August 25, 2003
Computer Design Yields Better, More
Efficient Therapeutic for Preventing Tissue Damage
(Philadelphia, PA/Princeton, NJ)
- The tedious laboratory trial-and-error method for
refining protein/peptide-based medicines could be accelerated
and complemented by an innovative in silico (on computer)
protein design method, according to researchers at Princeton
University, the University of Pennsylvania School
of Medicine, and the University of California
at Riverside.
Their findings, appearing in a recent issue of the
Journal of the American Chemical Society, could drastically
decrease the time it takes to move potential biopharmaceuticals
from the drawing board to the drug store. In this study,
the researchers modeled a peptide (a chain of amino
acids, such as a protein or protein fragment) called
Compstatin, which prevents the autoimmune-mediated damage
of organs during transplantation, and various inflammatory
diseases. The computer modeling and optimization process
cut down on trial and error and created a version of
Compstatin seven times more efficient and stable than
the original.
Since the function of a peptide depends on its form,
the researchers modeled the effects of substituting
each of Compstatin's 13 amino acid subunits with a different
amino acid. The novel in silico sequence design method
could then model how the altered amino acid sequence
folds together in comparison to the original peptide.
"It is a major challenge to design new peptides and
proteins that exhibit the desired function such as improved
inhibition for the complement system. The challenge
centers around the problem of selecting promising sequences
from the huge number of possible combinations and making
sure those sequences will have the desired three-dimensional
structure," said Christodoulos A. Floudas, PhD, a Professor
of Chemical Engineering at Princeton University, whose
laboratory developed the in silico de novo protein design
approach. "At the heart of this innovative technology
is a unique two-stage computer protein design method
that not only selects and ranks sequences for a particular
fold, but also validates the stability and specificity
of the fold for these selected sequences."
"It would have taken us months - or even years - to
synthesize and screen the 80 quadrillion possible peptide
sequences that the protein design program considered,"
John D. Lambris, PhD, a professor in Penn's Department
of Pathology & Laboratory Medicine and a co-author on
the study whose laboratory had discovered Compstatin
in 1996. "In the end, we came up with two analogues
to Compstatin - each created by altering one amino acid
- that performed its job even better than the original
protein."
Compstatin works by blocking human complement, the
immune system's passive alarm network that detects pathogens
in the blood. Unfortunately, complement can also attack
healthy tissue, and a variety of diseases are associated
with complement gone awry, such as multiple sclerosis
and hemolytic anemia. In addition, complement is thought
to play a role in the destruction of cells during strokes,
heart attacks, and burn injuries. The complement reaction
is actually a series of interlocking cascades, or chain
reactions, of biochemical events involving at least
30 proteins. Compstatin works by preventing the activation
of C3, a protein that functions at the point where all
the complement protein cascades intersect.
The two Compstatin analogues derived from the experiment
are superior in their ability to cling to and, hence,
prevent the activation of the C3 complement protein.
Based on these two analogs, more Compstatin analogs
have since been designed, some of which are 200 fold
more active that the original Compstatin, according
to Lambris. These new Compstatin analogs will be further
refined and tested until ready for clinical trials.
To create templates of the desired shape for Compstatin,
Dimitrios Morikis, PhD, a researcher at the Department
of Chemical and Environmental Engineering of University
of California, Riverside, identified the three-dimensional
structure of Compstatin in solution via nuclear magnetic
resonance (NMR) experiments, which he then computationally
refined.
The computational de novo protein design system, developed
at Princeton University by Floudas and postdoctoral
associate John Klepeis, is a technological advance made
possible by (i) a novel mixed-integer optimization model
that narrows 200 trillion amino acid sequences into
a short list of candidates that are likely to produce
a peptide of the desired shape, and (ii) a system called
ASTRO-FOLD that, using first-principles, predicts the
structures that would be formed by the candidate sequences.
The second step confirms and refines the first.
A distributed computing environment consisting of eighty
Linux-based computers was used for all the computational
predictions, and the predicted new peptides were subsequently
synthesized and experimentally validated in the Lambris
laboratory at Penn.
For
a printer friendly version of this release, click
here.
###
Editor's Note: Dr. John
D. Lambris and the University of Pennsylvania hold the
patent for Compstatin.
PENN Medicine is a $2.2 billion enterprise
dedicated to the related missions of medical education,
biomedical research, and high-quality patient care.
PENN Medicine consists of the University of Pennsylvania
School of Medicine (founded in 1765 as the nation's
first medical school) and the University of Pennsylvania
Health System (created in 1993 as the nation's first
integrated academic health system). Penn's School of
Medicine is ranked #2 in the nation for receipt of NIH
research funds; and ranked #4 in the nation in U.S.
News & World Report's most recent ranking of top research-oriented
medical schools. Supporting 1,400 fulltime faculty and
700 students, the School of Medicine is recognized worldwide
for its superior education and training of the next
generation of physician-scientists and leaders of academic
medicine.
Penn Health System consists of four
hospitals (including its flagship Hospital of the University
of Pennsylvania, consistently rated one of the nation's
"Honor Roll" hospitals by U.S. News & World Report),
a faculty practice plan, a primary-care provider network,
three multispecialty satellite facilities, and home
health care and hospice.
|
