable hydrogen bond: Estrogen receptor 17-estradiol 3-deoxyestradiol IC 50 = 0.9nM IC 50 = 180nM Lecture3_6.pse

24 I Interactions Three favorable benzene-benzene conformations can be identified as representative for - interactions: sandwich parallel displaced edge-to-face VdW ++, el.st. - VdW +, el.st. + VdW -, el.st. ++ overall: -2 kcal/mol overall: -3 kcal/mol overall: -3 kcal/mol ~4Å ~3.5Å ~1.7Å ~5Å

25 I Interactions - interactions can significantly contribute to protein-ligand interactions, but can also stabilize ligand s (or protein s) conformation. Example: Scytalone Dehydratase Protein-ligand interactions Ligand-ligand interactions Lecture3_10.pse

26 I.3.5 Cation- interactions Strong interaction between the electron-rich orbitals of an aromatic ring with adjacent cation (energetically equivalent to a hydrogen bond). Example: Acetylcholine binding to acetylcholinesterase + Lecture3_11.pse

27 ydrogen-bond interactions: I.3 Literature. Kubinyi ydrogen Bonding, the Last Mystery in Drug Design? in: Pharmacokinetic ptimization in Drug Research. Biological, Physicochemical, and Computational Strategies, B. Testa,. van de Waterbeemd, G. Folkers and R. Guy, Eds., elvetica Chimica Acta and Wiley-VC, Zürich, 2001, pp P. Murray-Rust, J.P. Glusker (1984) Directional hydrogen bonding to sp2- and sp3-hybridized oxygen atoms and its relevance to ligand-macromolecule interactions, J. Am. Chem. Soc. 106, interactions: C.A. unter (1993) "Aromatic Interactions in Proteins, DNA and Synthetic Receptors Phil. Trans. R. Soc. Lond. A 345, Cation- interactions: N. Zacharias, D.A. Dougherty (2002) "Cation-π interactions in ligand recognition and catalysis", TIPS, 23,

28 Protein-ligand interactions Types of interactions between protein and ligand - cation- steric/ van der Waals N N hydrogen bond electrostatic salt bridge

29 Protein-ligand interactions Dissociation constant for reaction A x B y xa + yb K d = A x B y A x B y

30 Protein-ligand interactions Conversion: K d G exp kbt k B T [300K] = kcal/mol G [kcal/mol] K i pm nm µm mm

31 Protein-ligand interactions Crude (and wrong) estimates of binding affinity: ydrogen bonds only 5 hydrogen bonds kcal/mol (if optimal geometry) nm nm Purine nucleoside phosphorylase: Lecture2_8.pse Simulation (minimized structure) E -Bond = kcal/mol E el.st. = kcal/mol E VdW = kcal/mol Measured: 11μM E ges = kcal/mol nm

32 Protein-ligand interactions Internal energy, protein Internal energy, ligand (difference in conformational energy: protein solvent) N N Desolvation energy, protein Desolvation energy, ligand Direct proteinligand interactions (-Bond, el.stat., VdW, ) Water-water interactions

33 Entropy (Gibbs) free energy of binding G G = TS (Energy-entropy compensation) Enthalpy In absence of external work: = U + pv, Entropy Measure of the extent of conformational space (x) accessible to the molecular system at a given temperature T Where U: internal energy (change in covalent and direct nonbonded interactions) pv: mechanical work

34 Entropy Entropy: Measure of the extent of conformational space (x) accessible to the molecular system at a given temperature T Lecture2_9.gif S t Lecture2_10.gif

35 Protein-ligand interactions Internal energy, protein Entropy, water (ligand solvent) Entropy, ligand (protein solvent) Internal energy, ligand (difference in conformational energy: protein solvent) N N Desolvation energy, protein Desolvation energy, ligand Direct proteinligand interactions (-Bond, el.stat., VdW, ) Entropy, protein (ligand solvent) Water-water interactions

36 ydrophobic effect ydrophobicity (attic greek: hydro = water; phobos = fear) is the physical property of a compound that is repelled from polar medium (e.g. water). ydrophobic molecules tend to be non-polar and prefer to bind to other hydrophobic compounds. Interaction: favorable N N N Interaction: depends on geometry and environment

37 ydrophobic effect Interaction: favorable Reasons: Entropy driven hydrophobic effect: Water molecules do not form hydrogen bonds with non-polar compounds stronger ordering of water molecules at the interface of the compound (due to fewer accessible hydrogen-bond partners lower entropy when ligand binds to hydrophobic binding pocket gain in entropy Enthalpy driven hydrophobic effect: ydrophobic binding pockets are not necessarily optimally hydrated (because water molecules cannot form favorable -bond interactions) favorable ligand-protein dispersion interactions are not negatively compensated by protein-water interactions

38 ydrophobicity Measure for hydrophobicity: partition coefficient logp is the ratio of concentrations of un-ionized compound between the water and octanol solution. log P log A A octanol water 0 0 A is A is hydrophobic hydrophilic logp > 0 logp < 0 Water ctanol Water ctanol

39 ydrophobicity log P values are approximately additive A molecule can be broken down into fragments with known hydrophobicity: logp logp i π i Example: log P(toluene) = log P(benzene) + (methyl) fragment i fragment i C (exp.: 2.7) values can be deduced by subtraction of appropriate log P values, e.g. (C) = log P(RC) - log P(R) More sophisticated computational log P calculations also take into account the extent of branching on alkyl groups, connectivity, etc. Computationally calculated logp values are called clogp.