that bind to and capture biowarfare agents are on the drawing board
at Livermore. The goal is for these molecules to quickly and efficiently
detect such deadly pathogens as botulinum toxin, anthrax spores,
or smallpox. Using synthetic chemistry, scientists produce these
new molecules that bind to unique sites on the surface of the toxin
or organism. Their two-pronged, or bidentate, structure is critical.
When a small molecule binds to a protein, the attachment is usually
weak, and the interaction between the two is short-lived. If, however,
two or more small molecules that bind to the protein are linked
together, their binding to the same protein may be thousands, even
millions, of times stronger. By targeting specific proteins, the
synthetic molecules will mimic some of the behavior in our immune
system where antibodies recognize molecular foreign entities in
our bodies and abnormalities such as cancer cells.
A single detector armed with
many of these synthetic targeting molecules could simultaneously
recognize an equal number of harmful biological agents that might
be used in a terrorist attack. Assays using antibodies, known as
immunoassays, are widely used to identify pathogens in the laboratory
and form the basis for many biowarfare detection systems fielded
to date. However, only seven good antibodies are currently available
for pathogen detection. Other detectors depend on recognizing the
bioagents DNA. But some pathogens, such as viruses,
require human exposure to only a small number of organisms to be
acutely toxic, says Livermore biochemist Rod Balhorn. With
so little DNA present in each virus and given the rapid variation
that occurs in the base sequences that make up the DNA, those pathogens
are typically very difficult to detect.
Similarly designed targeting
molecules could zero in on defective or overactive proteins in our
bodies and poison them, just as our natural antibodies do. These
antibodylike molecules can lock on to cancer cells or other pathogens
and kill themand only them. By targeting unique sites on other
proteins that cause diseasefor example, the proteases that
cause inflammation in arthritis or enable HIV to functionthe
synthetic molecules would block the activity of the protein without
entering its active site. The active site is a cavity on the surface
of a protein that is used by the protein to perform its function.
Similar active sites can be present in many proteins, both those
that are essential to cell function and others that cause disease.
The pharmaceutical industry
has already begun using this approach to develop drugs that function
as intended without blocking the activity of healthy cells or proteins.
Molecules that target unique sites on the surfaces of specific proteins
may soon lead to a new generation of drugs that have minimal side
Balhorn is leading the program
at Livermore to design synthetic molecules for bioagent detection
and cancer treatment. He and a team of Livermore investigators are
collaborating with scientists at Brookhaven and Sandia national
laboratories and the University of California at Davis Cancer Center.
Together, they are developing the methods needed to produce the
first of these synthetic antibodylike molecules.
Terminology is a little
tricky, he notes. It is tempting to call our new molecules
synthetic antibodies. But we are designing small molecules
that function like antibodies, not large proteins that are synthetic
versions of antibodies. So we use the term high-affinity ligands
to describe our molecules.
Ligand is a general
term used to describe a small molecule that binds to proteins or
other large molecules. The higher the affinity a ligand has for
a specific protein, the more tightly it binds to it. Research by
others has demonstrated that bidentate ligands have a vastly increased
affinity for the target protein, anywhere from thousands to millions
of times greater. Polyvalent ligandsmolecules that bind to
multiple sites on the surface of a proteinare observed in
many biological interactions that require very tight binding. The
seek-and-destroy antibodies of our immune system, which normally
operate quite successfully, are one example.
What were doing
is searching for two molecules that bind to two sites next to each
other on the surface of a protein, says Balhorn. Then
our synthetic chemist joins them together using a third molecule,
called a linker. The linker must be both flexible and robust, or
the new molecule will fall apart. This new synthetic ligand will
then behave pretty much like an antibody, binding tightly to the
The new bidentate molecules,
called high-affinity ligands (HALs), will have several advantages
over naturally occurring antibodies. They can be totally inorganic
(nonprotein) and can be synthesized in large quantities using methods
to ensure that each batch is structurally and functionally identical.
They will also be stable over a long period, making them excellent
candidates for long-term deployment in detectors for agents of biological
schematic diagram shows how a linker molecule will connect
molecules that bind to two sites on a protein. The goal is
to develop a process for designing and producing high-affinity
ligands for any structured surface. When two molecules are
connected with a linker, they bind with up to a million times
higher affinity than does each molecule alone.
bioagent detectors, HALs can be designed to target protein toxins
produced by pathogens as well as any major protein component of
pathogenic organisms. For the National Nuclear Security Administrations
Chemical and Biological National Security Program, work is under
way to develop HALs that bind to the Clostridium neurotoxins,
which include botulinum and tetanus, the most toxic substances known.
The Clostridium toxins attack the central nervous system
and cause spastic paralysis in the case of tetanus and flaccid paralysis
in the case of botulinum.
Balhorns team is laying
the groundwork for future development of HALs to target the Staphylococcus
enterotoxins, which cause acute intestinal symptoms such as those
associated with food poisoning, and ricin, a residue of castor bean
processing that causes major intestinal or respiratory complications.
The bodys response to toxic quantities of either of these
substances is swift and often fatal.
Work is also scheduled to
begin in the near future on HALs that bind to proteins in the spores
of Bacillus anthracis (anthrax) and in Yersinia pestis
(plague). Once these HALs are completed, efforts will focus on the
next highest priority agents: smallpox, Francisella tularensis
(a plaguelike illness), and Brucella melitensis (an organism
whose infections, often called Mediterranean fever, cause spontaneous
abortions). Creating synthetic ligands even for proteins with a
known structure is still a research project. Work began in 2000,
and Balhorn estimates that high-affinity ligands for these eight
bacterial toxins and threat organisms can be delivered in about
neurotoxins have three parts: the targeting domain and the
translocation domain, which together make up the heavy chain,
and the catalytic domain, which makes up the light chain and
is the toxic part of the molecule.
the structure of the target protein is known, the team uses that
structure to develop a HAL. Work on these molecules is a logical
progression from Livermores protein structure and computational
biology effort, with which Balhorn has been involved since its inception.
(See S&TR, April
Biology Looks at the Tie that Binds.) Using x-ray crystallography
and nuclear magnetic resonance (NMR) spectroscopy, high-resolution
structures for many proteins have been determined at laboratories
around the world, including Livermore. These include several types
of Clostridium toxins (botulinum and tetanus) and the Staphylococcus
All toxins in the Clostridium
family have three parts. The targeting (or binding) domain, which
binds to receptor molecules on the nerve cell membrane, and the
translocation domain, which makes a pore in the cell through which
the toxin passes, together make up what is known as the heavy chain.
The light chain, which contains the catalytic domain, is a protease
that is injected into the nerve cell and disrupts its functioning.
For the Clostridium
neurotoxins, the team is developing a HAL to bind to the targeting
domain, that fragment of the protein that recognizes and binds to
motor neurons. Of these neurotoxins, botulinum is considered a greater
threat than tetanus, but tetanus is easier to work with. Fortunately,
its targeting domain is sufficiently similar in structure to botulinums
that it serves as a model for botulinum.
In 1998, Livermores
x-ray crystallography group completed a high-resolution structure
of the binding domain of the tetanus toxin. Researchers then computationally
calculated the molecular surface of the protein to identify sites
where binding is likely to occur. We look for pockets on the
surface of the folded protein, places where another molecule would
be able to fit tightly, says computational chemist Felice
Lightstone. For the tetanus toxin, Lightstone found two appropriate
sites adjacent to one another on the binding domain.
For a HAL to be effective,
the sites designated for binding must be on a part of the toxin
that is conserved, meaning that these regions remain
essentially identical across all strains of a toxin. When bioagents
are being genetically engineered, areas such as these are difficult
to modify without altering the toxicity of the agent. Ideally, a
high-affinity ligand for tetanus toxin will be able to recognize
engineered and other unknown or related Clostridium toxins.
The next step involved selecting
compounds that might fit into the two sites. All of the 300,000
compounds in the Available Chemicals Database, a listing of all
commercially available compounds, were computationally inserted
(docked) into each site. The potential fit and interactions were
then assessed. The top 1,000 compounds were run again using a range
of structures for each compound representing the different bond
orientations and shapes, known as conformations, that each molecule
is likely to adopt. In this manner, the top 100 compounds were identified.
The calculations for each site took about 3 weeks on a Linux cluster
of 40 dual-processor personal computers.
Sandia National Laboratories
in Livermore has recently written new programs to expedite this
time-consuming process. Each compound is tested in 10 different
conformations to see which fits best into the rigid protein. This
provides a more realistic test of binding, because many of these
small molecules are not rigid and can adopt different conformations.
Computational docking projects typically have success rates
of anywhere from 10 to 40 percent, says Lightstone. Even
before we started using our new version of this program, our success
rate of identifying molecules that actually bind to the protein
was in the 40- to 65-percent range. Now, the likelihood of getting
a fit may be even greater.
The x-ray crystal structure for the tetanus toxin showing how
the amino acid chain is folded and (b) its calculated molecular
surface showing sites 1 and 2, predicted binding sites for ligands.
Once possible ligands have
been identified computationally, they must be tested in the laboratory
to see whether binding actually occurs. Mass spectrometry (MS) and
NMR spectroscopy are both effective for testing ligandprotein
binding. NMR examines binding in the solution state, while MS looks
at binding in the gas phase. MS typically requires much smaller
samples, but it cannot handle certain compounds or chemical buffers.
NMR can examine mixtures of compounds more easily and determine
which combinations bind best in solution. Both techniques can identify
where on the target protein binding is occurring.
The initial computational
screening process to find new compounds that bind to tetanus neurotoxins
resulted in 100 possible ligands that were predicted to bind to
one of two sites (site 1 and site 2) on the tetanus neurotoxins
targeting domain. Experiments using electrospray ionizationmass
spectrometry (ESIMS) suggested that 7 of the first 13 tested
compounds bound to the toxin. With ESIMS, ligand binding is
confirmed when a new mass peak appears at the expected mass-to-charge
ratio for the ligandtetanus complex.
antitumor drug doxorubicin was discovered to be the best fit at
site 1. The binding of this ligand to site 1 was later confirmed
by x-ray crystallography of doxorubicintetanus toxin and doxorubicinbotulinum
toxin complexes. For site 2, the same MS method was used to screen
1 of 100 compounds, six of which were observed to bind. The figure
below shows one of these ligands, lavendustin A, docked into site
2 in the predicted structure of the tetanuslavendustin A complex.
The six ligands predicted
to bind to site 2 were then screened for binding to the targeting
domain using NMR. The six molecules were tested individually, as
mixtures of different combinations of the compounds, and in the
presence or absence of the known site 1 binder, doxorubicin.
When examined by NMR, small
molecules exhibit weak, negative signals referred to as NOEs (nuclear
Overhauser effects). Large molecules such as proteins exhibit strong,
positive NOEs. When small molecules bind to proteins, the characteristics
of the NOE for the large molecule are transferred to the small molecule.
Thus, strong NOEs are detected for ligands that bind to the protein.
The NMR screening of mixtures
containing the six predicted site 2 ligands confirmed that four
bind to tetanus toxin in solution. Using a novel transfer NOE (trNOE)
competition assay, researchers have determined that three of these
ligands bind in the same site, presumably at site 2. The fourth
ligand was determined to bind in a third site distinct from site
1 and site 2.
NMR experiments were also
performed to evaluate how possible structural changes induced by
the binding of one ligand in site 1 could influence the binding
of the second ligand in another site. In these experiments, doxorubicin,
which was added first, remained bound to site 1 throughout the additions
of all six of the predicted site 2 ligands. The mixture containing
doxorubicin and lavendustin A produced the strongest positive trNOE
signal in the presence of the tetanus toxin. This experiment confirmed
that both lavendustin A and doxorubicin bind simultaneously to the
toxin, indicating that each must bind to a different site.
assay cannot define the location of the binding site, says
physical chemist Monique Cosman, leader of the NMR group at Livermore.
But since doxorubicin is known to bind to site 1, we know
that lavendustin A must bind to a different site, which may be site
By performing these trNOE
binding experiments with pairs of molecules that were determined
to compete for binding to the same site, Cosman developed a new
NMR method for identifying the relative strength of binding of each
ligand to a particular site on the protein. MP-biocytin, another
molecule that binds to site 2, did so with a relatively lower affinity
than lavendustin A. The affinity of the third ligand is similar
to that of lavendustin A, but it was not studied further because
it is too perishable.
predicted structure of the tetanuslavendustin A complex.
Lavendustin A is shown in purple binding to site 2.
Mass spectrometry was then
used to verify where the molecules are binding. Chemist Sharon Shields
developed a new method that combines MS with proteolysis, a process
in which a protein is digested by enzymes. This is unique,
she notes. Now we can study solution-phase biological processes
using a gas-phase mass spectrometric method.
She first treated the targeting
domain of tetanus toxin with proteases that make clips in the amino
acid chain either alone or on the tetanusdoxorubicin complex
using various ratios of doxorubicin to the neurotoxin. Then she
used matrix-assisted laser desorption ionization and ESIMS
to determine the pattern of enzymatic degradation that had occurred.
In the tetanusdoxorubicin combinations, doxorubicin prevented
the enzyme from digesting the protein at the binding site by limiting
access to the amino acids located in that region.
The figure below shows a
map of peptides (amino acid chains) produced by digesting the tetanusdoxorubicin
complex compared to the tetanus toxin alone. In this experiment,
Shields used the enzyme trypsin. The decreased abundance of peptides
indicates the location where binding is occurring. That location
contains amino acids 299304, 351376, and 394434.
Molecular docking calculations had predicted that doxorubicin would
reside near amino acids 356, 358, 359, 407, 409, 419, 427, and 437.
These predictions are a close match to MS results. Comparable locational
experiments using other enzymes had similar results.
Shields also found that the
presence of doxorubicin induces subtle changes in the tetanus toxins
three-dimensional structure, suggesting that the protein may envelope,
or wrap around, doxorubicin when it binds. Further experiments are
needed to confirm these results.
This map of peptides (amino acid chains) compares the doxorubicintetanus
toxin complex to the tetanus toxin alone. Amino acids in yellow
represent the peptides that showed a decreased abundance, which
indicates that binding is occurring. (b) Computational docking
studies predicted that binding would occur at the location shown.
The two match quite well.
a New Molecule
Synthetic chemist Julie Perkins
has the job of linking the two molecules that bind to sites 1 and
2 to create a new HAL. This is the critical step. She is experimenting
with linkers that will connect doxorubicin and MP-biocytin as well
as doxorubicin and lavendustin A. We know that each of these
compounds binds individually to sites 1 and 2, but because they
bind weakly, they can also float away, Perkins says. When
the compounds are linked together, they are much more likely to
She is starting with the
amino acid lysine as a linker. Lysine is an ideal building block
because it has three distinct functional groups upon which she can
perform synthetic chemistry experiments. Many derivatives of lysine
are commercially available as well. The molecules that have been
identified to bind into site 1 and site 2 can either be attached
directly to lysine, resulting in their close proximity, or with
a linker, which increases the distance between them. Increasing
the distance between the two compounds with a flexible chain may
also help increase the affinity of the ligand for the protein.
To achieve maximum
affinity of the ligand for the protein, we have to find the optimal
length and rigidity of the linker, says Perkins, and
that can only be done experimentally. She is experimenting
with a flexible glycol chain that can be attached to the lysine
to increase the distance separating the two ligands.
Once she has synthesized
each new compound containing the two linked ligands, conventional
binding studies will identify the highest affinity and most selective
ligand combinations. These studies will determine how tightly the
HALs bind and confirm that they selectively bind only to Clostridium
chemist Julie Perkins works to link two molecules, each of
which binds to two protein binding sites. The new molecule
will bind more strongly and securely to a specific toxin protein
than the individual molecules can.
For cancer therapy, the challenge
is to synthesize molecules that bind with high affinity to each
cancer cell without themselves generating an immune reaction from
the body. Targeting molecules therefore must be smaller and more
specific and have higher affinities than natural antibodies. They
should also not be made of proteins, which elicit an immune response
from the body.
The goal is to use these
small, exceptionally high-affinity molecules to deliver a lethal
radiation dose directly to a tumor. In this case, the HALs would
be tagged with radioactive isotopes and introduced into the body.
Research all over the world is focused on this new technique, known
as isotopically enhanced molecular targeting.
create new HALs for cancer treatment, Livermore is using the same
process developed for producing HALs that bind to toxins and pathogens.
The first project will be a HAL for a receptor protein found on
the surface of non-Hodgkins lymphoma, HLA-DR10. The crystal
structures of four HLA-DR molecules are known, and unique binding
sites on the HLA-DR10 protein have been identified using computer
models of the protein generated by computational biochemists Adam
Zemla and Daniel Barsky. Computational docking experiments are under
HAL developed for binding HLA-DR10 and targeting human lymphomas
will be designed to rapidly pass through the liver and kidney and
thus minimize the systemic damage that can occur when antibodies
carry radionuclides. We are striving to convert the meaning
of the word cancer from fear, pain, suffering,
and death to just another treatable disease,
1 and 2 on the HLA-DR10 molecule (a protein receptor for non-Hodgkins
lymphoma) have been identified.
of Unknown Structure
When a target proteins
structure is not known, the team will use a different route to design
and synthesize HALs. Computers cannot be used to predict the binding
of molecules to sites on these proteins. But NMR and MS processes
that are being developed and fine-tuned now for identifying ligands
that bind to known protein structures will identify ligands that
bind to unknown structures.
of molecules will be experimentally screened for their ability to
bind to the protein using a combination of Cosmans NMR technique
and mass spectrometry methods being developed by chemist Lori Zeller.
The molecules that bind will be segregated into sets that bind to
different sites. Perkins will then synthesize all possible combinations
of pairs of these small molecules using a series of different-size
linkers. With Livermores new Fourier transform ion cyclotron
resonance mass spectrometer, mixtures of the HALs and protein can
be quickly screened to identify the particular combination of ligands
and linkers that produce HALs that bind to the protein. This approach
should work well for creating detection reagents for pathogens.
In collaboration with groups at Porton Down Defense Science and
Technology Laboratory in England, Livermore researchers will design
the first HAL for a protein with an unknown structure to bind to
a protein on the coat of the anthrax spore.
will design a high-affinity ligand to bind to protein in the
spore coat of Bacillus anthracis (anthrax).
The Livermore team will soon
produce its first HAL for the Clostridium neurotoxins. To
know whether this work has been successfulwhether the ligand
works as designed in a bioagent detectorthe team will send
its results to the Department of Defenses Critical Reagent
Program to be assessed for quality and specificity.
the war against bioterrorism, the best defense begins with having
the best possible data. Work has begun on docking studies to identify
binding sites on the light chain of botulinum toxin. In this case,
the goal is to synthesize HALs that can distinguish between the
different types of Clostridium neurotoxins. That kind of fine-tuning
is essential for accurate bioagent detection and identification
during a crisis.
Key Words: antibodies,
bioterrorism, botulinum toxin, cancer treatment, Clostridium neurotoxins,
high-affinity ligands (HALs), mass spectrometry (MS), nuclear magnetic
resonance (NMR), protein structure, synthetic chemistry, tetanus.
information contact Rod Balhorn (925) 422-6284 (firstname.lastname@example.org).