Computer aided drug discovery: Design, synthesis and testing of novel anti-cancer agents

220 Pages·2016·2.97 MB·English

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COMPUTER AIDED DRUG DISCOVERY
Design, synthesis and testing of novel anti-cancer agents
ABRAM WASSEF

This thesis is submitted in fulfilment of the requirements for the degree of
Doctor of Philosophy

FACULTY OF PHARMACY
UNIVERSITY OF SYDNEY
2015
"If you don't believe in yourself, nobody else can"
Declaration
The work described in this thesis was conducted under the supervision of Prof David
E. Hibbs (Faculty of Pharmacy), Prof Paul W. Groundwater (Faculty of Pharmacy),
and Dr Jeff Holst in the Faculty of Pharmacy and in Centenary Institute. Unless
otherwise stated, it is the work of the candidate and is not currently being submitted
for any other degree.
Acknowledgments
First and foremost, I would like to convey my gratitude to Prof. David E. Hibbs my
supervisor for giving me the opportunity to experience pharmaceutical research. His
exceptional support and encouragement during the candidature of my PhD on both
professional and personal level, has given me the confidence to pave my career path.
I am sincerely grateful to Prof. Paul W. Groundwater for his continuing guidance,
support and humor. I specially wish to thank Dr Jeff Holst for his scientific
inspiration. Finally, I wish to thank Dr. Qian Wang who played an integral part of
my PhD.

During my candidature I developed many long-lasting friendships. I wish to express
my appreciation and thanks to those of whom I have shared laughter and good times
with. I am especially indebted to Ms. Vivian Liao for her kind friendship.

Finally, I wish to thank my parents for their tremendous love and ongoing support
throughout my life journey. I know they will be proud of me no matter what I do or
accomplish in life.
Poster Presentations
12th International Cancer Conference. 2011, Dublin, Ireland.
"Design, synthesis and testing of novel AMACR inhibitors"
ABSTRACT

The continuous enhancements of computational tools for drug discovery, have
greatly improved the pre-clinical stages of pharmaceutical research, to a higher level
of efficiency and greater speed. The combination between homology modelling
methods in structure-based drug design, and the chemoinformatics techniques in lead
optimization, has allowed successful development of small molecule inhibitors with
30 folds higher potency of best known ASCT2 inhibitors.

Three dimensional model of ASCT2 protein was constructed via fold recognition
technique, the preferred method in absence of highly similar protein sequences. This
model was used in virtual screening against commercial SPECs database comprised
of approximately 300 000 compounds of drug-like molecules to identify potential
inhibitors and characterize active site interactions through different docking
procedures. Visual analysis of the docking poses with correlation to the biological
results has allowed verification of the ASCT2 active site and determine the important
residues for strong ligand binding. Furthermore, the ASCT2 model has been used to
validate the biological results of the lead development stage through further docking
analysis.

AMACR homology model was built using the three dimensional X-ray crystal
structure of MCR with high sequence similarity and shared protein family. The
Maestro modelling software platform offered highly accurate model predictions and
further docking calculations in the virtual screening stage. The biological testing was
highly reliant on general cell viability results rather than specific AMACR inhibition
due to the high cost and difficulties associated with AMACR activity assays.
To conclude, computer-aided drug discovery in partnership with complementary in
vitro techniques have made major contributions in this thesis, to develop biologically
active molecules, demonstrating the high efficiency, great speed and cost-effective
advantages of molecular modelling.
CONTENTS

Declaration
Acknowledgements
Poster presentations
Abstract
List of Figures
List of Tables
Abbreviations

CHAPTER ONE
PROTIENS
Protein structural features 1
The hydrophobic effect 5
Protein structure prediction 6
First-principle methods 7
Techniques based on secondary structure prediction 9
Homology modelling 10
Template Identification 10
Protein Preparation 11
Sequence Alignment 12
Homology Model Generation and Evaluation 18
Threading 22
Protein Databases 24
Protein sequence databases 24
Protein structure databases 25

CHAPTER TWO
Computational Chemistry
Computational representation of molecules 27
Compound databases and search methods 28
Molecular docking 29
Molecular descriptors 33
Screening compound selection 35
Molecular Modelling Concepts 37
Computational chemistry and drug discovery 41
SBDD 43
Virtual Screening 49
LBDD 51
Pharmacophore Modelling 52
Chemoinformatics and LBDD 54
QSAR 55

CHAPTER THREE
Structure-based drug design of Alanine Serine Cysteine Transporter 2
inhibitors
Outcomes and significance 62
Introduction 63
Aims 74
Materials and methods 75
Homology modelling 75
Biological testing 77
Results and discussion 79
Molecular modelling 79
Biological testing 110
Lead optimization 113
Conclusion 123
Future work 125

CHAPTER FOUR
Structure-based drug design of Alpha Methyl Acyl Co-A Racemase (AMACAR)
inhibitors
Outcomes and significance 126
Introduction 127
Aims 142
Materials and methods 143
Homology modelling 143
Chemical synthesis 145
Biological testing 145
Results and discussion 147
Homology modelling 147
Chemical synthesis 157
Biological testing 161
Conclusion 169
Future work 170
Experimental 171
Appendix A 177
Appendix B 181
References 190