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The functional groups (ionization considered) of a drug and the bioactive conformation they must
adopt to sustain high-affinity and specific non-covalent interactions with the molecular target.
N
Drug-MT binding forces are the same that stabilize protein tertiary structure: H H
N N N NCH3
• Hydrogen bonds
N O
• Hydrophobic interactions H H3C
O H
• Electrostatic interactions
HO NH3
• Ion-dipole interactions •• N Bioactive conformation of STI-571
from X-ray coordinates (1IEP)
• Dipole-dipole interactions O STI-571(a.k.a. imatinib or Gleevec®) Via Protein Data Bank
• Charge-transfer complexes H (http://www.rcsb.org/pdb/)
Bioactive conformation
• ʌ-cation
Wentland-SC-9k
Protein Structure
Nearly all Natural Amino Acids have a Center of Chirality
O P3 O P1 O P2' O P4'
H H H H
Primary (1o) structure: N
N
N
N
N
N
N
N 20 Natural AAs have (S)- or L- absolute
[Amino acid sequence] P4
H
O P2
H
O P1'
H
O P3'
H
O
R H
configuration except Cys (R-) and Gly
+ O-
H3N L- L-glyceraldehyde (Fischer notation of
O absolute configuration)
Secondary (2o) structure: (R)- or (S)- Cahn-Ingold-Prelog notation
[Conformation of segments of
of absolute configuration)
backbone (e.g., D-helix, E-sheet)]
Wentland-SC-9m
..
N N N+
Threonine (R)-CH(OH)CH3 Thr T
CH2-S-S-CH2 •• •
H
•• Cysteine CH2SH Cys C H H
•
•
•
•
•
•
C C
O H2N Lysine (CH2)4NH2 Lys K 2Å 121.9o 1.4
5Å
D-Helix CH2 N
1.5
1.3
3
Aspartic Acid CH2CO2H Asp D C 115.6o
N
H
•
•
•
•
•
•
Proline Pro P
E-Pleated sheet +
-
N CO2
H H Wentland-SC-10a
Wentland-SC-10
H
Thr
H R O CH3
H R R
O H O H O
H
N N N N
N N N N
R RO O H O O
R H R R H
O
H O R H O R H O R H
H
N N N
N
N Glu N N N
O R R H R H
O-
O O O
R H
H R R R
H O H O H O
O
N N N
N N N N
O
R H O H O H O
O R R R
R
Wentland-SC-12c
Wentland-SC-13c
Inhibitor Substrate
thr315
glu286 koff
[E] [I] koff
thr315
CH2CH2
E·I E + I Ki = =
NCC kon [E · I] kon
CH3 CH H
O O O
H H N
N N N NCH3 "Slow tight-binding" inhibitors are characterized by:
- Slow (relative to diffusion control) "on rate"
N O
H3C - Very slow "off rate"
IC50 = 38 nM - Displacement of a structured H 2O from active site
N Wentland-SC-13d - Transition state analogue Wentland-SC-13f
Lineweaver-Burk Plots for Determination of Ki of a Competitive Inhibitor IC50 Value and Dose Response Curves
0.9 100
90
0.6
2X
[I]
1 0 1 2 3 4 5 6 7 8 9 10
Km 1 [S]
(mM-1) IC50 = Ki 1 + When [S] is 10-fold or more below its Km, then IC50 ~ Ki
1 [S] Km
1
Kmapp Km (1 + [I]/Ki)
Wentland-SC-14b
Wentland-SC-14a
X-H X-H
drug drug
O
N H N ..
N H O
..
Br O H N
H
X-H drug* X drug* X
irreversible O X
- Desolvation Penalty
O
S1 H H
S3 .. ..
O O
H2N
NH2 .. . . H .. .. . . + H2O
N H O O H O N H O N
..
+ N
H H
H H
HN
O X X
H2N O
Solvated drug and protein - unbound Drug - protein NCC
N
N
H Cl Enthalpic and entropic benefit in establishing H-bond contacts with MT may be offset by an
O uncompensatable desolvation penalty. Then why do this? SELECTIVITY and SOLUBLITY !!
S2
Wentland-SC-17
PPACK: inhibitor of human thrombin Wentland-SC-14f
HC O O
o
• Ion-dipole interactions ('G ~ -3 to -5 kcal/mol) • Dipole-dipole interactions ('Go ~ -1 to -3 kcal/mol)
H2C O O
CH3 O
-G H
Drug N H O +G Drug N·· +G
N
CH3 N H O
-G
+G
• Charge-transfer complexes ('Go ~ -1 to -7 kcal/mol) •S-Cation complexes ('Go ~ -0.5 to -1.5 kcal/mol) C
-G
OCOCH3 H H
CN CH2 +G
Drug Drug
H H
N O H3N CH2
(CH3)3N
Trp-84
C
HO CH2 Tyr CH2-Phe -G
N
H
N H
N AcO NOE's observed between the 4-acetyl methyl,
N H
PhCONH O 10 O
H OH 2-benzoyloxy phenyl and 3'-phenyl groups in
SS Stacking Edge-to-face
X O
3' O 13 DMSO-water solution.
OH 2
4
HO Vander Velde, D.G.; Georg, G.I.; Grunewald,
O O O
G.L.; Gunn, C.W.; Mitscher, L.A. J. Amer.
O O Chem. Soc. 1993, 115, 11650-11651.
2 H3C
• The larger the surface area the greater the effect (~ 28 cal/mole/Å )
Wentland-SC-18a
• H2O solvation of unbound ligand may have an uncompensatable enthalpic advantage
Wentland-SC-18
L1 High affinity binding is generally achieved via induced fit of MT around a ligand having optimized:
L2
L2 How do you achieve high affinity binding? “Stay tuned”
+ L2
Wentland-SC-18e
Teague, S. J. "Implications of Protein Flexibility for Drug Discovery." Nature Rev. - Drug Disc. 2003, 2, 527-541.
Wentland-SC-18c
CHEM-4330 - Spring, 2004 - Module 2 21 CHEM-4330 - Spring, 2004 - Module 2 22
OH H O NH2
Ser(-27)CH2 O Protein ATP N
O N HRP
H H O H substrate
H R' N N
N O N H O O
O
Tyr-43 O H O S H CH2Ser-88 O
O -
CH2 OH O P O P O P O
N O
H O- O- O-
H
H
H
Hydrophobic pocket formed
H N +
HN O OH OH
by Trp-79, -92, -108 H
O O R
Asn(-23) O N H anti-phosphotyrosine
TK antibody
Asp-128
O
H O H O H O H OPO3-2
H H H
N O N O N O R'
N H O
O S O S O S
O
signal Y
N N N CH2 O P O- B
-
biotinylated peptide
H H H H O
H H H H N SA
Binding stabilizes dipolar resonance contributors O
H
R
Weber, P.C.; Ohlendorf, D.H.; Wendoloski, J.J.; Salemme, F.R. Science 1989, 243, 85. Wentland-SC-20a N H