Validation of Receptor-Based Drug Design and Applications in the Study of IKKs, Truncated Taxane and LRH-1 Público
Hu, Haipeng (2011)
Published
Abstract
Validation of Receptor-Based Drug Design and Applications in the
Study of
IKKs, Truncated Taxane and LRH-1
By
Haipeng Hu
Since the first successful report of structure based drug design in
the 1990's, it has
been utilizing routinely in modern drug discovery. The performance
of the design based
on the fundamental assumption: a) the protein target does
not undergo conformational
change upon ligand binding or changes the same way independent on
the ligand type; b)
ligands which bind to the same protein share similar pharmacophore.
In order to verify
this assumption, a protein-ligand interaction survey with templates
from a selected
protein-ligand crystal structure database was performed. The result
indicates that over
99% crystal structures obey the structure fundamental assumption
which indicates the structure
base assumption is trustworthy in most cases. After verification of
the fundamental
assumption, it is utilized in several projects:
Liver receptor homolog 1 (LRH-1) is an orphan nuclear receptor (NR)
which
activates an array of genes responsible for development of
endodermal organs. Based on
the highly reserved structure properties of NRs, a series of LRH-1
antagonist candidates
were developed from known NRs agonists and antagonists, yielding
several compounds
with mild inhibition to LRH-1 but poor solubility based on in vitro
and in vivo assays.
Further work is currently in process to improve their activities
and ADME properties.
Two truncated taxane models were computationally generated by
replacing the
baccatin core with different fragments based on their structure
similarity with PTX, and
both of them lead to micro-molar level activities.
The inhibitor of Kappa B Kinases (IKKs) which bind with the rel
homology domain
of NFκB regulate the activation of NFκB by the
phosphorylation-induced ubiquitination
of the IκB proteins. Homology models were constructed and
investigated in silico. The
result provides a first-step to understand the mechanism of IKKs
inhibition and offers a
provisional guidance on the design and synthesis of novel IKKs
inhibitors.
In the end, a quantum chemical calculation was performed to prove
that the cuprate
intermediate formed between nucleophilic attach of the
dimethylcopper anion to the
β-unsaturated carbon has a square-planar structure.
Table of Contents
Table of Contents
List of Figures
..............................................................................................................III
List of Table
................................................................................................................
IV
Chapter 1: Bird View of Structure Based Drug Design
.................................................1
1.1
Introduction........................................................................................................1
1.2 Target Selection
....................................................................................................2
1.3 Drug Design
..........................................................................................................5
1.4 Outline of Subsequent Chapters
............................................................................7
Chapter 2: Protein Ligand Interaction Survey
...............................................................8
2.1 Interactions between Protein and Ligand
..............................................................8
2.2 Structure Base Assumption
.................................................................................11
2.3 True or False?
.....................................................................................................12
2.4 Experiment
Detail.............................................................................................14
2.5
Classification.......................................................................................................16
2.6 Case
Discussions........................................................................................19
2.6.1 Pose Difference: a. 1EPN & 5ER1
.........................................................19
2.6.2 Pose Difference: b, 1CVZ & 1BQI
.........................................................22
2.6.3 Protein Movement: a, 1SRF & 1VWJ
....................................................25
2.6.4 Protein Movement: b, 1DD6 & 1JJT
......................................................28
2.6.5 Solvent Effect: a, 1EGH & 1IK4
............................................................31
2.6.6 Solvent Effect: b, 1DMW & 4PAH
........................................................34
2.6.7 Metal Effect: 1C1U vs. 1KTT
................................................................37
2.7
Conclusions................................................................................40
Chapter 3: Computational Design of Liver Receptor Homolog 1
Antagonists Based on
Helix-12 Conformational Reorganization
....................................................................42
3.1 Nuclear Receptors
...............................................................................................42
3.2 Liver Receptor Homolog 1
.................................................................................44
3.3 Structural
Comparisons...........................................................................46
3.3.1 LRH-1 vs. Estrogen Receptor-α
..............................................................47
3.3.2 LRH-1 vs. SF-1
.......................................................................................48
3.4 Computational
Methods......................................................................................50
3.5 Analysis of Results
.............................................................................................52
3.5.1 SID-7969543 Analogs
............................................................................52
3.5.2 Tamoxifen
Analogs................................................................................59
3.5.3 Raloxifene Analogs
.................................................................................67
3.5.4 Steroid
Analogs......................................................................................72
3.6 Biological
Evaluation..........................................................................................77
3.7
Conclusions........................................................................................................79
Chapter 4 Truncated Taxane
........................................................................................81
4.1 Tubulin and Taxane Analogs
..............................................................................81
4.2 Simplified
PTX................................................................................................85
4.2.1 Replacement of the Baccatin Core
..........................................................85
4.2.2 Biological Evaluation
..............................................................................89
4.2.3 Computational Evaluation
......................................................................90
4.2.4
Conclusions.............................................................................................93
4.3 Truncated Taxanes
..............................................................................................94
4.3.1 Steroid
Analogs.......................................................................................94
4.3.2 Tubulin Binding Site
...............................................................................95
4.3.3 Ligand Preparation
..................................................................................97
4.3.4 Tubulin-Taxol Site Docking
...................................................................99
4.3.5 282 Site Docking Results
......................................................................103
4.4
Conclusions......................................................................................................107
Chapter 5: Homology modeling of IKKs and Analysis of Their
Binding Properties
through Molecular Modeling
.....................................................................................108
5.1 NFκB Activation
...............................................................................................108
5.2 Homology Models
............................................................................................112
5.3 Analysis on ATP Competitive Compounds
......................................................118
5.4 Mechanism Determination of IKKs Inhibitors
.................................................126
5.5
Conclusions......................................................................................................130
Chapter 6: Prediction of Structure of Cuprate Intermediate
......................................132
6.1
Introduction.....................................................................................................132
6.2 Experiment and
Discussion...............................................................................134
6.3
Conclusions....................................................................................................140
References
..................................................................................................................141
List of Figures
Figure 1.1 Process of structure based drug design
........................................................7
Figure 2.1 Structure and binding mode comparison among
vardenafil, sidenafil and
tadalafil
........................................................................................................................13
Figure 2.2 2D structures of ligands in 1EPN and 5ER1
.............................................21
Figure 2.3 Superimposed crystal structures of 1EPN and 5ER1
................................22
Figure 2.4 2D structures of ligands in 1CVZ and 1BQI
.............................................24
Figure 2.5 Superimposed crystal structures of 1CVZ and 1BQI
................................25
Figure 2.6 2D structures of MTB and short peptide CHPQGPPK
.............................27
Figure 2.7 Superimposed crystal structure of 1SRF and 1VWJ
.................................28
Figure 2.8 2D structures of MCL (left) and BDS (right)
............................................30
Figure 2.9 Superimposed crystal structure of 1DD6 and 1JJT
...................................31
Figure 2.10 2D structures of MCL and BDS
..............................................................33
Figure 2.11 Superimposed crystal structure of 1EGH and 1IK4
................................34
Figure 2.12 2D structures of HBI and LNR
................................................................36
Figure 2.13 Superimposed crystal structure of 1DMW and 4PAH
.............................37
Figure 2.14 2D structures of HBI and LNR
................................................................39
Figure 2.15 Superimposed crystal structure of 1C1U and 1KTT
...............................40
Figure 3.1 Structure of nuclear receptor's ligand binding
domain .............................44
Figure 3.2 X-ray crystal structure of LRH-1, labeled by
sub-sites and tunnels ..........47
Figure 3.3 Superimposed crystal structures of LRH-1 with
ER-α and SF-1 ..............49
Figure 3.4 Four lead compounds selected for LRH-1 antagonist
design ....................51
Figure 3.5 Docking and bioassay results of SID-7969543 in
SF-1 and LRH-1 .........53
Figure 3.6 Best docking poses of SID-7969543 analogs
3-1 to 3-9 ...........................59
Figure 3.7 Tamoxifen 2D structure and its binding pose in
ER-α and LRH-1 ...........61
Figure 3.8 Scaffold of analogs 3-15 to 3-18
...............................................................63
Figure 3.9 Tamoxifen analogs in LRH-1
....................................................................65
Figure 3.10 Raloxifene 2D structure and its binding pose in
ER-α and LRH-1 .........69
Figure 3.11 Raloxifene analogs which show steric conflicts
with H12 ......................71
Figure 3.12 The steroid analog in the bile acid receptor and
LRH-1 ..........................73
Figure 3.13 Steroid analogs with ring structures on R2
..............................................75
Figure 3.14 Steroid analogs with head group modifications
.......................................76
Figure 4.1 Atomic model of wild type β-tubulin
complexes with PTX ......................82
Figure 4.2 2D-structures of PTX and 282 and their
activities ....................................85
Figure 4.3 General structure of second generation T-taxol
mimics ............................86
Figure 4.4 low energy poses of compounds of 282 and
its analogs in the PTX tubulin
binding site
...................................................................................................................88
Figure 4.5 low energy poses of compounds 282 and its
analogs, 4-5 to 4-11, in 282
tubulin binding site and wild type PTX binding site
...................................................89
Figure 4.6 Reported steroid analogs which show effect on
preventing microtubule
disassemble
..................................................................................................................95
Figure 4.7 Comparison of wild type PTX binding site and
282 binding site .............97
Figure 4.8 Redundant Conformer Elimination (RCE) result of
the core region of the
steroid analogs.
............................................................................................................98
Figure 4.9 Docking results of steroids in tubulin-taxol
binding site .........................102
Figure 4.10 Docking results of steroids in 282
binding site .....................................106
Figure 5.1 NFκB activation pathways dependent on IKKs
...................................... 110
Figure.5.2 Structures of reported IKKs inhibitors
.................................................... 112
Figure5.3 Homology models of IKKs
.......................................................................
117
Figure 5.4 Compound Bayer A in IKK α unit and β
unit ..........................................121
Figure 5.5 Compound ML120B in IKK α unit and β
unit ........................................122
Figure 5.6 Compound NRDD1 in IKK α unit and β unit
..........................................123
Figure 5.7 Compound NRDD4 in IKK α unit and β unit
..........................................125
Figure 5.8 Compound BMCL-5a in IKK α unit and β
unit ......................................128
Figure 5.9 Compound NRDD2 in IKK α unit and β unit
..........................................129
Figure 5.10 Compound NRDD6 in IKK α unit and β
unit ........................................130
Figure 6.1 Conformation of the six isomers optimized with
B3LYP/6-31G*/ LANL2DZ.....136
Figure. 6.2 The lowest energy conformation within two
different series .................136
Figure 6.3. Calculated 1H (blue) and
13C (red) chemical shifts for lithiated 2a
and
lithiated 2b relative to TMS and compared with experimental
values (parentheses);
B3LYP/6-311+G*/(pCVDZ)/SDD method
...............................................................137
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