Annex 6
STFC RESEARCH PORTFOLIO—HIGHLIGHTS
DIAMOND LIGHT
SOURCE LTD
Professor Dame Louise Johnson, Director of Life
Sciences
Diamond is funded by the government (86%) through
the DIUS administered by STFC and by the Wellcome Trust (14%).
Diamond works closely with all the research councils, the Wellcome
Trust and the other funding agencies both through their formal
representation on advisory committees and through their funding
of users.
Diamond Light Source provides an intense source
of light and X-rays that are used in a range of experiments in
the life and physical sciences. Diamond began operation as a User
facility in 2007. Through its user programme in structural biology
with the Macromolecular Crystallography (MX) beam lines, Diamond
will contribute to the fight against the four communicable diseases
of the inquiry (influenza, tuberculosis, HIV/AIDS and malaria).
The MX beam lines exploit the intense X-rays to irradiate crystals
of biological macromolecules. The diffraction patterns from these
crystals allow the determination of the structures of the biological
macromolecules at the atomic level. Knowledge of structure provides
insights into biological function and the basis for a structure
based design of new therapeutic agents. Several academic user
projects, which are described in more detail below, are contributing
to drug design against specific targets from the causative organisms
of the four diseases.
Diamond will commence its industrial programme
in March 2008 and results from this will be driving the drug discovery
process to market. All the major pharmaceutical companies and
many of the small biotech companies have a structure based drug
design programme as a key component for new drug discovery, although
few companies are targeting TB and malaria.
In summary although Diamond Light Source does
not have its own programme to combat disease, Diamond is key to
the UK programme in structural biology by providing world-class
synchrotron radiation facilities and MX beam lines. The structural
biology results inform biological function and provide a basis
for logical drug design. Diamond is most suitably configured for
this role.
INFLUENZA
The two available anti-flu drugs, Relenza and
Tamiflu, approved in 1999 were both designed based on the knowledge
of the structure (determined in Australia) of the influenza virus
surface protein, neuraminidase. These successful drugs represent
one of the high points of structure based drug design.
New work is directed towards understanding how
the avian influenza virus can infect humans. The influenza virus
binds to its host cell through the binding of its second surface
protein, haemagglutinin (HA), to sugars on the surface of target
cells. In order to infect humans, avian influenza HAs need to
acquire changes in sequence that will allow them to bind to the
specific sugars ( 2,6 linked siallosaccharides) on human cells.
Understanding this switch in preference is a key to understanding
how avian viruses acquire the ability to pass between humans and
become pandemic. Scientists at the MRC National Institute for
Medical Research some years ago determined the structure of the
HA from the human virus that caused the 1918 Spanish flu pandemic
and from the structure they were able to explain why this strain
was so virulent (1). More recently in a user programme that will
exploit Diamond Light Source, their programme continues with a
study of avian H1 HAs and the HAs from the H5N1 avian viruses
and from viruses extracted from human patients. The results will
explain how H5 HA adapts to preferentially bind human receptor.
A promising start has been made (2).
TUBERCULOSIS
Although effective drugs exist for TB, current
therapy requires prolonged treatment, leading to compliance problems
and the emergence of multidrug resistance. There are further problems
in that the organism, Mycobacterium tuberculosis (Mtb)
can exist in a dormant state to be reactivated later. In the non-replicating
persistent state, the organism is believed to undergo a switch
in metabolism, using host lipid as an energy source. Current drugs
target the actively growing bacteria and are largely ineffective
against the dormant state.
The publication of the complete sequence for
Mtb in 1998 with the identification of ~ 3,900 open reading
frames that encode proteins has led to increased effort to functionally
annotate the proteins and to seek new drug targets that differ
from their counterparts in the human genome. Many distinctive
and unusual features have been noted, including a large number
of enzymes involved in lipid biosynthesis and metabolism (possibly
associated with dormancy) and a large proportion of the genome
dedicated to two families of unknown function. It has been estimated
that ~65% of gene products are of unknown function.
The genome information has stimulated an international
consortium for TB Structural Genomics formed in 2000. The work
of the consortium and other academic users has resulted in ~200
unique Mtb protein structures and a further ~250 ligand
complexes. This information has allowed the integration of data
from many other sources to illuminate the biological function
of proteins of previously unknown function (reviewed in (3)).
The information has also been used to develop a new series of
Mtb protein inhibitors (4).
In the user programme at Diamond, several groups
(from the Universities of Leeds, Birmingham and Cambridge, Kings
College and Birkbeck College) are addressing Mtb proteins
that include those that are targets against multi drug resistance
(DNA topoisomerase), those involved in mycolic acid and bacterial
cell wall pathways, those from the dormancy regulon, and a number
of other targets that also relate to worldwide international initiatives
to combat these diseases. The first paper from the MX beam lines
at Diamond (Lack et al (2007) Acta Cryst.F 64, 2-7) described
the structure of HsaD, a steroid-degrading hydrolase, from Mbt.
The enzyme is critical for the survival of M tuberculosis inside
human macrophages and is a potential target for therapy. The work
from a group at Oxford showed how the structure might be exploited
toward drug design.
It is anticipated that the structural biology
programmes will contribute to a better understanding of Mtb
biology and provide the basis for drug design. In order to
bring potential compounds to the clinic, new initiatives will
be needed to provide funding for the diseases of the poor.
HIV/AIDS
HIV/AIDS represents a second good example where
structure biology has led to effective drugs in the clinic. These
include the HIV protease inhibitors where intense effort first
based on the structures of a related retrovirus and then on the
HIV protease itself led to the commercially available products
such as Viracept, Agenerase and Aluviran approved in 1999-2000
and which are effective in the clinic.
In the user programme at Diamond further targets
are being pursued. The HIV reverse transcriptase is already a
target for therapy and is being further investigated (University
of Oxford) with new non-nucleoside and nucleoside inhibitors (5).
The HIV integrase executes the insertion of viral DNA into the
host cell genome, an essential multi-step process of the retroviral
life cycle involving host cell proteins (6). Structural studies
on the HIV integrase and cellular interacting proteins (Imperial
College) are leading to the definition of the mechanism of action
of new inhibitors.
MALARIA
Malaria poses an extraordinarily difficult disease
for drug design because of the complicated life cycle of the parasite,
its interactions with different hosts and the emergence of drug
resistant strains. Molecular targets for drug design include proteases
that hydrolyze hemoglobin, protein farnesyltransferase, heme detoxification
pathway, polyamine pathways, dihydrofolate reductase, artemisinin-based
combination therapies (ACTs), and enzymes of metabolic pathways
that are essential for parasite survival. Plasmodial surface proteins
have important roles in host cell invasion and are responsible
for antigenic diversity in this organism. In the longer term,
the answer to malaria is likely to come from vaccine development.
Vaccine development has yet to exploit structural approaches and
the interplay between antigen and immune response is more complex
than the interplay between a drug and its target protein. Nevertheless
knowledge of the three-dimensional structure of surface proteins
can facilitate our understanding their biological function, and
contribute to the development of therapeutic and vaccine strategies
against malaria (7).
Groups at the University of Oxford and at York
are using Diamond to tackle a number of specific proteins from
Plasmodium falciparum that include protein kinases that
are distinct from human protein kinases and which lend themselves
as good drug targets following the success of protein kinase inhibitors
for cancer treatment (8). Other targets include those proteins
involved in invasion of the red blood cell by the parasite, a
mitochondrial enzyme that is already a drug target, an enzyme
that is expressed in a stage specific manner in the parasite,
in addition to the enzymes dUTPase and thymidylate kinase and
their complexes with anti-malarial drug analogues.
REFERENCES
1. Gamblin, S J, Haire, L F, Russell, R J, Stevens,
D J, Xiao, B, Ha, Y, Vasisht, N, Steinhauer, D A, Daniels, R S,
Elliot, A, Wiley, D C, and Skehel, J J (2004) The structure and
receptor binding properties of the 1918 influenza hemagglutinin,
Science 303, 1838-1842.
2. Yamada, S, Suzuki, Y, Suzuki, T, Le, M Q,
Nidom, C A, Sakai-Tagawa, Y, Muramoto, Y, Ito, M, Kiso, M, Horimoto,
T, Shinya, K, Sawada, T, Usui, T, Murata, T, Lin, Y, Hay, A, Haire,
L F, Stevens, D J, Russell, R J, Gamblin, S J, Skehel, J J, and
Kawaoka, Y (2006) Haemagglutinin mutations responsible for the
binding of H5N1 influenza A viruses to human-type receptors, Nature
444, 378-382.
3. Baker, E N (2007) Structural genomics as an
approach towards understanding the biology of tuberculosis, J
Struct Funct Genomics 8, 57-65.
4. Arcus, V L, Lott, J S, Johnston, J M, and
Baker, E N (2006) The potential impact of structural genomics
on tuberculosis drug discovery, Drug Discov Today 11, 28-34.
5. Ren, J, and Stammers, D K (2005) HIV reverse
transcriptase structures: designing new inhibitors and understanding
mechanisms of drug resistance, Trends in pharmacological sciences
26, 4-7.
6. Al-Mawsawi, L Q, and Neamati, N (2007) Blocking
interactions between HIV-1 integrase and cellular cofactors: an
emerging anti-retroviral strategy, Trends in pharmacological
sciences 28, 526-535.
7. Bentley, G A (2006) Functional and immunological
insights from the three-dimensional structures of Plasmodium surface
proteins, Current opinion in microbiology 9, 395-400.
8. Doerig, C, and Meijer, L (2007) Antimalarial
drug discovery: targeting protein kinases, Expert opinion on
therapeutic targets 11, 279-290.
THE ROLE
OF E-SCIENCE
IN COMBATING
INFECTIOUS DISEASES
The drug discovery process is being greatly
accelerated by the use of GRID computing infrastructures. The
GRID infrastructures supported by STFC, EGEE (Enabling Grid for
E-Science) and GridPP (Particle Physics Grid), have been involved
in studies of Avian Flu and Malaria—and also of other infectious
diseases. Both of the infrastructures have substantial EC FP7
funding.
The Drug Discovery application software, where
scientists carry out "in silico" docking, has been running
on the EGEE production service since December 2004. In silico
docking enables researchers to compute the probability that potential
drugs will dock with a target protein. On a single computer, a
study involving 100,000 potential drugs might require six months
to complete—but can be accomplished in days using EGEE.
The next step in the development of GRID Software will be to increase
the performance of the application and compute millions of potential
drugs in only a few weeks.
In 2006, a collaboration of Asian and European
laboratories analysed 300,000 possible drug components against
the avian flu virus H5N1 using the EGEE Grid infrastructure and
similar facilities. To study the impact of small scale mutations
on drug resistance, a large set of compounds was screened against
the same neuraminidase target but with various, slightly different
structures. For the docking of 300,000 compounds against eight
different target structures of Influenza A neuraminidases, 2000
computers were used over four weeks—the equivalent of 100
years work on a single computer. Consequently, potential drug
compounds against avian flu are now being identified.
The WISDOM (Wide In Silico Docking On Malaria),
challenge identified over 46 million docked ligands during a one
month period in 2005—the equivalent of 80 years work on
a single PC. In this case, 1000 computers were simultaneously
used in 15 countries around the world.
The DENGUE project is also using in silico docking
to identify new potential compounds directed against proteins
that mediate essential functions for dengue virus infection and
replication whilst the AFRICA@home project is a grid based project
aiming at improving epidemiological monitoring of Malaria in Africa.
These grid projects have the potential to transform
into true e-Science projects, integrating in silico research with
experimental biology and chemistry.
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