Molekülvergleich, Pharmakophorhypthesen (GK/CS)

Transcription

Molekülvergleiche, Pharmakophorhypothese, QSAR-Studien, Design
• Molekülvergleiche ohne Rezeptorstruktur
• Ähnlichkeitsmaß
• Active Analog Approach
• Zusatzkräfte
• Differenzvolumina
• Feldbasierender Pharmakophor
• Vergleichende Feldanalysen
• CoMFA, CoMSIA, AFMoC
• Erste Designbeispiele
Literatur
• H.J. Böhm, G. Klebe, H. Kubinyi. Wirkstoffdesign - Der Weg zum Arzneimittel Lehrbuch, Spektrum - Akademischer Verlag (1996)
• Kubinyi, H.: Similarity and dissimilarity: a medicinal chemist’s view. In: 3D QSAR in drug design. Ligand-protein interactions and
molecular similarity. Kubinyi, H.; Folkers, G. und Martin, Y. C., Hrsg. Kluwer Academic Publishers, Dordrecht, 1998, S. 225-252; auch
veröffentlicht in Persp. Drug Discov. Design 9-11, 225-252 (1998).
• H. Kubinyi, Molekulare Ähnlichkeit. 1. Chemische Struktur und biologische Wirkung, Pharmazie in unserer Zeit 27, 92-106 (1998).
• H. Kubinyi, Lock and Key in the Real World. Concluding Remarks, Pharm. Acta Helv. 70, 259-269 (1995).
• D. Mayer, C. B. Naylor, I. Motoc und G. R. Marshall, A Unique Geometry of the Active Site of Angiotensin-Converting Enzyme
Consistent with Structure-Activity Studies, J. Comput.-Aided Mol. Design 1, 3 - 16 (1987)
• Cramer III, R. D., Patterson, D. E., und Bunce, J. D., Comparative Molecular Field Analysis (CoMFA). I. Effect of Shape on Binding of
Steroids to Carrier Proteins, J. Am. Chem. Soc. 110, 5959-5967 (1988).
• Klebe, G., Abraham, U., und Mietzner, T., Molecular Similarity Indices in a Comparative Analysis (CoMSIA) of Drug Molecules to
Correlate and Predict Their Biological Potency, J. Med. Chem. 37, 4130-4146, (1994).
• H. Gohlke and G. Klebe, DrugScore Meets CoMFA: Adaptation of Fields for Molecular Comparison (AFMoC) or How to Tailor
Knowledge-based Pair-Potentials to a Particular Protein J. Med. Chem., (2002) 45 4153-4170
• Goodford, P. J., Drug design by the method of receptor fit, J. Med. Chem. 27, 557-564 (1984).
Theoretische Methoden in der Chemischen Biologie
SS 2003 Philipps-Universität Marburg
Receptor
structurallyunbekannt
unknown
Rezeptor
strukturell
NH3
OH
HN
O
O
H
H
O
superposition
Ligand 3
Ligand 2
N
S
O
S
Ligand 1
HN OHNH2
NH2
N
O
N H
H
H
Comparison of Ligands only
Relative Differences in
Interaction Properties
+ Solvation Properties
Receptor
structurally
known
Rezeptor
strukturell
bekannt
O
O
NH3
N
H
O
O
O
OH
N
O
HN
H
O
Ligand 3
Ligand 2
N
NH2 H
S
Ligand 1
O
H
O
Protein - Ligand 1
N
O
H
N
O
Protein - Ligand 2
HO
Protein - Ligand 3
Affinity = Interactions(Protein/Ligand) + Solvation(Protein) + Solvation(Ligand)
Molekülvergleiche
Überlagerung von Molekülen nach ihrer Ähnlichkeit
Eigenschaftsbeschreibung in Abwesenheit der Bindestelle
• in den meisten Fällen: Struktur Zielprotein unbekannt
• aus der Kenntnis der vielfältigen Strukturvariationen
der Liganden und ihrer veränderten biologischen
Aktivität auf essentielle Bindungseigenschaften
zurückschließen
H
N
Suche nach einem
gemeinsamen
Pharmakophor
+
D
NH3
N
Histamin
P
A
Pharmakophor
(bei pH = 7 vorliegende,
positiv geladene Form)
Was ist gleich(er)?
(er)
Verschiedene Wirkmechanismen ähnlicher Moleküle
S
S
N
N
Cl
N
CH3
H3C
N
CH3
N
CH3
CH3
Promethazin
(H1-Antagonist)
Chloropromazin
(Dopamin-Antagonist)
R
N
CH3
a, R = CH3, Imipramin
b, R = H, Desipramin
(Uptake-Hemmer)
Verschiedene biologische Wirkungen von Steroiden
OH
OH
H
H
H
H
H
H
H
O
HO
Östrogen
Gestagen
OH
CH3
H
H
H
O
OH
CH3
H
H
H
O
Androgen
Anabolikum
OH
OH
H
H
H
H
O
H
H
CH3O
Norethynodrel
Mestranol
Unerwartetete Effekte bei der N- und C-Alkylierung
H3C
HO
O
a) R = H (Antagonist)
IC50 -AT1 = 0,3 nM
IC50 -AT2 = 4 500 nM
H
H 3C
N
N R
N
HO
N
CH3
O H
N
O S
O
Morphin, R = CH3
(Agonist)
Nalorphin, R = CH2-CH=CH2
(Antagonist)
R
b) R = CH2 CH(CH3)2
(Agonist)
IC50 -AT1 = 13 nM
IC50 -AT2 = 10 nM
Ligandenerkennung bei der DNA-Replikation
2,4-Difluortoluol als Thymidin-Isosteres
O
F
Me
Me
F
NH
N
H
O
N
Ribose
Me
N
F
H
H
H
4-Me-Benzimidazol
N
Ribose
N
H
N H
N
N
H
H
Adenin
Me
H
H
F
Ribose
2-4,Difluortoluol
O
Me
H N
O
H
N
Ribose
Thymin
S. Moran et al., J. Amer. Chem. Soc. 119, 2056-2057 (1997)
Enantiomere unterscheiden sich in ihren
biologischen Aktivitäten
CH3
CH3
CH3
O
(R)-(+)(S)-(-)Limonen
Geruch:
Orange
Limone
CH3
O
(S)-(+)(R)-(-)Carvon
Kümmel
Pfefferminze
Geruchs-Schwellenwerte (ng/l Luft) von stereoisomeren
Weinlaktonen
(3a,4,5,7a-Tetrahydro-3,6-dimethylbenzo-furan-(3H)-one)
5
CH3
6
4
3a
H 3C 3
CH3
CH3
7
7a
O
O
O
O
H 3C
O
3S,3aS,7aR
3R,3aR,7aS
0,00002 ng/l
> 1.000 ng/l
H 3C
O
3S,3aS,7aS
0,01 ng/l
H 3C
H3C
0,25 ng/l
120 ng/l
CH3
O
O
3S,3aR,7aS
CH3
O
O
O
O
O
3R,3aS,7aR
CH3
CH3
H 3C
CH3
H 3C
O
O
H 3C
O
3R,3aR,7aR
3S,3aR,7aR
3R,3aS,7aS
20 ng/l
0,1 ng/l
12 ng/l
H. Guth et al., Helv. Chim. Acta 79, 1559-1571 (1996);
O
N
N
Inhibitoren des Angiotensin
Konversionsenzyms (ACE)
OH
O
S
S
S
N
N
O
N
COOH
O
HOOC
OH
N
S
N
CH3
S
COOH
O
CH3
O
N
N
COOH
CH3
S
N
N
O
O
N
N
S
COOH
O
COOH
H
N
S
O
•Carbonylgruppe
O
•Zink-koordinerende Gruppe
O
CH3
P
N
H
O
HOOC
N
H
COOH
N
N
N
H
O
S
N
O
N
O
COOH
COOH
CH3
N
N
H
O
S
COOH
COOH
S
N
P
OH
O
COOH
O
N
H
O
COOH
HOOC
O
HOOC
COOH
CH3
HOOC
N
S
COOH
COOH
O
O
N
COOH
O
OH CH3
HOOC
P
N
N
O
H
O
COOH
S
S
S
N
O
•endständige Carboxylatgruppe
COOH
O
COOH
O
O
Gemeinsamer Pharmakophor?
N
N
H
SH
CH 3
N
O
COOH
Pharmakophor- & Konformationssuche:
Active Analog Approach
A
A
A
B
B
B
.....
B
Systematic Search
ΒΧ
ΒΧ
ΑΧ
C
ΒΧ
ΑΒ
.....
=
ΑΒ
ΑΧ
∩
Pharmakophor
Hypothese
ΑΧ
ΑΒ
B
B
C
ΑΧ
C
A
C
C
C
A
A
ΒΧ
ΑΒ
Eingeschränkter
erlaubter
Bereich
O
Inhibitoren des Angiotensins
Konversionsenzyms (ACE)
N
N
S
O
N
COOH
•Carbonylgruppe
N
HOOC
O
COOH
O
COOH
O
OH
N
•endständige Carboxylatgruppe
S
N
N
S
Gemeinsamer Pharmakophor?
OH
O
S
N
CH3
S
COOH
O
O
OH CH3
HOOC
P
N
N
O
H
O
COOH
CH3
O
N
N
COOH
CH3
S
N
N
O
O
N
N
S
COOH
O
COOH
H
N
S
•Zink-koordinerende Gruppe
H
N
H2N
O
O
O
CH3
P
N
H
N
O
N
H
COOH
N
N
O
S
HN
N
H
HOOC
N
O
N
O
O
COOH
N
P
OH
O
COOH
O
N
H
CH3
N
N
H
S
O
HOOC
COOH
S
COOH
Konformation?
O
COOH
NH2
HOOC
COOH
CH3
HOOC
S
Zn2+
COOH
COOH
O
O
N
COOH
O
O
S
S
S
N
N
H
SH
CH3
N
O
COOH
COOH
Molekülüberlagerung nach gemeinsamen Zentren
12
11
5
2
HO
3
1
12
9
12
10
6
10
5
7
N
2
3
4
17.2
9
9
11
8
5
3
6
1
1
17.3
Inhibitoren der ErgosterolBiosynthese
Starre Referenz oder
Ergebnis des Active Analog Approach
12
N
6
8
10
6
5
2
3
1
10
NH
7
4
17.5
4
17.4
Internes Kraftfeld +
Zusatzkräfte
Datenbanksuche nach einem
Pharmakophor
Beispiel: HIV-Protease
P1
o
8.5-12 A
P1'
o
o
3.5-6.5A
3.5-6.5A
H-Bond-d onor/acceptor
Ile A 50
N
N
H
OMe
Ile B 50
HO
H
OH
HO
O
H2O
O
OMe
R
O
1
OH
O
N
H
OH
R
HO
OH
O
O
A sp A 25
R
O
O
HO
N
HO
N
R
2
OH
A sp B 25
H
N
N
N
H
H
N
N
H
N
H
N+
H
N
R
H
H
H
N
N
H
H
N
O
H
O
N
N
N
N
N
N
H
H
N
N
N
N
H
Was macht
Moleküle ähnlich?
R
N
H
H
O
N
N+
H
R H
R
N
N
H
H
N
H
H
H
N
R
H
H
N
N
N
R
N
N
N
N
H
N
H
H
N
H
H
H
N+
H
N
R
N
N
H
N
H
R
N
N
H
O
H
N
H
N
N
H
N+
H
N
H
H
N
N
H
R
N
N
N
H
R
N
H
O
Verschiedener Bindungsmodus ähnlicher Moleküle
Phenylimidazole als Cytochrom P450cam-Inhibitoren
O
N
N
NH
N
1,0.10-7 M
N
NH
H3C CH3
Metyrapon
N
4,0.10-5 M
N
7,0.10-6 M
2,2.10-9 M
Modellverbindungen legen aktive Konformation fest
Calciumkanal-Blocker
aktiv:
R1
R1=
CH3
CH2
CH3
O
OH
O
O
17.1
Picrotoxinin
CH3
CH3
H
O
O
CH3
R2= OH
H
OH OAc
O
R2
CH3
OAc
CH3
O
O
OH
O
CH3
Überlagerung von Molekülen
nach ihrer Ähnlichkeit
OH
CH3
N
CH3
O
O
O
inaktiv:
O
O
O
O
O
OCOCH3
O
CH3
O
O
OH
O
O
OH
CH3
O
CH3
O
O
OH
O
O
O
O
CH3
O
O
OH
O
O
O
CH3
O
Picrotoxinin: Ligand des
Chloridkanals
O
O
O
O
OH
CH3
O
Volumen 1
aktiv
Überlagerung von Molekülen nach
ihrer Ähnlichkeit in Volumen und
physikochemischen
Eigenschaften
Volumen 2
inaktiv
Differenzvolumen
Volumenbereiche bereits
durch Rezeptor besetzt
Molekülbeschreibung durch räumliche
Gaussfunktionen
H2N
C
+
NH2
Physikochemische
Physikochemische Eigenschaften
Eigenschaften
sterisch
sterisch
elektrostatisch
elektrostatisch
hydrophob
hydrophob
H-Brückendonor/akzeptor
H-Brückendonor/akzeptor
HH2N
N
NH2
NH2
Ähnlichkeitsmaß
O
S
HN
HN
Referenz Ligand
Test Ligand
O PO O
3
Überlapp physiko-chemischer Eigenschaften
Pharmacophore Model from Ligand Superposition
O
F
H
N
HN
HOOC
N
S
HOOC
CF3
O
N
S
O
N
N
O
CH3O
CF3
RMS-Fit Cα-Atome
Superposition
Common
Pharmacophore
Assignment of Field-based Pharmacophores
red: molecule 1
blue: molecule 2
at each
grid point
arithmetic
arithmeticmean
mean
geometric mean
map field onto grid
.OR.
.OR .AND.
.
.AND.
approximate
grid by
gaussians
O
F
H
N
HN
HOOC
N
HOOC
CF3
S
O
N
S
O
N
N
O
CH3O
CF3
Steric fields
.AND.
.OR.
Hydrophobic
Hydrophilic
Electrostatic +/-
H-BondDonor/Acceptor
Steric
OR
Paired
Interactions
FlexS
HN
H2N
NH2
steric
NH2
O
HN
HN
hydrophobi
c
electrostati
c
H2N
+
NH2
NH2
S
PO3
HH2N
N
O
HN
S
Reference Ligand
Test Ligand
O
O PO
3
Overlap of Physico-chemical Properties
NH2
NH2
Test Ligand
NH2
NH2
HN
Reference Ligand
HH2N
N
Reference Ligand
Similarity Scoring
+
H-bond
Volume Check
O
H2N
NH
O
Test Ligand
Reference Ligand
Test Ligand
HN
Torsion
Torsion
HH2N
Torsion
N
Angle
NH2
Angle
Angle
NH2
90 180
0
90 180
HN
O
HN S
Lemmen, Lengauer & Klebe
1998
PO3
+
O
HN
O
S
O
O
PO3
O
Fast Flexible
Superposition
3D-QSAR (z.B. CoMFA-Methode)
In Studien der „normalen“ Quantitative Structure
Activity Relationships müssen alle Substanzen aus
einer einheitlichen Serie stammen.
3D-QSAR kombiniert den „normalen“ Ansatz mit der
Geometrie und kann deshalb auch Ähnlichkeiten
zwischen nicht-gerüstverwandten, aber funktionsverwandten Molekülen erkennen
Der Grundgedanke der Comparative Molecular
Field Analysis ist, anstelle von Strukturen,
Eigenschaftsfelder von Molekülen, die durch ihre
Wechselwirkung mit anderen Molekülen entstehen,
zu vergleichen.
.
,
..
..
Verb. -lg(IC50) S1 S2 S3
4.15
5.74
.
,
.... Sn E1 E2 E3
....
En
........
....
E(r)
3.89
8.83
6.74
0
LennardJonesPotential
CoulombPotential
r
-lg(IC50)= y + a S1 + b S2 + c S3 + ...+ h Sn + k E1 +m E2 + n E3 ... + z En
Data Set:
Inhibitors of
Thrombin,
Trypsin Factor
Xa
H
R1
O
N
H
R1
t-Bu
R2
N
SO2
SO2
N
-O C
2
Me
SO2
N
Me
R2
Me
Me
O
N SO2Me
Me
Me
SO2
Me
O
Me
...........
...........
CO2CH2Ph
H2N
+
NH2
SO2
N
Trypsin
Thrombin
Factor Xa
Affinity Prediction Training Set
FactorXa - CoMFA
Trypsin - CoMFA
Thrombin - CoMFA
9
8
8
7
7
6
5
predicted pK i
predicted pK i
predicted pK i
6
6
5
5
4
4
4
3
3
4
5
6
7
8
9
3
actual pKi
4
5
6
7
3
8
4
8
8
7
6
FactorXa - CoMSIA
Trypsin - CoMSIA
Thrombin - CoMSIA
9
5
actual pKi
actual pKi
7
6
predicted pK i
predicted pK i
predicted pK i
6
6
5
5
4
4
5
3
3
4
4
5
6
7
8
9
actual pKi
3
4
5
6
actual pKi
7
8
3
4
5
6
actual pKi
Affinity Prediction of Novel Compounds
Thrombin - CoMFA
9
FactorXa - CoMFA
6
predicted pKi
7
6
predicted pKi
7
8
predicted pKi
Trypsin - CoMFA
8
6
5
5
5
4
4
4
4
5
6
7
8
5
6
7
4
8
4
actual pKi
9
Thrombin - CoMSIA
9
8
6
FactorXa - CoMSIA
6
7
6
5
predicted pKi
7
predicted pKi
predicted pKi
Trypsin - CoMSIA
8
5
actual pKi
actual pKi
6
5
4
4
4
5
6
7
8
9
actual pKi
5
4
4
5
6
actual pKi
7
8
4
5
6
actual pKi
Steric Properties
steric occupancy
unfavorable
steric occupancy
favorable
Me
Me
SO2
H
N
iPr
O
H
N
iPr
CO2Me
Me
SO2
O
H
N
H
iPr
HN
NH2
pKi = 4.1
N
CO2CH2Ph
pKi = 6.1
HN
NH2
steric field
increase
hydrophobic
hydrophilic
decrease
increase
starting
point:
hydrophobic field
HN
NH2
HN
modelling:
NH2
H
CO2Me
SO2
H
N
H
N
O
predicted pKi = 6.4 (Thrombin)
+
SO2
H
N
H
N
N
O
predicted pKi = 8.0 (Thrombin)
O
S
N
Selectivity
Discrimination
O
O
O
N
N
S
O
8.38
6.77
N
O
N
O
S
H2N
+
NH2
O
5.68
7.10
N
O
O
H2N
+
NH2
CoMSIA
based on
Affinity
Differences
Steric Properties
Thrombin
Trypsin
CoMFA: Comparative Molecular Fields Analysis
• relative comparison of molecules
E(r)
• 3D-QSAR using interaction properties
=
...............................................................
OH
...............................................................
..................
.......................
......................
..........
.......................
......................
...............................................................
*
..........
.......................
......................
..................
.......................
......................
...............................................................
NH
..........
.......................
......................
..................
.......................
......................
.......................................................
...............................................................
.......................................................
...............................................................
.......................................................
...............................................................
.......................................................
O
...............................................................
.........................................................
..
O
...............................................................
.........................................................
NH
..
.........................................................
...............................................................
NH
..
.........................................................
...............................................................
..
.........................................................
...............................................................
..
.........................................................
...............................................................
..
.........................................................
OHOH
..
...............................................................
.........................................................
...............................................................
...............................................................
.........................................
......................
.......................................................
CoulombPotential
...............................................................
...............................................................
...............................................................
...............................................................
...............................................................
...............................................................
...............................................................
...............................................................
...............................................................
...............................................................
• set of training compounds required
LennardJones...............................................................
Potential
...............................................................
O 0
r
..
...............................................................
.........................................................
..
...............................................................
beyond van der Waals
CoMFA, generic probe
ligand information
Cramer et al., JACS 110 (1988) 5959-5987
molecular fields
correlate with exp. pKi via PLS
CoMSIA: Comparative Molecular Similarity Index Analysis
• Compare molecules by similarity
E(r)
.
• 3D-QSAR, generic physico-chemical properties
......
...............................................................
................................
*
S
...............................................................
.........................
OH
OH
O
...............................................................
NH
H
CoMSIA, generic probe
...............................................................
O
............................................................
...............................................................
...
O NH
............................................................
...
...............................................................
............................................................
NH
...
...............................................................
............................................................
...
............................................................
...............................................................
...
............................................................
...............................................................
...
............................................................
OH
OH
...............................................................
...
............................................................
...
...............................................................
............................................................
...
similarity indices
=
..................
.......................
......................
......
.......................
......................
...............................................................
NH
..................
.......................
......................
......
.......................
......................
...............................................................
N
NNH
HH
..................
......
.......................
.......................
......................
......................
...............................................................
r
......
.......................
......................
..................
.......................
......................
...............................................................
......
.......................
......................
..................
.......................
......................
O0
...................................................
...............................................................
...................................................
...............................................................
...............................................................
...... ......
....
...............................................................
...........
...
......
..................
.............................
......................
...............................................................
...............................................................
...............................................................
...............................................................
O
O
...............................................................O
........ ....
...............................................................
...................................................
...............................................................
...............................................................
......
.........
...........
Gaussian
...............................................................
................
ligand information molecular similarity fields
Klebe, Abraham, Mietzner, J. Med. Chem., 37 (1994) 4130-4146
AFMoC: Adaptation of Fields for Molecular Comparison
• tailor DrugScore potentials to a particular protein
• 3D-QSAR including protein specific information
....
........ ....
2
3
1
2
0
1
1
0
-1
-2
-ln(g(R) / gref(R))
-ln(g(R) / gref(R))
3
2
-ln(g(R) / gref(R))
........... ...
.........
3
................
1
-1
0
-2
-1
2
1 -2
3
2
1
2
4
5
R 3[Å]
R 3[Å]
4
6
5
4
6
5
6
R [Å]
...... ......
...... ......
........... ......
......
...............................
.
.........................
protein information
ligand information
Gohlke, Klebe, J. Med. Chem. 2002, in press
modified potential fields
3D-Struktur
bestimmung
3D-Struktur des
Proteins
vorgeschlagener
Ligand
biologisch
aktiver Ligand
Testung
Ligandendesign
synthetisierte
Verbindung
Synthese
C a rb o x yp e p tid a s e A
lip o p h ile
B in d e ta s c h e
lip o p h ile
B in d e ta s c h e
Z n 2+
Z n 2+
{
O
H
N
O
O
N
H
R
N H2
O
H2N
O
HO
+
+
N H2
O
N
H
H2N
N
H
In h ib ito r
S u b s tra t
ACE
...P ro -P h e -H is -L e u ...
S u b s tra t
P y r-T rp -P ro -A rg -P ro -G lu -Ile -P ro -P ro T e p ro id e 1 0 0 n M
P y r-L y s -T y r-A la -P ro
P h e -A la -P ro
A la -P ro
R2
O
R3
N
H
0 .0 5 µ M
1 .4 µ M
250 µM
O
H
N
O
O
R2
O
O
R1
O
S u b s tra t
O
IC 5 0 = 3 3 0 µ M
IC 5 0 = 2 2 µ M
COOH
N
O
CH3
COOH
N
O
R1
HS
CH3
HOOC
O
In h ib ito r
N
HOOC
O
H
N
IC 5 0 = 2 0 0 n M
COOH
N
HS
O
IC 5 0 = 2 3 n M
COOH
Oxyhämoglobin
β 2 -N-Term
β 2 -His2
O
-
O
-
P
O
β 1 - His143
Desoxyhämoglobin
O β 2-His243
O
O
O
O
P
O
-
O
β 1 -His2
β 1 -N-Term
β 1 - Lys 82
Diphosphoglycerat
setzt Affinität des Hämoglobins
zu O2 herab, regelt O2 -Abgabe
Vermessen der Abstände zwischen polaren Gruppen im
Hämoglobin Tetramer, Blockieren der Umlagerung
Konkurrent zu allosterischem Effektor DPG
β 2-1
N
N
β 1-1
R=H
R = OCH2COOH
OHC
Schiffsche Base
kovalente Verknüpfung
H
N
β 2-1
β 2-His 2
-O
3S
β 1- His 143
R
β 2-His 143
SO3-
O
COO-
N
H
β 1-1
SO3H
β 1-His 2
CHO
R=H
R = OCH2COOH
HO
R
OH
SO3H
β 1- Lys 82
Additionsprodukt

Molekülvergleich, Pharmakophorhypthesen (GK/CS)

Transcription

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