The identification and characterisation of antimicrobial peptides from snake and scorpion venom.

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by  Caroline Fixter

The identification and characterisation of antimicrobial peptides from snake and scorpion
venom.
HARRISON, Patrick Liam.
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THE IDENTIFICATION AND
CHARACTERISATION OF
ANTIMICROBIAL PEPTIDES
FROM SNAKE AND SCORPION
VENOM
By
Patrick Liam Harrison
Submitted in partial fulfilment for the degree of Doctor of
Philosophy (PhD)
Biomedical Research Centre, Sheffield Hallam University
October 2014
Dedication
This thesis is dedicated to the memory of Thomas O ’Shea and Trevor Harrison
Very different men, who shared common decency, a belief in fairness and pride in who
they were. If everyone were like you the world would be a better place.
Quote
((It is not long since conditions in the mines were worse than they are now. There are
still living a few very old women who in their youth have worked underground, with the
harness round their waists, and a chain that passed between their legs, crawling on all
fours and dragging tubs of coal. They used to go on doing this even when they were
pregnant. And even now, if coal could not be produced without pregnant women
dragging it to and fro, I fancy we should let them do it rather than deprive ourselves of
coal. But-most of the time, of course, we should prefer to forget that they were doing it.
It is so with all types of manual work; it keeps us alive, and we are oblivious of its
existence. More than anyone else, perhaps, the miner can stand as the type of the
manual worker, not only because his work is so exaggeratedly awful, but also because it
is so vitally necessary and yet so remote from our experience, so invisible, as it were,
that we are capable of forgetting it as we forget the blood in our veins. In a way it is
even humiliating to watch coal-miners working. It raises in you a momentary doubt
about your own status as an Intellectual’ and a superior person generally. For it is
brought home to you, at least while you are watching, that it is only because miners
sweat their guts out that superior persons can remain superior. You and I and the editor
of the Times Lit. Supp., and the poets and the Archbishop of Canterbury and Comrade
X, author of Marxism for Infants—all of us really owe the comparative decency of our
lives to poor drudges underground, blackened to the eyes, with their throats full of coal
dust, driving their shovels forward with arms and belly muscles of steel”
-George Orwell-The Road to Wigan Pier, 1932
Acknowledgments
First of all thank you to my supervisors Dr. Keith Miller & Prof. Peter Strong for all
their support and willingness to allow me freedom of thought and to try new things. Not
everything worked out but I hope the direction we have travelled, represented in this
thesis, will be something we can look back on with fondness. Thank you also to Prof.
Stephen Evans, Dr. George Heath and Dr. Ben Johnson at the University of Leeds you
have been truly remarkable collaborators and this thesis would look radically different
without you. Also where would I be without my friends and colleagues Dr. Mohamed
Abdel-Rahman and Mohamed Tawfik.
To Prof. Thomas Smith, whose decision to employ me as placement student within his
laboratory in 2008 represents the start of this journey and I certainly wouldn’t be where
I am today without you kindness, I must also thank Dr. Jeanette Gittens and Dr. Tim
Nichol for their help, support and friendship over the last six years. I’m sorry for all the
stolen pens, tip boxes, lab coats and mess I make-I only hope you can forgive me!
And to Nicola, I don’t think you realise the high regard people hold you in. The passion
for your research, your role within science and the position you hold is only transcended
by the warmth and kindness you do it with. Thank you for all your help and support
over the last six years.
This PhD experience wouldn’t have been the same without (Dr) Robert Bradshaw and
Adam Bagshaw, in the three years I have lived at Kelham Island you have provided
more fim, laughter and true friendship then most people experience in a lifetime. I’ve
spent all my money on Kelham best, incredibly bad football bets and slow horses and I
wouldn’t change it for the world.
To my friends for who this big purple book means absolutely nothing. You’re an
eclectic bunch to say the least and long may you stay that way. Never stop being who
you are and become what society considers acceptable.
Apart from the fancy title, an even if I fail the viva, it matters little because without
starting this PhD I wouldn’t have met my beautiful girlfriend. Words can’t express how
much I love you. When I think of the future I don’t for one second consider the job I
will have or things I will own I think of us building a life and a family, spending time
together because to be truly happy is the biggest prize of all.
But lastly I save the biggest thank you to my parents whom I love dearly. You have
given me everything I could have ever wished for and this thesis is yours as much as
mine. Wherever I am or whatever I’m doing I always think of being at home. The mark
of happy home is it makes you relaxed and comfortable and whenever I am there I
always do. To me it will always be home.
Abstract
The need for new antimicrobial agents is becoming one of the most urgent requirements
in modem medicine. In the search for new antimicrobial drugs, in recent years, a large
amount of research has been undertaken to both identify antimicrobial peptides (AMPs)
and elucidate their mechanism of action. AMPs are ubiquitous in nature and have
favourable properties that make them attractive for drug development including potent
activity, low resistance rates due to their membrane disruptive mechanism of action, and
selectivity to prokaryotic membranes.
Venoms are an under exploited source of AMPs, in this thesis AMPs have been
identified, biologically characterised and their mechanism investigated. From snake
venom two novel AMPs (6-7KDa) along with four potential phospholipase A2 (PLA2)
proteins have been identified (12-14 KDa). One of these peptides, isolated from black
mamba venom (Dendroaspis polylepis) exerts moderate antimicrobial activity and has
low cytotoxic properties making it an ideal candidate for future drug development.
From scorpion venom, three AMPs (1-4 KDa) have been biologically characterised, one
of which, Smp43, is postulated to have a di-helical structure and exhibits good
antimicrobial activity especially against Gram positive organisms (4-64 pg/ml) and
exhibits negligible haemolytic properties at concentrations up to 512 pg/ml. The
mechanism of action of Smp43 and a shorter peptide termed Smp24 has been
determined using liposome leakage assays, atomic force microscopy (AFM) and quartz
crystal microbalance-dissipation (QCM-D). Smp24 caused pore formation in synthetic
prototypical prokaryotic membranes and induced the formation of non lamellar lipid
structures and caused lipid segregation in a prototypical eukaryotic membrane whilst
Smp43 exerted its effects through a mechanism of diffuse limited aggregation (DLA)
which, until now, has not been described as an AMP mechanism of action.
In summary, this thesis has identified novel AMPs which can subsequently feed into
drug development pipelines, provides further evidence of the membrane disruptive
mechanism of AMPs whilst enhancing our understanding of these mechanisms.
v
Table of Contents
0 Dedication - 1 0
Quote-ll
0 Acknowledgments-lll
0 Abstract-VO
0 Table of contents - VII0
0 List of figures-XII
0 List of tables-XVII
0 Abbreviations-XVIII
Dedication......................................................................................................................................i
Abstract................................................................................................................................... v
Table of Contents.........................................................................................................................vi
List of figures...............................................................................................................................ix
List of tables.................................................................................................................................xi
Abbreviations..............................................................................................................................xii
1 CHAPTER 1 INTRODUCTION TO ANTIMICROBIAL PEPTIDES................................................1
1.1 Introduction..............................................................................................................................................2
1.2 Mechanisms of antimicrobial resistance........................................................................................3
1.3 Strategies in antibiotic drug discovery............................................................................................7
1.4 Antimicrobial Peptides.........................................................................................................................8
1.5 AMP conformation................................................................................................................................9
1.6 Structural Characteristics of AMPs.................................................................................................12
1.7 Membrane characteristics.................................................................................................................16
1.8 Natural resistance towards AMPs..................................................................................................20
1.9 Stratergies for AMP production.....................................................................................................21
1.10 AMP mechanism of action...............................................................................................................23
1.11 AMPs from venom...............................................................................................................................35
1.11.1 AMPs from snake venom.....................................................................................36
1.11.2 AMPs from scorpion venom....................................................................................................41
1.12 Atomic force microscopy...................................................................................................................68
1.12.1 Operation characteristics of AFM..........................................................................................69