View
1.502
Download
4
Category
Preview:
DESCRIPTION
http://proteinsandwavefunctions.blogspot.com/2011/02/drug-design-and-ph.html
Citation preview
1
Drug Design and pH!Jan H. Jensen!
Department of Chemistry!University of Copenhagen!
http://propka.ki.ku.dk/~jhjensen!
2
Drug Design and pH!Getting the protonation state right
on the ligand
and the protein!
The protonation state determines!
Charge and hydrogen bonding properties!
3
4
pKa value => charge as a function of pH!
q(pH ) = 11+10 pH − pKa
5 1ACJ.pdb!
The protonation state determines charge and hydrogen bonding properties!
6
Determining pKa values for ligands!
Experimental:!Spectroscopic feature vs pH!
pH!N
MR
Shi
ft!
Computational:!
Hammet-Taft rules !
PH+ P + H+ !
pKa = pKmodel + ρ σ ii
substituents
∑
pKa = ΔGrxn / RT ln(10)
7
Ligand pKa prediction software using Hammet-Taft rules !
Epik!http://www.schrodinger.com/products/14/4/!
Marvin!http://www.chemaxon.com/marvin/sketch/index.jsp!
MoKa!http://www.moldiscovery.com/soft_moka.php!
ACD/pKa DB!http://www.acdlabs.com/products/phys_chem_lab/pka/!
8
Drug Design and pH!Getting the protonation state right
on the ligand
and the protein !
The protonation state determines!
Charge and hydrogen bonding properties!
9
Standard pKa values for residues !
10
Picture of non-standard!Protonation state in active site!
Non standard pKa values for residues in proteins !
11
Simple rules for pKa Predictions?!
pKa = 4.8!
pKa = 4.5!
pKa = 5.0!
pKa = 4.8 - 0.3!
pKa = 4.8 + 0.2!
pKa = 4.8 - 0.5 + 0.2!
AH A- + H+!pKa = ΔGrxn/1.36!
12
�
pKa = pKamodel + ΔpKa
Desolv + ΔpKaHB + ΔpKa
Chg-Chg
Model pKa values:
C-End=3.20, Asp=3.80, Glu=4.50, His=6.50, Cys=9.00, Tyr=10.00,
N-End=8.0, Lys=10.50, Arg=12.50.
PROPKA1: Li, Robertson & Jensen Proteins 2005!(PROPKA3: Olsson, Rostkowski, Søndergaard, Jensen JCTC 2011)!
PropKa!
13
DpKa: Hydrogen Bonding!! !∆pKa= -0.8 , if D < d1!
∆pKa= -0.8 (D-d2) / (d1-d2), if D < d2!! !!! !∆pKa= 0.0, if D > d2!∆pKa
D (Å)d1 d2
F0
0.00.0
O
O
D
HO
Li, Robertson & Jensen Proteins 2005!
14
4.5 Å15.5 Å
N15.5Å=443∆pKa= +0.43
aNLocal=13∆pKa= +0.91
Asp102
Arg46
Leu103
b
-1.20
-1.20
-0.48-0.46
Asp148
Asp102
Arg46+0.73
-2.40
c
Example: Asp102 in RNase H1!
pKa = 3.8 + 1.3 - 3.3 - 1.7 = +0.1!
Exp = < 2.0
Li, Robertson & Jensen Proteins 2005!
15
Ca 20,000 hits last 12 months! Included in PDB2PQR and Vega-ZZ (*)!
16
17
PROPKA-VMD interface!
Rostkowski, Olsson, Søndergaard, Jensen BMC Struct. Biol. 2011!
18
(a) Asp /Glu
-2
0
2
4
6
8
10
12
-2 0 2 4 6 8 10 12Experimental pKa values
PR
OP
KA
Pre
dic
tio
n
(b) Cys
2
4
6
8
10
12
14
2 4 6 8 10 12 14Experimental pKa values
PR
OP
KA
Pre
dic
tio
n
(c) His
0
2
4
6
8
10
0 2 4 6 8 10Experimental pKa values
PR
OP
KA
Pre
dic
tio
n
(d) Lys
2
4
6
8
10
12
14
2 4 6 8 10 12 14Experimental pKa values
PR
OP
KA
Pre
dic
tio
n
RMSD = 0.7!N = 210!
RMSD = 1.2!N = 41!
RMSD = 1.0!N = 11!
RMSD = 0.7!N = 24!
19
P + L P·L
PH+ + L PH+·L
H+ H+Ka
f Kac
Kb+
Kb0
Kobs = Kb0 1+10 pKa
c − pH
1+10 pKaf − pH
pKa values can change upon ligand binding!
Kobs =[PiL]+ [PH + iL][P][L]+ [PH + ][L]
=[PiL][P][L]
1+ [PH+ iL]
[PiL]⎛⎝⎜
⎞⎠⎟
1+ [PH+ ]
[P]⎛⎝⎜
⎞⎠⎟
= Kb0
1+ [H+ ]
Kac
⎛⎝⎜
⎞⎠⎟
1+ [H+ ]
Kaf
⎛⎝⎜
⎞⎠⎟
20 20
pKa values can change upon ligand binding!
Implication number 1:!
Inhibition constant is pH dependent!
Kobs = Kb0 1+10 pKa
c − pH
1+10 pKaf − pH
21 21 21
pKa values can change upon ligand binding!
Implication number 2:!
Change in Ki wrt pH means !
change in protonation stateupon binding!
−∂ log(Kobs )
∂pH= qc − qf
Kobs = Kb0 qfqc
q = 11+10 pH − pKa
22 22 22 22
pKa values can change upon ligand binding!
Implication number 3:!
Docking score using static
protonation state must be corrected!
�
ΔGb = −RT ln(Kb0) − RT ln 1+10pKa
c − pH
1+10pKaf − pH
⎛
⎝ ⎜
⎞
⎠ ⎟ = ΔGb
0 + ΔGb,pH0
23 23 23 23
pKa values can change upon ligand binding!
Implication number 4:!
ΔH measured by calorimetry will be
buffer dependent and must be corrected!
ΔHcorrected = ΔHobs − (qc − qf )ΔHion
ΔHion is ionization enthalpy of buffer!
24
Effect of Ligands: PROPKA 2.0!
�
pKa = pKamodel + ΔpKa
Desolv + ΔpKaHB + ΔpKa
Chg-Chg
PROPKA 2: Bas, Rogers & Jensen Proteins 2008!PROPKA3.1: Søndergaard & Jensen, in progress!
Atom typing!H-bond donor/acceptor!
Charged groups!Ligand ionizable groups/pKmodel!
25
xxx.pdb!
pKmodel!
xxx.pka new_xxx.pdb!
PROPKA!
new_xxx.pdb!edit!
PROPKA!
new_xxx.pka!
Edit = !new pKmodel or!
new atom types!
26
N29!
pKmodel!pKa!
C25!C91!
10.3!12.0!
3.2!
Experiment!
1K1L.pdb -> 1K1L.pka!
new_1K1L.pdb!
new_1K1L.pka!
27 Bas, Rogers & Jensen Proteins 2008!
28
Summary!Implications for docking!
Protonation state of ligand can be estimated computationally!
Protonation states of active site residues are not!always “standard”!
Protonation states can change upon binding!
In which case docking score must be corrected!
29
Questions Now?!
Questions Later?!
Leave a comment on!http://proteinsandwavefunctions.blogspot.com/2011/02/drug-design-and-ph.html!
Recommended