New synthesis and screening
technologies and the allure of access to previously undruggable targets are
driving an explosion of new company formation and deal-making around macrocycles
and constrained peptides.
While it remains to be seen
whether the in vitro promise of these platforms will translate into
viable drug candidates, the clinical successes of macrocyclic natural products
provide tantalizing hints of what could be achieved by the systematic
exploration of this compound class.
Macrocycles may be capable of
hitting new classes of targets because their ring structure causes them to
behave differently than most small molecules.
Macrocycles are chemically
defined by a ring structure of at least 12 atoms. They are typically 500-2,000
daltons in size. In contrast, most small molecules weigh less than 500 daltons,
which has been considered the upper limit for a compound to be cell permeable
and orally bioavailable.
"The easy targets have now been done; enzymes and GPCRs
largely have been addressed through small molecules," said Ensemble
Therapeutics Corp. CSO Nick Terrett. "Protein-protein
interactions with large surface areas are very difficult to address with small
molecules, and macrocycles are a very effective way of getting to a size that
allows enough interaction with the protein."
A similar approach is to create
constrained peptides by artificially linking linear peptides into specific
structures possessing improved drug-like properties including cell
Ensemble is one of at least 12
biotechs developing platforms for synthesizing or screening macrocycles
and constrained peptides (see "Building Cycles," A8).
As a group, these companies are
enjoying a rush of attention from big pharma - there have been at least 27
discovery partnerships with biopharma partners in the last five years (see "Cycle
"There is no doubt that within the last 3-4 years
it has been a lot easier to get pharma's attention from a collaboration
standpoint," said Tranzyme
Inc. VP of IP and operations Mark Peterson. Tranzyme partnered its
macrocycle discovery platform with Bristol-Myers
Squibb Co. in 2009.
Indeed, collaboration looks to
be essential to solving the puzzle of cell access. At this point, all the lead
programs disclosed thus far are aiming at extracellular targets.
The model macrocyclic drug that inspired these development
efforts is cyclosporine, a fungal-derived natural product developed as an
immunosuppressant more than 30 years ago by Sandoz AG (now a unit of Novartis
AG). Approved by FDA in 1983 as Sandimmune, the drug is an orally
bioavailable and cell permeable 1,200-dalton cyclic peptide made up of 11 amino
Cyclosporine suppresses the
immune system by binding to cyclophilin A, which then drives the formation of a
protein-protein interaction that inhibits calcineurin. NMR studies have shown
that cyclosporine can adopt different conformations depending on its chemical
environment, which may explain how it can possess drug-like properties despite
"Cyclosporine is the poster child for this field because
it violates Lipinski's Rules, and there are lots of other cyclic peptide
natural products with molecular weight over 1,000 that are cell permeable. Since
these compounds are well outside what is normally considered drug-like, their
structures might suggest a path toward the design of synthetic, non-Lipinski
compounds as we go after more challenging targets like protein-protein
interactions," said Scott Lokey, associate professor of chemistry and
biochemistry at the University
of California, Santa Cruz.
In 1995, Christopher Lipinski
consolidated observations from the literature into a set of five rules related
to drug absorption. Lipinski's Rules state that molecules with molecular
weights above 500 daltons, more than five hydrogen-bond donors or more than 10
hydrogen-bond acceptors are likely to be poorly absorbed. (see
BioCentury, Jan. 28, 2002).
Terrett noted that cyclosporine's
conformational flexibility allows it to adopt a form with increased
hydrophobicity when the molecule needs to get through a cell membrane.
This flexibility is "an
inherent positive aspect of macrocycles, but it can be hard to computationally
predict," he said.
Other naturally derived macrocycles include the antibiotics erythromycin and vancomycin, and the
However, natural macrocycles
are chemically complex and difficult to synthesize, which has prevented the
large-scale synthesis of compound libraries. In addition, computational
challenges make SAR difficult.
Early attempts to design
macrocycle drugs were based on screening peptide libraries against targets of
interest, then attempting rational design of analogs with improved
Doug Treco, CEO of Ra
Pharmaceuticals Inc., told BioCentury these efforts were largely
unsuccessful. "There are almost no examples of anybody taking such a
peptide and then using medicinal chemistry to successfully make it into an
orally available drug," he said.
While peptide libraries could
be generated using phage display and mRNA display, a major obstacle was that
peptides could not be systematically cyclized or otherwise structurally
constrained in a way that would confer drug-like properties.
"The limitation was that you could only use natural amino
acids and generate disulfide-linked peptides," said Patrick Reid, CSO of PeptiDream
To solve this problem,
companies including Ra and PeptiDream set out to develop chemical methods to
improve the drug-like properties of peptides by constraining their structure
and increasing their diversity, often in conjunction with platforms that
enabled the screening of large libraries of cyclic molecules.
PeptiDream was founded in 2007 based on technology developed
by Hiroaki Suga at the University
of Tokyo that enables incorporation of modified unnatural amino acids
into mRNA display peptide libraries. This includes the incorporation of
N-methylation, a modification that increases a peptide's ability to permeate
cells (see SciBX: Science-Business eXchange, Jan. 26).
Reid told BioCentury PeptiDream has active target
discovery deals with eight companies, including AstraZeneca
LLC unit, Amgen
Tanabe Pharma Corp., Daiichi
Sankyo Co. Ltd., Pfizer
Inc., BMS and Novartis. The remaining partnership is undisclosed.
He also said the company is
planning an IPO on the Tokyo Stock Exchange next year.
Ra was founded based on technology from Jack Szostak's lab at Harvard
Medical School and Massachusetts
General Hospital. Ra also is using an mRNA display peptide library to
display peptides that contain unnatural amino acids (see BioCentury, July 16).
Treco said differences in
peptide library design are the key differentiating factor between the
"We've made progress in
generating unique molecules with a mixture of natural and unnatural amino
acids," he said. "Our feeling is, if we can build in enough features
that will confer lipophilicity and hydrophobicity in the right configurations
to a molecule, we can probably work with molecules in the 700- to 1,100-dalton
Indeed, the challenge for
macrocycle and constrained peptide technologies is not just to identify potent
candidates, but to improve medicinal chemistry properties to make the peptides
cell-penetrant and more drug-like.
For that reason, Aileron
Therapeutics Inc. CSO Tomi Sawyer said his company decided to focus on
structure-based design of stapled alpha helical peptides, rather than on
extensive screening efforts.
"The beauty of it is that
after five years and literally many thousands of stapled peptides, we have a
pretty good knowledge base to define proprietary rules for how to lead
optimize, in terms of length, charge and hydrophobicity," he said.
In 2010, the company signed the largest disclosed deal in the
space when it partnered with Roche
to develop stapled peptides to target intracellular protein-protein
interactions. Aileron received $25 million in technology access fees and
R&D support and is eligible for up to $1.1 billion in milestones, plus
royalties (see BioCentury, Aug. 30, 2010).
Another player developing constrained peptides to inhibit
protein-protein interactions is Protagonist
Therapeutics Inc., which is engineering disulfide rich peptides using a
combination of approaches including computational design, phage libraries and
directed evolution. CEO Dinesh Patel said disulfide rich peptides can improve
stability in vivo and can offer "the potency of biologics and the
pharmacokinetics of small molecules."
Protagonist has discovery deals with therapeutic peptide companies
Pharma A/S and Ironwood
In the past three years, two additional companies have been
built around constrained peptide technologies. In 2009, Bicycle
Therapeutics Ltd. was founded to generate bicyclic peptides containing
natural amino acids using phage display. Bicyclic peptides contain two cyclic
loops that can interact with their target, allowing them to exhibit bivalent
binding similar to mAbs (see BioCentury, Nov. 2, 2009).
Bicycle obtained a non-exclusive license to use CLIPS
(chemical linkage of peptides onto scaffolds) technology from Pepscan
Therapeutics B.V. in phage display. The companies are collaborating on
therapeutic peptide projects.
Pepscan CTO Peter Timmerman told BioCentury his company is
seeking co-discovery partnerships to apply its technology to specific targets
nominated by the partner. Partners include Johnson
& Johnson, Phylogica
Ltd., Zealand and Alvos Therapeutics Inc. (now part of Arrowhead
In 2010, Lanthio
Pharma B.V. was founded to use a Lactococcus lactis expression
platform to generate peptides structurally constrained by lanthionine bridges.
CSO Gert Moll said the company expects to announce the close of a series A
round within the next few months (see BioCentury, Feb. 20).
In parallel with efforts to
develop cyclic peptides, at least half a dozen companies have developed
new chemical approaches to synthesize smaller, non-peptidic macrocyclic
compounds that could offer improved cell permeability and retain enough potency
to block protein-protein interactions.
Ltd. began its efforts using PEMfinder, a platform designed to
synthesize cyclic peptides, but has since added to its capabilities by
developing MacroFinder, a platform that can synthesize non-peptidic molecules
400-800 daltons in size. CSO Daniel Obrecht said molecules in this size range "intrinsically
are a better starting point for achieving cell permeation and oral
bioavailability and act more like small molecules."
Polyphor announced macrocycle discovery partnerships with
Novartis in 2010 and with Boehringer
Ingelheim GmbH this year (see BioCentury, July 16).
Peterson said Tranzyme took a
similar tack with its MATCH (macrocyclic template chemistry) platform.
"We wanted to stay within
the small molecule realm," he said. "Unlike people now trying to
explore the intermediate space, our focus was on trying to capture the
advantages of macrocycles in terms of potency and selectivity but to do it
within a small molecule package, between 400 and 600 daltons."
Ensemble's DPC (DNA-programmed
chemistry) platform synthesizes non-peptidic macrocycles called Ensemblins,
which are typically 600-1,000 daltons. The technology uses DNA as a template to
generate macrocycles using synthetic building blocks.
Terrett said this approach can
be used to generate highly diverse libraries of macrocycles containing
different ring sizes and different domains, some of which are often found in
naturally occurring macrocycles, such as polyketides and terpenoids.
Since April 2009, Ensemble has entered into three partnerships
to use its macrocycle discovery platform with BMS, Pfizer and Roche's
When Genentech chose Ensemble
as a partner in June, James Sabry, VP of partnering at Genentech, specifically
pointed to protein-protein interactions as an area where the company was
interested in exploring the potential of Ensemblins (see BioCentury, June
plc obtained a similar DNA-encoded library technology when it acquired
Praecis Pharmaceuticals Inc. in 2007. Barry Morgan, VP of molecular discovery
research at GSK and former VP of chemistry at Praecis, said the platform has
been used to generate over a billion macrocyclic molecules up to 1,000 daltons
In 2010, Oncodesign
S.A. entered the macrocycle development space when it in-licensed
macrocyclic chemistry technology that had been developed at J&J by Jan
Hoflack, who led J&J's European medicinal chemistry team.
Hoflack, now CSO and head of
drug discovery at Oncodesign, told BioCentury the company is focusing on
Nanocycles, which are macrocycles that weigh 300-400 daltons and are generally
composed of ring structures of 12-18 atoms. Oncodesign is using its platform to
develop selective kinase inhibitors and plans to eventually use the technology
on other classes of targets.
Last week, Oncodesign signed a deal with Sanofi
to discover and develop inhibitors against undisclosed kinase targets. In
January, the biotech announced a deal with Ipsen
Group to discover and develop leucine-rich repeat kinase 2 (LRRK2)
The newest disclosed company in the space is Encycle
Therapeutics Inc., which was spun out of the University
of Toronto by MaRS
Innovation to commercialize the work of Andrei Yudin, a professor of
chemistry at the university. The company is developing compounds dubbed nacellins
using proprietary amphoteric cyclization reagents.
While the technology can be used to cyclize peptides or
non-peptidic molecules, Yudin said he plans to focus on smaller ring structures
of 9-18 atoms. The company was incorporated in January and has raised an undisclosed amount of seed funding largely from MaRS Innovation.
In addition to these non-peptidic macrocycle approaches, Forma
Therapeutics Holdings LLC is attempting to design molecules that
disrupt protein-protein interactions in cancer through a four-year partnership
with Boehringer Ingelheim announced in January.
CEO Steve Tregay said
the company is not specifically developing macrocyclic compounds but is aiming
to address some of the same problems as macrocycles using its
diversity-oriented synthesis (DOS) platform, which engineers extensive
stereochemistry into small molecules to maximize the potential to disrupt
protein-protein surface contacts.
While much of the excitement
over macrocycles is due to their potential to disrupt intracellular protein-protein
interactions, every currently disclosed lead program in the space targets an
extracellular protein. This reality reflects the challenge of developing a
potent and cell-penetrant macrocyclic compound.
Tranzyme and Polyphor are the
only companies with macrocyclic compounds in the clinic. Polyphor's lead
compound is POL6326, a conformationally constrained peptide that antagonizes
CXC chemokine receptor 4 (CXCR4; NPY3R). It is in Phase II testing to treat
multiple myeloma (MM) using autologous transplantation of hematopoietic stem
Tranzyme's lead compound is
TZP-102, an orally administered ghrelin receptor agonist in Phase IIb testing
to treat diabetic gastroparesis.
Two weeks ago, Aileron
announced it hopes to start clinical development of its lead internally
developed program in 2013. The compound, ALRN-5281, targets the growth
hormone-releasing hormone (GHRH) receptor.
Aileron's most advanced
protein-protein interaction disrupting stapled peptide is a dual Mdm2 p53
binding protein homolog (MDM2; HDM2) and Mdm4 p53 binding protein homolog
(MDM4; MDMX) antagonist. The stapled peptide is in preclinical
development and is partnered with Roche. Sawyer said Aileron plans to publish
detailed results describing a stapled peptide developed as part of this
The targets of preclinical lead
programs that have been disclosed are also extracellular, including Ra's
program targeting the plasma enzyme kallikrein, and Ensemble's program
targeting interleukin-17 (IL-17), which is expected to enter the clinic in
"There is no question
there is a simple approach when the target is extracellular and when you have
IV administration, and there is no question the first stories will happen in
that area," said Juerg Zimmerman, head of global discovery chemistry,
oncology & exploratory chemistry & infectious diseases at Novartis.
"The most difficult area
is intracellular targets, and there is a challenge to get these macrocycles
into the cell, but there is no question it can be overcome," he said. "The
real value of these molecules is that they will be able to interfere with
GSK's Morgan voiced similar
conclusions. "Most people engaged in drug discovery are accepting of the
fact you can get macrocycles and peptides that are effective biochemically, in
cells and in vivo. However, it is the translation to the clinic that
will be the critical next step for the field," he told BioCentury.
Spiros Liras, head of medicinal
chemistry in cardiovascular, metabolic and endocrine diseases at Pfizer, said
the pharma's interest is in galvanizing the scientific community to solve the
issue of cell permeability. "From the get go, we have decided that it wasn't
going to be a topic that any single group could possibly solve alone," he
Pfizer is working with Lokey
and collaborator Matt Jacobson, professor of pharmaceutical chemistry at
the University of California, San Francisco, to computationally predict
drug-like properties for macrocycles.
Separately, Lokey and Jacobson
this year founded a macrocycle company that is operating in stealth mode.
Therapeutics Inc., Cambridge, Mass.
Inc. (NASDAQ:AMGN), Thousand Oaks, Calif.
Research Corp. (NASDAQ:ARWR), Pasadena, Calif.
plc (LSE:AZN; NYSE:AZN), London, U.K.
Therapeutics Ltd., Cambridge, U.K.
Ingelheim GmbH, Ingelheim, Germany
Squibb Co. (NYSE:BMY), New York, N.Y.
Sankyo Co. Ltd. (Tokyo:4568; Osaka:4568), Tokyo, Japan
Therapeutics Inc., Toronto, Ontario
Therapeutics Corp., Cambridge, Mass.
Therapeutics Holdings LLC, Watertown, Mass.
Inc., South San Francisco, Calif.
plc (LSE:GSK; NYSE:GSK), London, U.K.
Medical School, Boston, Mass.
Group (Euronext:IPN; Pink:IPSEY), Boulogne-Billancourt, France
Pharmaceuticals Inc. (NASDAQ:IRWD), Cambridge, Mass.
& Johnson (NYSE:JNJ), New Brunswick, N.J.
Pharma B.V., Groningen, the Netherlands
Innovation, Toronto, Ontario
General Hospital, Boston, Mass.
LLC, Gaithersburg, Md.
AB (SSE:MVIR B), Huddinge, Sweden
Tanabe Pharma Corp. (Tokyo:4508; Osaka:4508), Osaka, Japan
AG (NYSE:NVS; SIX:NOVN), Basel, Switzerland
S.A. (Dijon, France)
Inc., Tokyo, Japan
Therapeutics B.V., Lelystad, the Netherlands
Inc. (NYSE:PFE), New York, N.Y.
Ltd. (ASX:PYC; Xetra:PH7), Subiaco, Australia
Ltd., Allschwil, Switzerland
Therapeutics Inc., Redwood City, Calif.
Consortium for Drug Discovery (CQDM), Nuns' Island, Quebec
Pharmaceuticals Inc., Boston, Mass.
(SIX:ROG; OTCQX:RHHBY), Basel, Switzerland
Inc. (NASDAQ:TZYM), Durham, N.C.
of California, Santa Cruz, Calif.
California, San Francisco (UCSF),
of Tokyo, Tokyo, Japan
of Toronto, Toronto, Ontario
Pharma A/S (CSE:ZEAL), Glostrup, Denmark