Silico Drug Discovery Based on the Identification of a Novel “Druggable”
Surface Pockets on the ras Oncogene
Opening a New Door to the Development of World’s First Anti-cancer Drug Targeting
discovered substances (low molecular weight compounds) that exhibit anti-tumor activity
by inhibiting the functions of the ras
oncogene products (Ras),*1 which are the cause of approximately 20%
of human cancers. These compounds may serve as a scaffold for the development of molecularly
targeted anti-cancer drugs (molecularly targeted drugs)*2
for Ras. The reserch achievement was published online in Proceedings of the National Academy of Sciences of the United States of
Despite its importance as
an anti-cancer drug target, there has been no effective molecular targeted
therapy for Ras at present (Fig. 1). Since
the first determination of the crystal structures of Ras in the late 1980s, researchers
have considered that no effective strategy would be available for the
development of Ras inhibitors because of the absence of well-defined surface
pockets suitable for drug binding (Fig. 2).
cooperation with Takashi Kumasaka of Japan Synchrotron Radiation Research
Institute (JASRI) and Masaki Yamamoto of RIKEN, the research group determined
novel crystal structures of Ras and recognized “druggable” pocket structures on
their surface for the first time in the world (Fig. 2). Moreover, We have applied structure-based drug design*3 utilizing
the structural information on these pockets and found three compounds that fit
into one of the pockets (Fig. 3) and have potent activity to block binding of
Ras to their multiple target proteins such as Raf kinases and phosphoinositide
3-kinases (Fig. 4). Furthermore, the
compounds, named “Kobe family compounds” in the published paper, displayed significant anti-tumor
activity on a xenograft*4 of human colon carcinoma
cells carrying the active ras
mutation (Fig. 5).
to a patent search, the Kobe family compounds have not been registered as anti-cancer
drugs. Kobe University applied for a
national patent for these compounds (including the screening method for Ras
inhibitors) as the candidates for the development of new anti-cancer drugs in
2011 and will soon apply for a US patent.
global pharmaceutical companies such as Genentech*6, an affiliate of
Roche,*5 and Abbott Laboratories*7 have devoted much effort
to exploring and developing Ras inhibitors. Our reserch achievements have recently
been published in leading scientific journals such as PNAS, intensifying the competition in this research field. However, the novel inhibitors discovered in this
study are quite different from theirs in terms of the mechanism of action. Moreover, the novel inhibitors show stronger biochemical
and cellular activities and, furthermore, they exhibit a significant anti-tumor
effect in the mouse xenograft model of human colon cancer unlike the compounds
reported by the companies (Fig. 5). Although the inhibitory activity is not particularly potent for the
clinical application at present, the Kobe family compounds may serve as a lead scaffold for the
development of the world’s first anti-cancer drug targeting Ras.
to the publication of this research achievements, a joint press conference attended
by representatives of seven media outlets was held at Kobe University Graduate
School of Medicine on 25 April 2013, as shown in the picture.
*1ras oncogene products (Ras)
name “ras” is an abbreviation of “rat
sarcoma virus” from which it was discovered. There are three ras oncogenes, H-ras, K-ras and N-ras in mammals. Their products,
collectively called Ras, belong to a family of small G proteins, i.e. guanosine
triphosphate (GTP)-binding proteins, and regulate intracellular
signaling pathways controlling cell growth, differentiation, apoptosis and cell
mobility. They exist in the genome of normal cells as the ras proto-oncogene and are converted to the ras oncogenes when the activities of their products are hyperactivated
by point mutations.
anti-cancer drugs (molecularly targeted drugs)
designed to detect a specific property of cancer cells at the level of signaling
molecules and to target such molecules are collectively called molecularly
targeted drugs. Different from chemotherapeutic
drugs, which are designed to kill normal cells as well as cancer cells, molecularly
targeted drugs are expected to achieve better therapeutic effects with less
side effects because they affect cancer cells only.
Rational drug design is the inventive process of finding new medications based on the knowledge
of a biological target. The drug is most commonly an organic small molecule
that activates or inhibits the function of a biomolecule such as a protein,
which in turn results in a therapeutic benefit to the patient. Structure-based
drug design, aided by computer modeling techniques, involves the design
of small organic molecules that are complementary in shape and charge to
the biomolecular target with which they interact and therefore will bind
A graft of tissue
transplanted between animals of different species; it may be concordant,
occurring between closely related species, in which the recipient lacks natural
antibodies specific for the transplanted tissue, or discordant,
occurring between members of distantly related species, in which the recipient
has natural antibodies specific for the transplanted tissue. The nude mouse, with an inhibited immune system due to a greatly reduced number of T cells,
is valuable to research because it can receive many different types of
tissue and tumor grafts, as it mounts no rejection response. These xenografts
are commonly used in research to test new methods of imaging and treating
pharmaceutical and health-care company with its head office located in Basel,
Switzerland. Established in 1896, Roche
built its foundation by manufacturing vitamins.
Since the 1950s, it has developed and sold diazepam (sold under the
trade name of Cercine in Japan), which has become the global standard for
anxiolytic drugs. It has dominated the
market of anxiolytic drugs and generated a significant profit for Roche. Since the 1990s, Roche has focused on the
development of anticancer drugs.
and world-leading biopharmaceutical manufacturer in the United States. When Roche first bought Genentech in 1990, it
was a small biotechnology company in San Francisco, the United States, with
some promising anti-cancer drugs under study but lacking the funds to continue development. However, because of the enormous financial
power and the expertise of Roche in clinical development, Genentech now has many
anticancer drugs that have become huge successes such as Avastin for breast, lung,
and colorectal cancers, and Herceptin for breast cancer.
pharmaceutical and health-care company in Illinois, the United States, which was
established in 1888. It develops and
provides a wide range of medicinal products such as HIV test agents, Humira for
rheumatoid arthritis, Kaletra for HIV, and the antiepileptic drug Depakote.
Press conference held at Kobe University Graduate School of Medicine(Kusunoki
Campus) attended by seven media outlets.
Starting from the left, Dr. Kumasaka, Associate Professor Shima, and
1 Current status of the development of
molecular targeted anti-cancer drugs:
a number of molecularly targeted anti-cancer drugs against intracellular
signaling molecules related to oncogene addiction are currently available on
the market, there is no effective drugs targeting Ras.
2 Comparison between the newly solved
and already-known structures of Ras used in this research
newly determined structure (right, M-Ras) possesses a surface pocket between
the two switch regions which are important for recognition of various
effectors, including Raf, PI3K and PLCe (Fig. 1). In
contrast, the already-known structure (left, H-Ras) does not possess a pocket
in the corresponding region.
3 Inhibitory mechanism of the selected
compounds on Ras-mediated cancer signaling
The compounds which bind to the surface pocket of Ras inhibit the interaction
between Ras and its effectors, thereby preventing signals essential for
cancer cell growth and proliferation.
Fig. 4 Screening method for low molecular
weight compounds which inhibit Ras function (1)
1) Screening for the candidate compounds which bind to the surface pocket of Ras
by computer-docking simulation, (Step 2) examination for inhibitory activity of the selected compounds in vitro and in cellular system using cancer cells carrying active Ras
K-RasG12V), and (Step 3) examination
for in vivo anti-tumor activity of
the compounds using a xenograft model in the nude mice transplanted with human
colon cancer cells bearing K-RasG12V.
Fig. 5 Screening method for low molecular
weight compounds which inhibit Ras function (2)
the Kobe Family compounds were administered in the nude mice transplanted with
colon cancer cells bearing activated Ras (K-RasG12V), a significant inhibitory
effect of the compounds on tumor growth was observed compared to the control.