1. Network Summary
This is a report for the ARC on the formation of the Australian
Protease Network. Proteases are enzymes that are essential for all
forms of life. They account for 2% of the genomes of most
organisms, including humans, and they control activation, synthesis
and turnover of proteins in all organisms. Proteases are pivotal
regulators of physiological processes during conception, birth,
growth, maturation, ageing, diseases and death. Genetic and
environmental factors can disturb the balance of protease-catalysed
human physiology leading to abnormal development (left), poor
health, disease and death. Proteases are also essential for replication
and transmission of viruses, parasites (below left) and bacteria (below centre) that
cause infectious diseases in humans and animals; for the proliferation of insects and
agricultural pests that damage plant crops and spread infection through animal stocks;
and for growth and yields of all marine (below right) and terrestrial food sources.
Because of their importance in health and disease, a few proteases have already been
targeted by leading academic and multinational pharmaceutical companies, who have
successfully developed exquisitely selective and non-toxic drugs for the treatment of
HIV/AIDS, high blood pressure, and stroke/coronary infarction. Proteases are also used
in domestic washing powders, cheese manufacture, meat tenderisation and processing,
and baking. The field is clearly 'ripe for the picking', with a growing number of protease
inhibitors in clinical drug trials funded by leading pharmaceutical companies.
Despite these very compelling reasons to study proteases, our
understanding of their detailed roles in many diverse processes remains
limited and hence our ability to harness them for the benefit for
humankind is compromised. It is, however, very clear that there are
enormous, untapped, but tangible, benefits to be derived from increasing
our research effort into these enzymes, particularly with regard to
promoting and maintaining good health, and developing an
environmentally sustainable Australia.
Australian scientists have made many major, innovative
contributions to understanding the role and importance of proteases.
However, these efforts have been uncoordinated and little
networking has been undertaken. In this regard, the establishment of
an Australian Protease Network has the potential (through national
and international initiatives and incentives) to bring researchers
interested in proteases, their inhibitors, and receptors together for the
first time. Moreover, Network participants have over 100 research collaborators overseas,
and these connections can also be more extensively utilised through a highly interactive
Network. It will greatly enhance and extend current protease research activities, facilitate
the recruitment of new researchers to the field, help cultivate and seed more intensive and
extensive research collaborations than currently feasible, improve our understanding of
protease biology, expand the capacity and horizons of Australian protease research, and
ultimately facilitate translation of this knowledge into benefits for society.
The Network aims to enhance research capacity by
facilitating national and global research collaborations;
seeding new research directions in Australia; enhancing
communication between national and international
researchers by coordinating specific conferences, meetings,
workshops, and research/researcher exchanges; promoting
more effective transfer of technology and skills; raising
awareness of proteases and their biology in the scientific and general community by
developing and fostering educational programs; enabling sharing of equipment,
educational materials and educators; and encouraging and facilitating the exploitation of
proteases, inhibitors, and receptors for pharmaceutical and industrial applications. In
these ways the Network will value add to Australia's contributions to protease biology
and chemistry, while also creating new opportunities for, and more effective training and
mentoring of, the next generation of Australia's research leaders and managers through
an innovative succession plan.
2. Proteases and their Importance to all Life.|
2.1 What Are Proteases?
Proteases are enzymes that are essential to all life. They are
biology's version of Swiss army knives (1) that cut up biological
polymers (called polypeptides) composed of amino acids, the
common building blocks for all life. Humans, mammals and other
organisms extract amino acids from their environment (diet) or
synthesize them, link them together in long assemblies, following
which proteases control their lengths and folded shapes through a
variety of mechanisms leading to proteins. Proteins are
responsible for all biological processes that characterise carbon-
based life. Proteases (2) are essential for the synthesis of all proteins, controlling protein
composition, size, shape, turnover, activation and ultimate destruction. Their actions are
exquisitely selective, with each protease being responsible for splitting proteins at very
specific sequences of amino acids under a preferred set of environmental conditions.
2.2 Why Are Proteases Important?
There are over 500 human proteases (3), accounting for 2% of all human
genes (DNA sequences that code for amino acids), and similar
numbers of proteases occur in every mammal (vampire bat, right),
plant, insect, marine organism and in every infectious organism that
causes disease. Proteases (also called proteinases or peptidases) play
pivotal roles in regulating conception, birth, digestion, growth,
maturation, ageing, and death of ALL organisms. Proteases regulate most physiological
processes by controlling the activation, synthesis and turnover of proteins. Different proteases are
also essential in viruses, bacteria, parasites and insects for replication and disease
transmission. As proteases are such potent biological regulators with high potential for
tissue destruction, they are tightly regulated by a variety of naturally occurring inhibitors.
In medicine, proteases represent important targets for medical
intervention because of their essential regulatory roles in human
physiology. With regard to such regulatory proteases, it is now known
that single amino acid mutations in at least 50 human proteases result
in hereditary/genetic diseases (3), a few of which are listed in
Also, other genetic or environmental conditions can result in an over-
or under-abundance of a particularly crucial protease or natural
inhibitors/activators of proteases, leading to abnormal physiology and disease.
Based on understanding the roles of proteases in the replication
of viruses, blockbuster drugs have been developed to block
(inhibit) viral proteases required for replication of HIV and are
currently the most effective treatments for HIV/AIDS. Other
drugs block an important human protease (thrombin) involved
in blood clotting and are now among the most effective
treatments for stroke and coronary infarction; others block
another human protease
(ACE) that raises blood pressure and are among the best treatments for hypertension.
Other protease inhibitors (4) are being developed to treat parasitic, fungal, and viral
infections; inflammatory, immunological, and respiratory conditions; cardiovascular and
neurodegenerative disorders including Alzheimer's disease, and cancers. Human
proteases such as kallikreins have also been identified as important prognostic indicators
of diseases. For example, prostate specific antigen is a kallikrein used
in the diagnosis of
prostate cancer. A number of other proteases are experimental vaccines in current
development to fight infectious diseases.
In our environment, proteases are key regulators of the life of
insects and other agricultural pests, key regulators of growth and
health of farm animals, and principal regulators of plants and
marine food sources. Research into these relatively under-studied
proteases has the potential to contribute spectacularly to our
economy by improving plant and animal health through enhanced
growth and treatment/prevention of parasite infections, crop protection through new
herbicides and pesticides, and increased or faster production of food resources.
3. Network Background
3.1 Network Scope
The Australian Protease Network was formed in 2004 by over
8 0 research groups (Appendix 6) from 28
universities/institutions/hospitals/companies in 6 states of
Australia (Queensland, New South Wales, ACT, Victoria, South
Australia, Western Australia). Each of these groups represents
multiple researchers including postgraduate and undergraduate
students working in the area of proteases, protease inhibitors and
protease receptors, supported by the Australian Research
Council, National Health and Medical Research Council, host institutions, industry, and
local and national charitable organizations. The participants have individual links to
collaborators in 20 countries (Belgium, Brazil, Canada, China, Denmark, France,
Germany, Hong Kong, Ireland, Italy, Japan, Korea, New Zealand, Poland, South Africa,
Sweden, Switzerland, Thailand, UK, USA). One of our first initiatives has been to fill an
unmet need, to build both National (www.protease.net.au) and International
(www.protease.net) protease network registers, with the blessings of the International
Proteolysis Society (www.protease.org). This reveals the scope of our vision, to draw not
only on Australians but also on researchers around the globe to catalyse research
collaborations, make new connections, enhance the capabilities, and expand the horizons
of Australian as well as international researchers.
The Network capitalises on an area (protease research) of
national research strength, and will coordinate it (for the first
time) through high profile National and International
collaborations to target fundamentally important processes in
life, ageing, health, and death that are associated with
National Research Priorities (5). Network participants have
formulated a wide ranging spectrum of initiatives and
strategies specifically designed to promote, extend, and link both current and anticipated
research and educational activities both nationally and globally. All participants share
common interests in the nature, properties and importance of protease enzymes or their
receptors or their inhibitors in biology. However their collective interests and expertise
are also interdisciplinary, extending beyond proteases and transcending the traditional
boundaries defined by the disciplines involved in their research portfolios, namely
genomics, genetics, transcriptomics, proteomics, bioinformatics, immunology,
molecular/cellular/developmental/structural biology, physiology, inflammation,
microbiology, cancer biology, neurobiology, enzymology, glycobiology, pharmacology,
cardiovascular research, chemistry, computing, and the design and development of drugs,
vaccines, and diagnostic agents.
3.2 Network Aims
Australians have made innovative contributions to understanding and regulating
proteases. However this initiative aims to network their efforts by value-adding to current
protease research through promoting national and international collaborations to improve
our understanding of biology, seed new innovative research efforts at the cutting edge of
the field, and encourage ultimate exploitation of proteases/inhibitors/receptors for
pharmaceutical and industrial applications.
The principal objectives are to build a highly interactive research
and educational protease network within Australia; to catalyse the
exploration of new frontiers and opportunities for developing
important new protease-related research programs relevant to life,
ageing, disease and death; and to coordinate and target a significant
proportion of protease research effort at problems of national or
international significance. Ultimate health and environmental
outcomes will have long lasting potential to create exciting and lucrative new
opportunities for the Australian economy.
Specifically the Network aims:
- To value-add to current protease research by promoting more effective/extensive
national and international collaborations to improve our understanding of biology.
- To unite, for the first time, the efforts of those Australians currently researching the
biology and chemistry of proteases (including structures, functions and control),
while also increasing awareness of the importance of proteases among other
Australian scientists who could be potential recruits into the Network.
- To increase the capacity, and expand the horizons, of Australian protease research
through developing more intensive links with current international collaborators,
while sourcing potential new collaborations via more effective international
- To facilitate global networking by building, maintaining, and communicating
through, national and international website registers of protease researchers; using
them to catalyse more extensive collaborations, communications, and
information/researcher exchange through specialist meetings, workshops, and
- To create new networking, management and leadership opportunities for established
and younger scientists, fostering student and postdoctoral exchange of Australian and
- To provide financial, vocational, mentoring and grant writing support to current or
prospective protease researchers, especially younger investigators.
- To promote interdisciplinary research approaches and education programmes by also
connecting Australian and global researchers through the rapidly growing disciplines
of genomics, proteomics, transcriptomics, bioinformatics, as well as more traditional
disciplines of genetics, structural/molecular/cell/developmental biology, enzymology,
physiology, immunology, microbiology, pharmacology, chemistry & drug discovery.
- To create opportunities for sharing equipment, techniques and new technologies,
infrastructure, and knowledge through lab visits and web-based document
- To connect research groups, individual students and researchers with potential end
users including each other, and to engage the community through Network activities.
- To generate new opportunities for, and facilitate commercial exploitation of,
proteases/inhibitors/receptors through future recruitment of pharmaceutical, biotech
and industrial participants.
These networking initiatives have been designed to promote
research collaborations, encourage lateral thinking, train and
educate participants in new activities and diversify their interests,
all towards improving our capacity to understand biology.
Separate initiatives will be described to facilitate the ultimate
exploitation of information accrued on proteases/inhibitors/
receptors for pharmaceutical and industrial applications.
3.3 Network Structure
The Australian Protease Network has an interim management committee comprising 10 people:
ACT Node Coordinator:
NSW Node Coordinator:
Vic Node Coordinator:
Qld Node Coordinator:
SA Node Coordinator:
WA Node Coordinator:
Fairlie will coordinate the overall program, supported by two Early
Researchers namely Drs. Hooper and Tyndall and a full time Network
Administrator. Assoc. Professor Pike (Victoria), Professor Alewood
(Queensland), Professor Hogg (New South Wales),
Dr. Baker (ACT), Professor Kumar (South Australia), and Professor
Australia) will act as local coordinators for each of the State nodes.
An International Protease Network website register
(www.protease.net) is also being
created to facilitate global communications and collaborations between protease
researchers and end users. A core group of eminent international protease researchers
have been enlisted by the Australian Protease Network as scientific advisers and conduits
to the international community. Expatriate Professor Chris Overall will chair this
advisory group which currently comprises:
Professor Chris Overall
North American Degradomics Group
University of British Columbia, Vancouver
Professor Guy Salvesen
North American Degradomics Group
The Burnham Institute, San Diego
Professor Ben Dunn
President of the International Proteolysis Society
University of Florida College of Medicine, Gainesville
Professor John Mayer,
Council Member UK Biochemical Society,
University of Nottingham Medical School, Nottingham
Professor Yoshiaki Kiso,
Director Center for Frontier Research in Medicinal Science,
Kyoto Pharmaceutical University, Kyoto
The network will endeavour to recruit International protease researchers, as opportunities
arise, for relocation to Australia. Network recruits who relocated to Australia between
Oct 2003 - May 2004 are Professor John Dalton (Dublin City University to University of
Technology, Sydney), Dr. John Deadman (Thrombosis Research Institute, London to
AMRAD, Melbourne), Dr David Dougan (Heidelberg University) and Dr. Kaye Truscott
(Freiberg University) to La Trobe University, Melbourne. Among international
participants who are expatriate Australians are Prof. Chris Overall (UBC, Canada), Prof.
Terry Spithill (McGill, Canada), Prof. Toni Antalis (George Washington, USA), Prof.
Paul Brindley (Tullane, USA), Drs Donmienne Leung and Michael Kelso (SCRIPPS,
USA), Dr. Matt Glenn (Yale, USA), Assoc. Professor Andrew Abell (Canterbury, NZ), Dr. Catherine Gilchrist (Auckland, NZ).
3.4 Network Participants
Over 80 Australian research groups have so far joined the
Network and supplied 1 page entries to www.protease.net.au on their specific protease
research activities and interests. Their names, research (Appendices 3, 4 and 5), and web links
(Appendix 6) are shown below.
Over 100 international researchers from 20 countries are
listed collaborators in the individual entries to www.protease.net.au by Australian
Network participants. These and many other protease researchers will be recruited to the
international network www.protease.net
The international participants complement/augment the skill base of the Australian team
to enhance discovery and broaden investigative capabilities in protease research. Among
expected outcomes that unifying collaborations between Australian and International
protease researchers could produce are the discovery of new serine, metallo, cysteine,
aspartic and threonine proteases, identification of new mutations in proteases that lead to
hereditary diseases, classification of new clans or families of proteases, unravelling of
new protease cascades, finding of new cellular receptors and pathways influenced either
directly or indirectly by proteases, characterisation of new protease functions and new
three dimensional structures, newly revealed enzymatic properties, establishment of new
roles for proteases in physiology and disease, validation of proteases as new drug targets,
creation of new inhibitors as new drug leads, development of proteases as prognostic aids
for diagnosing diseases, and as new vaccines. This initiative also forms a development
pipeline for identification of new knowledge on the biology of proteases, their structures,
and their functions in vitro and in vivo.
4. Summary: Status of International Protease Research
Historically, the importance of proteases in humans has been under-
rated, dismissed in the past as enzymes used mainly to degrade
proteins such as digestion of ingested food. We now know that
proteases (2) are pervasive mediators of most biological processes, present
in the GI tract, blood, cells, the brain, heart and all other organs, and
even in the airways. In fact every organism uses proteases in a
sophisticated network of endogenous regulators of cellular function. The challenge is to
unravel the highly specific roles carried out by each protease in every living organism
and to determine their respective importance to life, health, ageing, disease, death and
ultimately their value to man in medical, industrial and other applications. The following
areas of international activity are considered by us to represent some of the most
important issues in the field, yet are currently under-explored and would benefit
significantly from intensified and coordinated new research effort in Australia.
4.1 Genetic variants of proteases, protease inhibitors and receptors
An increasing number of hereditary diseases (3) are becoming
associated with mutations in protease enzymes (Appendix 1),
suggesting a need for more genetics/bioinformatics studies of
cDNA sequences in diseased individuals, for directed efforts at
identifying the properties of protease knockout animals, and for evaluating the properties
of proteases with specific types of mutations.
4.2 Proteases and Infectious Diseases
In relation to infectious diseases, the success of inhibitors of HIV
proteases (6) in the treatment of HIV/AIDS has spurred on efforts (albeit
limited) to target proteases important in the replication of other viruses
(e.g. Hepatitis C (7), Cytomegalovirus (8), Rhinovirus 3C (9), SARS (10), Dengue (11)).
There is also a significant research effort to block parasite proteases
that mediate the major parasite-induced diseases like malaria
(plasmepsins) (12) , schistosomiasis (cathepsins) (13), and hookworm (right)
infections (cathepsins) (14).
An exciting development in recent years was the
discovery of proteasomes (right) (15), a cylindrical
multidomain protease enzyme that functions much
like a sausage machine in destroying proteins.
Cells use such proteases to selectively
turnover and remove oxidised or otherwise damaged proteins, in
addition to destroying regulatory proteins for which a short
half-life is critical for their function. While it is known that
ubiquitin marks such proteins for destruction, the precise mechanisms
by which proteins are selected for ubiquitylation and selectively
recognized by proteasomes remains largely unknown. The interplay between
proteases and molecular chaperones appears to be a particularly important new field of
protease research, and recent studies showing that inhibitors of proteasomes induce
apoptosis has sparked interest in therapeutic possibilities for this class of protease too.
4.4 Proteases and Protein Folding
One category of damaged proteins are the so
called `mis-folded' proteins (16) now associated
with over 20 amyloidogenic diseases,
including Alzheimer's disease and other
neurodegenerative diseases. These are thought
to involve mis-folded proteins that aggregate into neurotoxic species of as yet unknown
composition. Proteases responsible for formation of these aggregating `mis-folded'
proteins are thus assuming prominence as prospective drug targets, most notable progress
being made for Alzheimer's disease.
4.5 Proteases and Aging
In the early 21st century we live in an ageing community, with
mounting pressure to find new and effective treatments for diseases of the aging, like Alzheimer's disease, arthritis, osteoporosis,
inflammatory syndromes, cancers, diabetes, high blood pressure and
heart diseases. All of these conditions are associated with proteases,
the inhibition of which can potentially lead to effective treatments
Inhibitors of BACE (beta secretase) show considerable promise for
reducing amyloid formation (right) associated with Alzheimer's disease
and are in early clinical trial. Inhibitors of tumour necrosis factor
alpha convertase (TACE)
and interleukin converting enzyme (ICE/caspase-1) are being trialed for
TNFα and IL-β are known to be key pro-inflammatory agents. A great deal
of effort has
been devoted to developing neutrophil elastase inhibitors for
controlling irreversible lung
destruction in diseases such as chronic obstructive pulmonary disease
and cystic fibrosis,
though many drug trials have been discontinued. Cathepsin K inhibitors
to Phase III clinical trials for osteoporosis, while inhibitors of complement proteins and
MMPs are in development for varied inflammatory conditions. Inhibitors of matrix
metalloproteases and caspase-1 have shown some promise for treating cancers, though
the former have stalled in Phase III clinical trials. Inhibitors of
dipeptidyl peptidase IV(left) (17) are in clinical development of
diabetes. Thrombin inhibitors are now prescribed in man for
treating stroke and coronary infarction, while inhibitors of other
proteases involved in blood coagulation (e.g. factor Xa, VIIa) are
in clinical trials. Inhibitors of angiotensin converting enzyme
(ACE) are currently used to treat hypertension, while renin
inhibitors are in trials for the same purpose. All of this work
(Appendix 2) speaks to the promise of protease inhibitors for
medical applications, including those related to National Research Priorities in Australia.
4.6 Proteases and Development
At the other end of the age spectrum, proteases play vital roles in
conception, birth and developmental biology. Problems of infertility,
endometriosis, healthy foetus development, and healthy births have
assumed paramount importance in modern Australian society.
Endometrial proteases and the roles of deubiquinating enzymes are
being studied in Australia and globally in relation to contraception,
infertility, and developmental biology.
4.7 Proteases and Inflammatory Diseases
Major problems in young Australian children are asthma and allergies. Mast cell tryptase (18) is a protease that has attracted a lot
of attention for the treatment of asthma with encouraging clinical
responses to inhibitors. Exciting developments in more recent
times were the discoveries of proteases in dust mites (left),
scabies and other allergens and the identification of protease
activated receptors (PARs) (19) which are sensors that are activated by proteases in the
airways and many other tissues. There has been a significant increase in research on
PARs in recent years with their detection in a wide range of cells & tissues of the central
nervous system, vasculature, intestine, airway epithelium, pancreas, skin, joints, etc and
predicted roles for PAR ligands in asthma, inflammatory diseases, and cancers.
Australians are at the forefront of this research.
4.8 Proteases, Diagnostics and Vaccines
In recent times proteases have been considered as potential diagnostics and vaccines. The overexpression of proteases such as matrix
metalloproteases in cancers and inflammatory disorders, and kallikreins
and cathepsins in cancers, has raised the prospect of using them as
prognostic markers of disease. One kallikrein is now referred to as
prostate specific antigen (20), and others look to be promising markers for
ovarian and colon cancers. Proteases are also being examined as potential
vaccines in parasite and viral infections, and could lead to vaccination programmes in
less developed countries where diseases like malaria, schistosomiasis, and Dengue fever
are rife. With regard to toxins, protease such as those produced by Clostridium tetani (tetanus toxin) represent important vaccine target antigens and similar toxin-associated
proteases may also represent suitable candidate vaccine antigens, for example, Bacillus anthracis (anthrax toxin). Similarly, proteases produced by other infectious agents that
play important somatic roles within the organism per se may also prove to be important
4.9 Proteases and Cell Death
Finally, cell death (21) is mediated by proteases. A great deal of
international research, as well as research by Australians, is
currently focussed on understanding the mechanisms of protease-
mediated cell death in development and disease. Cysteine proteases
such as caspases 2, 3, 7, 8, 9 and 10, as well as serine proteases like
granzyme B are used to kill harmful cells, including damaged cells, cancer cells (right),
autoreactive immune cells and virus-infected cells. A better understanding of proteases in
cell death may lead to new generations of drugs for the treatment of degenerative
disorders, heart disease, autoimmune diseases, stroke, cancer and ageing.
5. Audit of Australian Protease Research
5.1 Audit Summary
An audit of Australian protease research was conducted in January 2004 and Researcher
profiles are collected in a database (Appendix 6) that is searchable by key word. A
summary of some of the important information in the data base is shown in Appendices 3-6. Some of the strengths and opportunities created by the establishment of an
Australian Protease Network are described below.
It was clear from the audit of current Australian activity that Protease research is an area
of National Research Strength, but that it is largely in individual researcher laboratories
and may therefore suffer a lack of researcher communication, stimulation of ideas, and
availability of valuable reagents and expertise. However, the survey also revealed that
substantial complementarity would be gained through highly interactive national
There are around 100 research groups in Australia which
have protease research as a significant component of their
research portfolios. About 65% of these groups are in
Victoria and Queensland. The Victorian research effort is
primarily driven by biology, particularly molecular and
cellular biology, genomics, genetics, bioinformatics,
enzymology and immunology, with a particular strength
in proteinaceous inhibitors highlighted by an NHMRC
Program grant team working on systems biology of
serpins (left). Other features of Victorian-based research
include a number of independent efforts on the biology of
serine, cysteine, and metallo proteases, and two new ARC QEII fellows working on
relationships between chaperones and proteases in cellular removal of damaged/toxic
Research in Queensland is driven more by interests in gaining molecular insights to
protease structures and functions through structural biology, chemistry, drug design,
molecular pharmacology, microbiology, proteomics, genomics
and developmental biology. Three ARC Professorial Fellows
are working on synthesis, structures, and design of small
molecule protease inhibitors. Kallikreins, caspases, ADAMTS
and toxin-generating proteases are also prominent features of
Research on microbial, viral and parasite proteases also represents a national strength and
is studied by multiple researchers in Qld, NSW, WA and Vic. Insect proteases are being
studied in Victoria, Qld and ACT including at CSIRO.
Research in NSW focuses on bioinformatics and data mining,
particularly of the serine protease family, and the biochemistry and cell
biology of proteases that play important roles in asthma and cancer.
Researchers are working with industry to develop inhibitors of mast cell
proteases for the treatment of asthma and the use of protease fragments
to inhibit tumour growth.
South Australian research features caspases in mammals and insects, ubiquitination,
reversible ubiquitin marking of proteins for destruction by proteases, and roles of
dipeptidylpeptidases in disease, areas that are also studied in ACT, NSW and Victoria,
making these strengths as well.
Western Australian research has a major strength in protease activated receptors. These
are proteins (G protein-coupled receptors) found on surfaces of a wide range of cells
including inflammatory, cancer and airway cells. They are activated by trace levels of
extracellular proteases and are particularly important in allergies, asthma and cancers.
Pockets of researchers in Victoria and Queensland also work on PARs, but there is little
current interaction between the states in this area of national strength.
Overall, Australian research groups characteristically use wide ranging interdisciplinary
approaches to protease research with most investigators working in more than three
disciplines (Appendix 5) from genomics, genetics, bioinformatics, transcriptomics,
proteomics, structural/developmental/molecular/cellular biology, immunology,
enzymology, physiology, immunology, microbiology, pharmacology, chemistry & drug
discovery. There is considerable scope for harnessing these knowledge bases and
interdisciplinary skills, supplemental to protease expertise, for educational purposes as
well as research cross-fertilization.
A significant strength of Network participants is that many have been very successful in
publishing (> 1500 papers since 1998), attracting funding including research grants (>300
ARC, NHMRC & other grants), and commercialising their research through patents,
consultancies, contracts, and startup companies. This augers well for a network
environment that promotes a free flow of information exchange and sharing of research
capability, grantsmanship skills, and commercialisation experience and knowhow.
There are many opportunities for Australian
researchers to band together and tackle important problems in a
more concerted manner. More collaborative research can
be expected to address the roles and specific classes of proteins in
regulating life processes in humans and other organisms, resulting
in new knowledge that is important to a better understanding of
life, ageing and death.
New protease inhibitors, diagnostics and vaccines can also be expected to result down the
track from more effective networking both in Australia and overseas. Based on protease
inhibitors that are already in clinical trials (Appendix 2), we can expect that a more
extensive and collaborative Australian-led effort on protease research will result in new
drug leads for clinical trials for the treatment of important diseases in Australia, such as
stroke and heart disease, diabetes, cancers, arthritis, and Alzheimer's disease.
6. Proposed Research Directions, Configurations, Infrastructure and Facilities
(a) Proposed Research Directions
Most of the protease research that will be undertaken by network participants will be that
for which funding is already awarded through individual research grants from
organizations like ARC, NHMRC, NIH, companies, local institutions, charitable
organizations, etc. A substantial component of the network budget will therefore be used
to value add to that research effort through specific networking initiatives such as
conferencing, workshops, research/researcher exchange, young investigator promotion,
and educational activities.
The remainder of the budget will be used to expand Australia's research capacity,
particularly focussing on stretching the horizons of Australian protease research,
catalysing and supporting high-risk new research activities that have the potential to
change the landscape of Australian protease research.
Network participants have so far identified 12 new research directions that could result
from establishment of the Network and help to push Australian protease research further
to the forefront of international protease research. They are now foreshadowed as areas
currently worthy of increased research collaboration and greater focus in Australia over
the next 5 years:
- Protease Genetics.
It is only relatively recently that
associations have been made between mutations in
protease enzymes and hereditary diseases. Further
systematic examinations of the effects of protease
knock out mice and effects of protease mutations on developmental biology
and disease development in animals would be valuable adjuncts to clinical
studies of genetic defects in disease. We also propose to team up with the
Network on Genes and Environment in Development
- Viral Proteases.
New studies towards identifying
and inhibiting new proteases required for viral
replication/infection would be important. Current
awareness is high in Australia and overseas of
HIV/AIDS, and `new' infections by viruses like
SARS, bird influenza, and flaviviruses like Dengue and West Nile.
Comparatively small efforts by Australian protease researchers are ongoing,
but would benefit from more collaborations and recruitment of new Australian
protease researchers into these areas, with the promise of new information
about viral infection (the scourge of the 21st Century) and potential
development of new antiviral leads, vaccines, or diagnostic kits.
- Proteases in the Tropics.
Discovery of new
proteases in tropical parasites and in venomous
creatures, together with the validation of those
proteases as drug targets, is a worthwhile objective
already being pursued to limited extent by Australian
protease researchers who are at the forefront of these
areas. Australia is the closest developed nation to
substantial South East Asian populations infected by tropical diseases like
malaria, hookworm infections (above), schistosomiasis, etc. It is also home to some of
the world's most venomous animals, from snakes and spiders to marine
animals, and toxins isolated from these creatures are providing valuable clues
to new medicines.
- Proteases in Protein Turnover and Destruction.
Mechanisms by which
intrinsically short-lived regulatory proteins, or misfolded, oxidised
or otherwise damaged proteins, are marked and recognized for proteolytic
destruction and removal from an organism deserve more
intense research focus due to their importance. Researchers
in Canberra, Adelaide and Melbourne are currently
investigating these areas but could benefit significantly from
initiatives designed to exchange researchers and research
information through enhanced networking within Australia
Proteases in the Cell Nucleus.
The nucleus is the site of central functions
such as gene transcription, which are vital to maintenance
of normal healthy cells. A number of proteases and their
inhibitors have recently been found in the nucleus, their
important functions being turnover of transcription factors
and chromatin remodelling. The identity of
proteases and their inhibitors in the nucleus is being
investigated mainly by researchers in Melbourne, but this work would be
considerably enhanced by interaction with researchers in other states, allowing
Australian research to take a leading role in this important
new area of research.
- Intramembrane Proteolysis.
There is a growing number of
proteases that have been identified to process intramembrane
substrates. Whether such processes actually occur in the
membrane is not yet certain. However this a very important
class of under-studied enzymes that promise to tell us
something new about membrane proteins (right) and their biology. Membrane
biology is a frontier science and the important role of proteases in generating
and regulating membrane proteins deserves Australian research effort. A
workshop on Membrane Protein Structure is being held in Melbourne on 6
- Identification of Protease Substrates In Vivo.
Despite a great deal of
research having been carried out to assess the
function of individual proteases, the functional
profiles of many proteases, particularly those inside
cells, remains incomplete. This is in part because the
complete range of in vivo substrates is not known. At
a national level, a computer (Linux computer cluster,
right)-assisted bioinformatic approach is being used to
build models that allow scanning of the proteome for cleavage sites for a
particular protease, based on knowledge of its cleavage preferences. Putative
substrates can then be verified both in vitro and in vivo to provide a better
understanding of protease function. Such computer programs are intended to
become national and international resources which could considerably aid the
identification of in vivo substrates for proteases.
Proteases in Apoptosis and Tumours.
Australians have been at the forefront of unravelling the
mechanisms leading to cell death, and there is
continuing research on proteases that mediate cell death
and on tumour resistance to apoptosis mediated by
proteases. The development of orally active and highly
selective inhibitors of each of the proteases identified as
important in these mechanisms would provide valuable
in vivo tools for this research (caspase-8, left). Increased international
connections, information flow, and researcher exchange programs in this fast
moving field would also significantly help Australian protease researchers to
advance their efforts towards understanding and interfering with cell death.
- Proteases in Developmental Biology.
Proteases are crucial
in conception, birth, and developmental biology.
Australians are currently examining endometrial proteases,
caspases and the roles of deubiquitinating enzymes in
relation to contraception, infertility, endometriosis, healthy
foetus development, developmental biology, and birth.
However these efforts barely scratch the surface of what is
needed to understand the important roles of protease
enzymes in developmental biology. This network will make significant new
links between Australian and international protease- and non-protease
researchers to identify these roles, including fostering links with researchers in
the Network on Genes and Environment in Development
- Protease Activated Receptors.
Protease activated receptors (PARs) are being
increasingly found on different types of human cells, and seem likely to be
only the first of many groups of extra- and intra- cellular receptors for
proteases. PARs are already implicated in the airways as sentinels for sensing
trace quantities of proteases, and have been implicated in a variety of
inflammatory disorders, cancers and proliferative diseases. Australian
researchers are at the forefront of studies on PARs relevant to
asthma, allergy, inflammation and cancer, with asthma and
allergies being particularly problematic for young Australian
children. A present difficulty in this field is the lack of truly
selective and potent small molecule agonists and antagonists that
can be used as tools to properly validate the roles of these
receptors in biology. The network will encourage collaborative
interactions within Australia and with overseas researchers to advance
Australian capacity in this field.
Proteases As Diagnostics and Vaccines.
Australians have already made
important contributions to proteases like
kallikreins and metalloproteases that are
used as diagnostic markers of cancer.
Further efforts to associate protease
overexpression with diseases could find
application in the development of new
diagnostics. Similarly, Australian
researchers are in the process of developing experimental vaccines based on
proteases associated with parasites (hookworms, malaria, schistosomiasis) and
viruses (Dengue, RSV, West Nile). What is needed, that the network could
potentially provide, is some coordination and collaboration (through networking)
of these efforts towards the development of new diagnostics and new vaccines.
- Proteases in Insects and Plants.
Many plants are now known to produce high
concentrations of proteins that inhibit proteases, and these proteinaceous
inhibitors provide the plants with significant protection against pests and
pathogens. For example, certain serine protease
inhibitors from tobacco (Nicotiana alata) either
expressed in transgenic plants or supplied in artificial
diets affect growth and mortality of Helicoverpa
armigera and H. punctigera larvae, the major insect
pests for cotton in Australia. One research effort
between Melbourne and Brisbane is seeking to use these
protease inhibitors to enhance insect resistance in
transgenic cotton. Researchers in Canberra and Melbourne are characterising
insect proteases, which potentially represent very important targets for new
inhibitor-based insecticides. Overall the field of plant and insect protease research
is very much under-studied in Australia and has the potential to generate lucrative
new opportuntities for Australia in herbicides, insecticides and pesticides.
In addition to enlisting recruits to, and enhancing more intensive collaborations among,
current research teams through currently funded projects, the Network will use some of
its funding to initiate or enhance the above twelve proposed research directions through
creation of extensive team-based research programs. The Network will, once funded, call
for interested participants to fall into purpose-built teams to collaborate on the research
frontiers described briefly above or modified versions that may result from future
Network meetings between February-July. The National Network meeting in Brisbane
(Jan 22, 2004) clearly identified key players in each of the above initiatives, but the
Network wishes to expand those groups into much larger teams and to provide the
cohesive links necessary to make important and significant inroads to these frontiers.
(c) Infrastructure and Facilities
Network Participants' Institutes, Universities, Centres and Hospitals are listed in section 8.5 of this report. Access to Facilities and Infrastructure at those 32 institutions is through
individual researchers listed in our audit, most of which have contributed protease-
specific summaries of research activities and interests in links under Appendix 6. In
addition, the Network participants have collaborators in 20 countries and our preliminary
efforts to build an international protease network (www.protease.net) will help facilitate
global exchange of research and researchers, as well as access to infrastructure and
facilities around the world.
7. National Benefits
National benefits resulting from the establishment of an Australian Protease Network will include:
7.1. Capturing the National Benefits
Many internationally important discoveries on key biological roles of proteases,
suggested by the diverse range of physiological and biological functions already known
for proteases in humans and organisms. This new information will be essential in
understanding details of fundamental biological processes that are a matter of life and
New diagnostic kits, which can be expected to be developed based on Australian
research, since proteases are already recognized as prognostic indicators of diseases (e.g.
cancer, asthma, chronic inflammation, etc).
New inhibitors for proteases validated as important in disease, which could fuel the
creation of new Australian startup companies, with economic benefits for the country.
Proteases are already well recognized by the pharmaceutical industry as viable drug
targets, blockbuster drugs currently being used in man to treat HIV/AIDS (HIV protease
inhibitors), stroke and coronary infarct (thrombin inhibitors), hypertension (ACE
inhibitors). The industry needs both validation of other proteases as drug targets and new
selective inhibitors of those proteases for future commercial success.
International access to a highly skilled research network for collaborating
pharmaceutical/biotech companies and academic research groups.
New opportunities for student exchange, student and postdoctoral employment,
sabbaticals, value-added joint grant applications, opportunities for industry support,
product marketing and commercialisation, and global information and researcher
Increased Australian visibility in this very important field of basic and applied
research, enrichment of Australia's capabilities in interdisciplinary biological-chemical
research, increased commercial involvement in what is becoming a very lucrative
industry, and many discoveries important to the biology of life, ageing and death, and
maintenance of good health.
End-user engagement, including other network participants working on proteases in
different areas, pharmaceutical and other companies, hospitals, educators, and the general
A Young Investigator Program with initiatives to fast track the next generation of
researchers for management and leadership roles in Australian science. Components of
this program will include student travel bursaries for workshops, conferences, lab
exchanges, participation in and representation at network activities,
fellowship/grant assistance through organized mentoring, formal employment/vocational
Marketing and advertising of protease research, researchers, publicity for selected
network activities and reporting of clinical or other international successes to the
Educational materials and programmes which will emerge as a result of the
networking activities with outreach especially to university and hospital teaching.
In addition to generating the significant and synergistic benefits described above, the
Australian Protease Network will endeavour to ensure that these benefits are retained
within Australia. In this regard, the perceived benefits may be essentially grouped into (a)
scientific advances, b) commercialisation, and (c) education.
With regard to scientific advances, significant national benefit will be captured in the
form of increased numbers and quality of publications as well as higher citation rates of
members of the Network, both of which will further enhance the international reputation
of Australian researchers. An annual conference will provide a major opportunity for
organized and wide-ranging scientific exchange and targeted research recruitment. The
national and international websites will provide a convenient forum for reporting and
publicising Network activities, advances, and benefits. Scientific advances and these
activities will, in turn, facilitate increased postgraduate education opportunities within
Australia, enhance further scientific exchanges between states and countries, encourage
the return of expatriates, and relocation of other highly regarded scientists to Australia.
With regard to commercialisation, increased communication between Network members
as well as increased scientific productivity will result in increased capture and
exploitation of intellectual property, with concomitant effects on the national economy.
Sharing of commercialisation knowhow and experience can facilitate the mentoring of a
new generation of entrepreneurial scientists.
Finally, one of the main mechanisms for capturing the benefits derived from the
establishment of the Australian Protease Network will be in the area of education at both
undergraduate and postgraduate levels, where new knowledge generated will enhance
Network members' ability to teach at the cutting edge of protease research. The network
will also be producing web-based reports on conferences, workshops and training
programs, listings of material and equipment resources, highlighting scientific papers,
and soliciting expert comments on topical issues of public interest. These reports will be
valuable end-user targeted resources of interdisciplinary information and public relations
materials for use by educators, students, researchers and the general community.
8. Annotated Hyperlinks to Relevant Websites
8.1 Aligned Web Sites
International Protease Network register of researchers.
International Proteolysis Society official web page.
Network on Genes and Environment in Development
Australian Protease Network : 1st National Meeting
Institute for Molecular Bioscience
University of Queensland,
Brisbane, Queensland, Australia
Workshop on Membrane Protein Structure
Lecture Theatre, 7th floor
Walter & Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Victoria, Australia
Australasian Proteomics Society : 9th Lorne Proteomics Society
29th Lorne Conference on Protein Structure and Function
[Protease Session on February 9]
XVIIth International Congress on Fibrinolysis and Proteolysis
March 22-24, 2004
IBC's ScreenTech(R) World Summit 2004
discovery and development conference featuring four in-depth scientific
programs: Protein Kinases and Phosphatases, Protease Inhibitors,
Neurodegenerative Diseases, Advances in HTS & Assay Technologies.
June 26 - July 1, 2004
FASEB Summer Research Conference
Ubiquitin and Protein Degradation
Saxtons River, Vermont, USA
September 6 - 10, 2004
Joint 59th Harden/EMBO Conference
The Ubiquitin Proteasome System in Health and Disease
Cirencester (Cotswolds), England
June 5-9, 2005
4th International Symposium on Serpin Structure, Function and Biology
8.3 Individuals, Societies, Organizations
The American Society for Cell Biology
Website devoted to the exchange of scientific knowledge related to areas of cell biology.
The Cell Death Society
This site is primarily concerned with mechanisms of cell death and apoptosis.
This apoptosis and cell death related website is a non-profit initiative, maintained by PhD students.
Interactive cell biology resource.
European Cell Death Organization
society aims to facilitate the exchange of scientific information,
developments and links between researchers and research into cell death.
The Protease Consortium
A website devoted to proteolytic enzymes as therapeutic targets for cancer.
American Society for Biochemistry and Molecular Biology
Scientific and educational organisation for the advancement of the sciences of biochemistry and molecular biology
Australian Proteome Analysis Facility
centre working with the aim of using new technologies to aid in the
discovery of therapeutic, diagnostic and quality markers for
biotechnology, agricultural and academic industries.
The Proteome Society
for scientific information exchange, scientific discussion and a
general information resource concerning proteomic sciences.
A protease and protease inhibitor web server.
8.4 Sequence & Structure Data Bases
MEROPS: The Protease Database
resource and database for peptidases, (also known as proteases,
proteinases and proteolytic enzymes) and their protein inhibitors.
SCOP: Structural Classification of Proteins
Database containing structural classification of proteins, proteases, peptidases etc.
HIV Protease Database
Database of three-dimensional structures of HIV proteases and complexes.
The Calpain Family
Website devoted to the calpain family of proteases.
ProLysED: The Bacterial Proteases Database
of annotated SWISSPROT and PDB primary datasets containing additional
information such as predicted structures, known inhibitors, biochemical
Classification of peptidases into families, clans, and catalytic type based on structural similarities.
A Protein Degradation Resource
Information resource on protein degradation.
Ubiquitin and the Biology of The Cell
Free web-based copy of the book Ubiquitin and Biology of The Cell, with additional structural information and other resources.
8.5 Network Participants - Institutions, Universities, Centres, Hospitals
Australian National University
Baker Heart Research Institute
Box Hill Hospital
Heart Research Institute
Institute for Molecular Bioscience
Institute for Medical and Veterinary Science
La Trobe University
Murdoch Children's Research Institute
Peter MacCallum Cancer Center
Queensland Institute of Medical Research (QIMR)
Queensland University of Technology (QUT)
Royal Melbourne Institute of Technology (RMIT)
Royal Children's Hospital
Royal Prince Alfred Hospital
Royal North Shore Hospital
St George Hospital
St Vincent's Hospital
University of Adelaide
University of Canberra
University of Melbourne
University of Queensland (UQ)
University of New South Wales
University of South Australia
University of Sydney
University of Technology, Sydney
University of Western Australia
Victor Chang Cardiac Research Institute
Walter and Eliza Hall Institute of Medical Research