Receptor-Ligand Interactions
What is a Molecule?
Ĥ Ψ = EΨ
Ĥ is the Hamilton operator defining the operations that need to
be performed with the set of wave functions Ψ (psi) of the
electrons of a molecular system.
109.5°
(sp3)
120°
(sp2)
180°
(sp)
R1 CCN: 122°
H
N CNC: 116°
O R2 peptide
bond: planar
Darstellungen von Aspirin®
8 7 9
HO O
6 10 12
O 1 5 11
OH 2 4 13
3
Worum es geht, am Beispiel der „Aspirin-Story“
Salicin
(aus Weidenrinde, Entzündungshemmer)
Arachidonsäure
HO
COOH
O-β-D-glucopyranosid
COX
COX
COOH COOH
OH O O COOH
O O
OOH
Salicylsäure Acetylsalicylsäure
PGG2
(Aspirin®, Prodrug)
10.10.1897 Erstsynthese
durch Felix Hoffmann (Bayer)
Prostacyclin Thromboxan A2
• inhibiert COX-1 und COX-2 (1991 entdeckt) Pharmakologischer Effekt
Strukturbasierter Entwurf von Wirkstoffen
Ser530
• Molecular Surface
• Solvent Accessible Surface (SAS, Conolly, 1985)
• Solvent Excluded Volume
Solvent-accessible surface
(SAS, molecular surface)
vdW surface
Probe
sphere
Lee-Richards
surface
Wechselwirkungspartner
• Protein + Wirkstoffmolekül
• Protein + Protein
• RNA + Protein
• DNA + Protein
• RNA + Wirkstoffmolekül
• Lipid + Protein
…
Kristallstruktur der 30S Untereinheit des Ribosoms
(PDB 1giy @ 5.5 Å)
Protein + „kleines Molekül“
Rezeptor Ligand
O
N O
H2N N HN
OH
N N
O OH
NH2
Polare WWs
Lipophile WWs
Aromatische WWs
Optimale Interaktion
O O
Enthalpischer Beitrag
solvated receptor-ligand complex
• Brechen und Bilden von H-Brücken
• Bilden lipophiler Kontakte
HO
∆G = ∆H − T∆S
Energy coordinate
∆ Ea ∆Ed
∆E
Interaction coordinate
The thermodynamics of protein-ligand interaction
K eq ≡
k forward
=
[PL]
Kd = Ki =
[P] ⋅ [L]
k backward [P] ⋅ [L] [PL]
Equilibrium constant Dissociation constant
[PL]
∆G = ∆G° + RT ln
[P ] ⋅ [L]
Equilibrium condition: ∆G = 0 (steady state)
[PL] 1
∆G° = − RT ln ( )
= − RT ln K eq = − RT ln = RT ln(K i ) = 2.303 ⋅ RT log(K i ).
[P][L] Ki
• hydrogen-bridges (“hydrogen-bonds”),
• ionic and polar interactions,
• arene-arene (“aromatic”) interactions, and
• dispersive interactions (vdW interactions).
Entropic Contributions
High-entropy state
HO
O + Lys
H 3N
N
+
Phe
Hydrogen bridge
O (ionic interaction)
H 3N
O
Aromatic
interaction
Enthalpy-driven Entropy-driven
Tyr43
Tyr33
a) b)
HO O HO O HO O
O O
λ=0 λ=1
∆G = ∑ ∆Gi
i
Thermodynamic Cycle
∆G 1
P+L PL
(Protein + Ligand) (Protein-Ligand complex)
∆G2 ∆G4
∆G 3
P+D PD
(Protein + Dummy) (Protein-Dummy complex)
Summation (integration)
over all intervals ∆∆ == ∆∆G
∆∆G
∆∆
∆∆G G44-- ∆∆G
G22
The IC50 Value
IC 50
Concentration of
Ki =
[Ligand ]
1 + reference
Kd
Cheng-Prussoff
Non-specific binding
IC50
Concentration of test compound
Screening Methods
24 well
96 well
HTS Workstation
Wechselwirkungstypen
Nicht-kovalente Wechselwirkungstypen
O H N
hydrogen bonds
O H O Dopt = 2.8 – 3.2 Å
H
O H N
+
O H N
O H
H ionic interactions
Dopt = 2.7 – 3.0 Å
+
N
O H H
hydrophobic interactions
CH3 H3C
+
N
cation-π interaction
-
metal complexation
2+
Zn S
Lipophile Gruppen
O Cl
O S
apolare Heterozyklen
Die Wasserstoffbrücke
Covalent limit (40 kcal/mol)
H X--H--X
O O [HF2]-
R R
H2N
O H O PO(OH)2
H2N
very strong
Cl3
O H N CH3 Hydrogen-bonds
strong
Hydrogen-bonds
weak
Hydrogen-bonds
NH4+ ···F-
very weak
NH4+ ROO- OH···O=C
Cl3CH···O=CMe2 Hydrogen-bonds
NH···O=C OH···OH C=CH···OH
NH···S C=CH···O
NH4+···Cl- NH4+ ···π NH···NH CH···FC
CH···Cl- CH···S
NMe4+···X- (NO2 )3CH···O
C≡CH···π CH4···π
OH··· π NH···π CH···ClC CH4+···Ar
100°-180°
β
α >150°
2.8 – 3.2 Å
- ∆H ° • gerichtete WW
O-H ••• N (29 kJ × mol-1, 2.88 Å) • definierte Geometrie
O-H ••• O (21 kJ × mol-1, 2.70 Å)
N-H ••• N (13 kJ × mol-1, 3.10 Å)
N-H ••• O (8 kJ × mol-1, 3.04 Å).
Die Natur als Vorbild
zum Beispiel …
(Trp)
NH
HO OH
O
HN
HO O H
N OH
O P O
O
OH
(Val)
Phosphoramidon
PDB: 5TMN
Zn2+
R Kd / µM
X = -NH- X = -O- X = -CH2-
OH 0.76 660 1.4
Gly-OH 0.27 230 0.3
Phe-OH 0.08 53 0.07
Ala-OH 0.02 13 0.02
Leu-OH 0.01 9 0.01
Geometrie von H-Brücken (II)
Ligand
Ligand
r
r
α −
ω
Receptor Receptor
Bindung von Metallionen
Receptor
Zn2+
“Zinc finger”
DNA Bindung
„Lipophile“ Wechselwirkungen
δ⊕
δ⊕ δ⊕
δ
δ⊕ δ⊕
δ⊕
+
r r r
r
α
ω
Cation-π
π Edge-to-Face Face-to-Face Aliphatic
Aromatische Wechselwirkung
Multiple Bindungsmoden
Soakingexperimente mit
Trypsin + Guanidiniumbenzoat
Sp
ez
ifit
äts
tas
ch
e
katalytisches Ser195
Böhm et al. (1996)
Bindungsmoden verschiedener Inhibitoren
stärkere Bindung
geänderte Struktur des Rezeptors
der Ligand bindet nicht in der berechneten theoretisch
„optimalen“ Konformation
Movie:
Bindung des Substrates (purple) an die
ribosomale A-Site ändert die Struktur des
Peptidyl-Transferase-Zentrums
T. Martin Schmeing, Kevin S. Huang, Scott A. Strobel
and Thomas A. Steitz, Nature 438, 520-524 (2005)
What is a molecule?
HO O 8 7 9
6 10 12
O
1 5 11
OH 2 4 13
3
2D structure Molecular graph
∑ k (r − r )
2
E stretching = b 0
bonds
Federkonstante Gleichgewichtslänge
(„Steifheit“)
Kraftfelder: Bending-Energy
Ebending = ∑ kθ (θ − θ 0 )
angles
2
Federkonstante Gleichgewichtswinkel
(„Steifheit“)
Kraftfelder: Torsion-Energy
qi q j Bij Aij
E non −bonded = E Coulomb + E vdW = ∑∑ + ∑∑ 12 − 6
i j 4π ε 0 rij i
j rij rij
Ladungs WW Dispersions WW
(„Lipophile“ WW)
Demo Benzaldehyd
Conformer Generator: Torsion Angle Distribution
Potential Energy
Relative frequency
p(τ) E(τ) /
kJ/mol
0 0
0° τ 180° 0° τ 180°
Torsion angle
p (τ )
E (τ ) ∝ − ln
pref
„Inverse Boltzmann method“
DOCK (Kuntz)
DOCK-Hit
Cysteinprotease-Inhibitor
Optimierung
(Malaria)
LUDI (Böhm)
• Finde WW-Zentren
HD: blau
HA: rot
Lipo: grün
• Plaziere Fragmente
• Verknüpfe Fragmente
Energy landscape
Local optimum
Global optimum
Barrier to local search