Computational Studies of Neuroactive Peptides for Treating Neurological
Disorders and Disease
A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy
Jierong Wen
Master of Biotechnology with Distinction, RMIT University
School of Science
College of Science, Technology, Engineering and Maths
RMIT University
December 2020
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Declaration
I certify that except where due acknowledgement has been made, the work is that of the
author alone; the work has not been submitted previously, in whole or in part, to qualify for
any other academic award; the content of the thesis is the result of work which has been
carried out since the official commencement date of the approved research program; any
editorial work, paid or unpaid, carried out by a third party is acknowledged; and, ethics
procedures and guidelines have been followed.
Jierong Wen
09th December 2020
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Acknowledgements
The present work cannot be made without the help and support from many people.
Thanks to my supervisory team, Andrew and David, you always help and support me during
my Ph.D. study and for my future career.
Andrew, you inspired me to step into the field of computational biology since my Master's
program. You guided me to pave the way for learning the drug discovery and design through
computational methods with your knowledge and patience, whenever I needed. I learned
that professional success was not only achieved via hardworking but also enthusiasm for the
study. You let me know that thinking critically and creatively is the most important thing
during research. Also, I appreciated your financial support for the publication and my
international academic conference travel.
David, you were happy to share the up-to-date experimental outcomes without exception,
providing a crucial basis for my computational research interests. You have proved that the
great success was based upon passion, vision and attention to even minor errors. I also want
to thank you for your generosity in providing me with the opportunities for joining in the
cooperation work that I was interested in, and your support when I was confronted with
problems during study.
The computational study in this thesis was designed based on the experimental results. Many
thanks to Dr. Jeffrey McArthur and colleagues at the University of Wollongong for conducting
the experiments and providing the fundamental knowledge that this thesis can reply on.
Thanks to the insightful suggestions regarding Chapter 4 of this thesis provided by Dr. Quentin
Kaas, Dr. Han-Shen Tae and Assoc. Prof. Rilei Yu. The computational resources in this thesis
were provided by the Pawsey Supercomputing Centre (Australia), National Computational
Infrastructure (NCI) and CSCS Swiss National Supercomputing Centre (Switzerland) via the
PRACE Project Access scheme.
I was grateful for the help from Assoc. Prof. Samantha Richardson, SEH Research Training
Services, School of Graduate Research (SGR) and RMIT Scholarship team for supporting me
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during the COVID19 pandemic. I also appreciated the subsidy from the SGR team and the
School of Science for my international conference travel.
My parents invariably support me during my study. They encourage me with their efforts and
let me know that I should never stop pursuing my dream. Thus, I can be more confident and
focus on my study.
Financial support
This research was supported by the Australian Research Council (DP150103990).
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Table of Contents
Chapter 1 : Introduction – Nicotinic Acetylcholine Receptors and Voltage-Gated Ion Channels Targeted
by Conotoxins ......................................................................................................................................... 3
1.1 Overview ....................................................................................................................................... 4
1.2 nAChRs .......................................................................................................................................... 4
1.2.1 Structure of nAChRs .............................................................................................................. 5
1.2.2 nAChR Stoichiometries .......................................................................................................... 8
1.2.3 nAChR Multiple Binding Interfaces ....................................................................................... 8
1.3 Voltage-Gated Calcium Channels ................................................................................................. 9
1.3.1 Structure of VGCCs .............................................................................................................. 10
1.3.2 VGCCs Multiple Binding Sites .............................................................................................. 12
1.4 Conotoxins .................................................................................................................................. 13
1.5 Conotoxins as Versatile Tools ..................................................................................................... 14
1.5.1 Conotoxin Interactions with nAChRs................................................................................... 14
1.5.2 Conotoxin Interactions with Voltage-Gated Ion Channels .................................................. 19
1.5.3 The Potential of Conotoxins as Analgesics .......................................................................... 24
1.6 Computational Approaches Assist in Drug Design: General Observations and Overview ......... 25
1.7 Aim .............................................................................................................................................. 26
1.8 References .................................................................................................................................. 28
: Methodology ...................................................................................................................... 43
2.1 Homology Modelling .................................................................................................................. 44
2.1.1 Background.......................................................................................................................... 44
2.1.2 Searching for Sequence Similarity ....................................................................................... 45
2.1.3 Model Building .................................................................................................................... 46
2.1.4 Model Evaluation ................................................................................................................ 46
2.1.5 Examples of Application ...................................................................................................... 47
2.2 Molecular Dynamics Simulation ................................................................................................. 50
2.2.1 Background.......................................................................................................................... 50