Modern pharmaceutical, food, materials
and nanotechnology industries increasingly rely
on the rationalisation and prediction of molecular
structure, stability and function in order to
optimise their products, reduce the time and cost
of development and increase their success rate.
Molecular model of tRNA
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The methods of computer simulation and molecular
modelling, such as Monte Carlo (MC) and molecular
dynamics (MD), continue to come of age making
significant contributions to a wide variety of
experimental fields, ranging from molecular biology
and drug design to nanotechnology and biomaterials
design. Concomitant rapid advances in computational
power have enabled these technologies to tackle
physical, chemical and biological molecular phenomena
of unprecedented high complexity (e.g., protein-protein
interactions), long time scales (e.g., protein
folding) and/or long length scales (e.g. polymer-nanoparticle
interactions). The key advantage of MC and MD
computer simulation methods over various experimental
techniques lies in their ability to allow scientists
to describe in exquisite atomistic detail the
behaviour of individual molecules. These methods
are also able to track the time evolution of the
structure and interactions of molecules from the
femto to the microsecond scale. This level of
sophistication enables the analysis of nearly
every conceivable property of single molecules
or bulk materials.
Our research efforts are aimed at investigating
the molecular forces that determine the stability
and activity of biomolecules, the behaviour of
polymeric drug delivery systems, and the specificity
and strength of drug-protein interactions. Furthermore,
we aim to develop computational algorithms and
methods that impact drug discovery and delivery,
particularly in major diseases such as diabetes,
cancer and Alzheimer's disease. These developments
and their outcomes have great potential for the
generation of intellectual property of significant
value to the pharmaceutical, biomaterials, nanotechnology
and software industries.
Molecular model of Bovine Rhodopsin used as
the template for most 7TM receptor comparative
models.
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We have international collaborations with Prof.
Jannis Samios (National University of Athens,
Greece), Prof. John Finney (University College
London, UK) and Prof. Miguel Costas (National
University of Mexico).
The Biomolecular Modelling Group has interests
in a number of specific areas:
(1) Protein flexibility
and solvation in drug design.
The influence of water is critical in determining
their specificity, geometry and affinity of biomolecular
interactions. This arises from the entropic effects
and desolvation penalties that determine the magnitude
of the free energies of binding. In recent years
we have been developing methods for incorporating
an explicit treatment of hydration into computer-aided
drug design (see Figure 1). The next step is to
implement a realistic method for the dynamic hydration
of ligand-protein complexes within docking and
structure-based drug design applications that
can deal with water-mediated contacts and desolvation.
In the case of protein-protein interactions, it
is also essential to determine the magnitude of
water-mediated interactions on the free energies
of binding between two protein molecules or between
one of the proteins and a drug molecule. These
are outcomes of significant importance for the
pharmaceutical industry, since the lack of success
in many drug discovery projects can be partly
attributed to neglecting the aqueous environment
in which biological interactions take place.
Figure 1. Snapshots of Monte
Carlo computer simulations of a ligand-protein
complex in vacuo and in explicit solvent, showing
the development of a hydrogen-bonding network
around the bound ligand.
Protein flexibility at both the levels of local
sidechain rearrangements and large inter-domain
conformational changes also plays a crucial role
in drug-protein and protein-protein interactions
of therapeutic interest. Recently methods have
been developed for predicting and/or incorporating
the effects of protein flexibility in drug design
(see Figure 2). Further research is now required
to be able to predict protein conformational changes
upon binding to a drug or second protein, as is
the case of the insulin receptor (see below).
Many current therapeutic targets involve proteins
that undergo conformational changes as part of
their normal function (e.g. insulin receptor,
protein kinases, GPCRs), creating the need in
the pharmaceutical industry for an appropriate
method of characterising and predicting such conformational
changes and the way they affect the design of
drugs. The joint treatment of explicit hydration
and protein flexibility will allow for the modelling
of ligand-induced conformational changes in aqueous
solution, creating an accurate approach to the
modelling of ligand-protein interactions.
Figure 2. Comparison of predicted
conformation (shown in pink) of a ligand binding
site in a protein against experimentally-observed
conformation (shown in green).
(2) Drug-protein
interactions.
We have recently been involved in the development
of new ligand-protein docking optimisation methods
and the analysis of conformational, hydrogen-bonding
and hydrophobic properties of ligand binding sites
(see Figure 3). We are working on developing a
description of the steric properties of binding
sites and to identify regions within a binding
site of unique geometric and overall interaction
properties. This will solve the problem often
found in drug design when selecting, prioritising
and partitioning the large number of hydrogen-bonding,
hydrophobic and steric features of a binding site
or protein interface.
Figure 3. An analysis of the
hydrophobic properties of binding sites reveals
subtle differences when shape, extent and steric
crowding are considered.
At the same time, these new methods can be applied
to drug discovery efforts in therapeutic areas
such as diabetes and cancer. In the case of diabetes,
small insulin-mimetic molecules that can be taken
orally have been recently developed through the
use of a pharmacophore model of insulin and further
work is being carried out to explore novel molecular
scaffolds.
(3) Protein-protein
interactions.
Protein-protein interactions involve extended
interfaces whose complementarity determines the
free energy of interaction. We have recently been
involved in the development of new methods for
computing protein-protein interaction free energies.
We are developing these methods by looking at
selected "mutants" of protein complexes
in order to disentangle their steric, electrostatic,
hydrophobic and water-mediated contributions.
Molecular dynamics simulations help determine
the role of the dynamic plasticity of amino acid
sidechains and water molecules in determining
the strength and specificity of interaction.
(4) Drug loading
and delivery in nanoparticles.
In the area of drug delivery, biodegradable copolymeric
materials have been used for some time to achieve
surface erosion for the controlled delivery of
embedded drug molecules. The delivery of drug
molecules is dependent upon the rate of solvent
penetration, pH and ionic force, responsible for
the gradual degradation of the polymeric surface.
Dendrimeric materials have also been used to physically
encapsulate drug molecules through hydrophobic
interactions or steric impediment. However, currently
there is limited knowledge of the molecular mechanisms
responsible for the successful loading and delivery
of drug molecules. We can use computer simulation
methods to provide insight into the molecular
mechanisms underlying the interactions of the
drug with the designed chemical components of
the nanoparticle and the role of additives in
enhancing these interactions.
One application of polymeric nanoparticles has
been the targeting of the blood-brain barrier
to enhance the delivery rate and specificity of
treatments for analgesia and Alzheimer's disease.
Computer simulation methods are being used to
investigate the molecular structure of encapsulated
drug molecules in copolymeric biodegradable materials,
the mechanism of penetration of water and its
pH and ionic force dependence, and the mechanism
of interaction of the drug with the various chemical
polymeric components that might influence its
loading and delivery. The aim is to aid the optimisation
of the formulation of copolymers in order to enhance
the incorporation of water soluble peptides.
(5) The hydrophobic
effect.
The hydrophobic effect is the archetypal solvent-induced
force, arising from the intermolecular ordering
processes in water that occur in the vicinity
of non-polar species in aqueous solution. This
phenomenon has been widely studied due to its
importance in many chemical and biological processes:
the solubility of drug molecules, the adsorption
of surfactants onto surfaces, the formation of
micelles and biomembranes, the interactions between
macromolecules and the association of ligands
and proteins in solution, and the folding and
stability of proteins.
Figure 4. Snapshot of a molecular
dynamics computer simulation of an aqueous solution
of methane (coloured in pink) in the presence
of NaCl (coloured in green and blue), showing
the hydrophobic aggregation of a methane cluster.
We have conducted a substantial number of computer
simulations in order to characterise the temperature,
pressure and salt concentration dependences of
hydrophobic interactions in aqueous solution (see
Figure 4). However there is still controversy
about the effect of water density and cooperativity
in hydrophobic interactions.
Interestingly, other highly hydrogen-bonded liquids
such as hydrazine and formamide exhibit solvophobic
effects similar to those of water. It remains
unclear what molecular processes are involved
in the formamide/hydrazine solvation of non-polar
species. These solvents provide an excellent experimental
and theoretical framework to contrast their physico-chemical
solvophobic properties with those of water. They
may also provide alternative routes for the preparation
and stabilisation of micellar solutions and biomembranes.
We are investigating hydrophobic and solvophobic
effects in aqueous and non-aqueous solvents by
characterising the solvent-induced interactions
of small non-polar molecules and their temperature,
pressure, concentration and ionic force modulation.
Computer simulation techniques are used to characterise
the free energy changes and the solvent structure
and dynamics in simple but realistic systems by
modifying the solute concentration, size and curvature,
temperature, pressure and/or salt concentration.
(6) Protein denaturation
and stabilisation.
Chemical reagents such as urea, guanidium chloride
and ethanol exhibit characteristic molecular interactions
with proteins during their denaturation. Interestingly,
these agents have the ability to increase the
solubility of non-polar molecules in water and
to increase the critical micelle concentration.
The molecular mechanisms behind such observations
are still not well understood. These denaturants
seem to act as anti-hydrophobic agents and it
is believed that their molecules either bind directly
to non-polar surfaces or disrupt the structure
of water. It is important for the food and biopharmaceutical
industries to be able to predict the conditions
that favour the stability of proteins in, for
example, foodstuffs and biological reagents.
Computer simulations are being used to determine
the structure and dynamics of hydration in model
systems like water/urea and water/alcohol/urea
solutions, where there is experimental (structural
and thermodynamic) data available. In the case
of proteins, computer simulations are being used
to determine the nature of the interactions of
the protein surface with such denaturant agents,
as well as the degree of solvent accessibility
at different denaturant concentrations and temperatures
when compared to water accessibility. This will
help determine the extent of protein chemical
degradation under various solvent formulations.
(7) The mechanism
of cryoprotection.
Aqueous mixtures of solvents such as DMSO, glycerol,
and ethylene glycol are widely used as cryoprotective
agents to preserve biological tissues during freezing.
It is believed that these agents suppress crystallisation
in cell water by inducing the formation of a glassy
state, preventing hyperosmotic injury of the tissues
caused by sodium chloride. An analogous mechanism
is said to allow the stabilisation of proteins
by sugars at low hydration levels. However, there
is the need for molecular modelling and computer
simulation studies to assist the explanation of
the molecular mechanism of cryoprotection, as
some solvents have the above properties and others
do not. This knowledge would help with the design
of better solvent mixtures to improve the cryopreservation
properties and cooling/heating rates used.
In recent years we have carried out a number
of computer simulations to investigate the effect
of temperature and DMSO concentration in aqueous
solutions near room temperature. These studies
have validated recently developed intermolecular
potentials of DMSO and have shed new light on
the hydrogen-bonding structure that develops in
water/DMSO mixtures. We are now interested in
investigating the inhibition of the crystallisation
of water under various concentrations and temperature
conditions in order to characterise the suggested
formation of a glassy state (vitrification). We
are particularly interested in determining what
molecular properties of a solvent in aqueous solution
allow it to have cryoprotective properties.
Contact Details of Program Leader
Name: Dr Ricardo L. Mancera
Institution: WABRI - Curtin University
GPO Box U1987, Perth WA 6845
Phone: +61 8 9266 1017
Fax: +61 8 9266 7485
E-mail:
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