™

www.oncogenex.ca
Bringing hope to life.™

Antisense technology
DNA, RNA, and Protein Basics
In living organisms, DN A car r ies all of the always partners with G. The sequence or order of
instructions for building the proteins that make up these nucleotides establishes the cell’s recipe for
an organism, coded in small sections called genes. making proteins.
DNA consists of a constant backbone made of
In a process called transcription, DNA is used as a
sugar and phosphate molecules as well as variable
template to manufacture an RNA molecule, called
nucleotides or bases (Adenine, Thymine, Guanine,
messenger RNA (mRNA). mRNA communicates
Cytosine, commonly known as A, T, G and C). DNA
the genetic message found in DNA to other areas
resembles a ladder, forming a twisted, double-
of the cell so protein production can occur. Like
stranded structure with the nucleotides making up
DNA, RNA is made up of nucleotide base pairs and
the rungs of the ladder and the backbone forming
a sugar-phosphate backbone. During translation
the sides of the ladder. One strand of the ladder
phase, mRNA travels to the ribosome, which is the
(sense) matches exactly with its complementary
cell’s machinery that assembles proteins based on
strand (antisense); the nucleotides that make up
the instructions contained in the mRNA.
the rungs of the ladder are very specific in how they
match each other. A always partners with T and C

How Antisense Works

While traditional drug therapies are based on
designing compounds that block or inhibit disease-
causing proteins, antisense therapies focus on
preventing the production of disease-causing
proteins. Antisense drugs are based on small DNA-
like or RNA-like constructs that bind to the protein-
coding strand of genetic message (mRNA), blocking
the translation of the disease-causing protein. By
binding to mRNA, antisense drugs prevent the
genetic code from being read by the ribosome, which
is responsible for translating and manufacturing
proteins; additionally, the bound antisense/mRNA
complex is enzymatically degraded so the protein
cannot be synthesized.

A nti s en s e th er ap y b lo ck s th e
tr ansl ation phase of protein
synthesis by binding to the specific
genetic segment of mRNA that
codes for production of a specific
disease-causing protein. OGX-011
binds to the segment of mRNA that
codes for clusterin.

The OncoGenex Antisense Story

In November 2001, OncoGenex established a co- 90% and inhibited clusterin expression in lymph
development relationship with Isis Pharmaceuticals nodes by greater than 95%. OGX-011 is currently
for the development of OGX-011, the lead product being evaluated in Phase 2 clinical trials in prostate,
in the OncoGenex pipeline. OGX-011 is a second- breast and non-small cell lung cancers.
generation antisense compound designed to knock
In March 2005, OncoGenex and Isis expanded their
out clusterin, a cell survival protein that is usually
antisense drug development collaboration to include
expressed in tumor cells in response to standard
additional second-generation antisense cancer drug
anti-cancer therapies. By inhibiting clusterin, OGX-
candidates, including the second product candidate
011 sensitizes resistant tumors to conventional
in the OncoGenex pipeline, OGX-427. OGX-427 is
cancer therapeutics. Data from a Phase 1 clinical
designed to inhibit production of Heat Shock Protein
trial demonstrates that OGX-011 is well tolerated,
27 (Hsp27), a target that has been associated with
achieves excellent drug concentration in target
treatment resistance and prevention of cell death
tissue, and inhibits the clusterin target in prostate
in various cancer cells. OGX-427 is slated to enter
cancer and lymph nodes. OGX-011 inhibited clusterin
the clinic in early 2006.
expression in prostate cancer cells by greater than
 Contact Information
Scott D. Cormack, President and CEO
™
OncoGenex Technologies Inc.
400-1001 West Broadway, Vancouver, BC, Canada V6H 4B1
Telephone: 604.736.3678 | Fax: 604.736.3687
Bringing hope to life.™ www.oncogenex.ca

Evolution of Antisense Technology

The first researchers who worked on antisense
technology saw the possibilities of new methods of
drug design. However, that promise has not yet been
fully realized. First-generation drugs have demanded
daily, intravenous dosing, and their lower specificity for
their target mRNA keeps them from being as potent
as is desirable. New developments in the chemistry
of antisense give further hope to developing potent,
long-lasting antisense ther apies that are more
conveniently adminstered.
The first antisense constructs studied were based
on the natural backbone structure of DNA. These
constructs had an extremely high affinity for their
t ar get s e quence s . Ho w e v er, s tr uc t ur e s b a s e d
on naturally occurring DNA are subject to swif t
degradation by nucleases and proved to be unsuitable
for therapeutic uses.
In an ef for t to make antisense technology more
amenable to therapeutic use, scientists attempted to
alter the backbone of the antisense molecules. The first
successful backbone chemistry modified the phospho-
diester structure in the DNA backbone to a phospho-
rothioate structure, which increased the construct’s
stability and made the technology more amenable
to therapeutic use. However, these constructs still
had plasma half lives of only hours, and the modified
DNA backbone decreased the affinity of the antisense
molecule to its target mRNA sequence.
To increase the stability of the antisense compound,
a second-gener ation chemistr y w as developed,
adding the 2’MOE (2’-methoxyethyl) modification to
the oligonucelotide backbone. A further improvement
incor por ates both fir st-gener ation and second-
generation chemistries into “gapmers”: antisense
sequences that have their ends modified with 2’MOE
chemistr y while retaining at their centers first-
generation chemistry. The 2’MOE modified ends protect
the construct from degradation, giving significantly
improved half life and binding affinity, while the first
generation center permits enzymatic degradation
of the mRNA /antisense complex. Gapmer second-
generation chemistry drugs have increased half-lives
of 5- to 10-fold over first-generation chemistry and
increased affinity to target mRNA.
The improved affinity of second-generation drugs is
primarily attributable to their design and composition.
Second-generation drugs are composed of both RNA-
like and DNA-like nucleotides, while first-generation
drugs are entirely DNA-like. Because RNA hybridizes
more tightly to RN A than to DN A , the second-
generation drugs have a greater affinity for their RNA
targets and, therefore, greater potency. With increased
potency, second-generation drugs are more active at
lower doses.
Additionally, second-generation chemistry with gapmer
design significantly slows degradation of the drugs by
protecting the drug from destructive nucleases. The
resulting slower clearance from the body allows for
less frequent dosing, and in the future may allow for
oral delivery, a useful feature for long-term use given
added patient convenience.

“0” “1st ” “2 nd”

Generation Generation Generation

Phosphodiester (P=O) Phosphorothioate (P=S) 2’MOE (modified P=S)

Characteristics: Characteristics: Characteristics:

(1) Highly unstable to nucleases (1) Better stability to nucleases (1) Best stability to nucleases
(2) Good affinity to target mRNA but still degrades (2) Increased affinity to target mRNA
(2) Decreased affinity to target mRNA

Result: Result: Result:

(1) Rapidly degrades (1) Unknown tissue concentration (1) Confirmed tissue concentration
(2) Never advances to human trials (2) Unknown target regulation (2) Confirmed target regulation
(3) Daily dosing (3) Once a week dosing