Method’s PowerExpands itsApplicability to Earlier-Stage R&DEllyn Kerr

Cengent Therapeutics (San

Diego) will be announcing it

has confirmed the precise

mode of structural interac-

tion of a drug lead against a major dia-

betes target.

The firm has developed, and applied x-

ray crystallography to analyze the activity

of, novel inhibitors to protein tyrosine

phosphatase-1B (PTP1B) that reportedly

exert a prolonged glucose-lowering effect

in a mouse diabetes model. The inhibitors

represent a new class of potential diabetes

drugs—that avoid the side-effect weight

gain typically associated with other dia-

betes therapeutics.

“We believe this is the first time the

precise interaction of the PTP-1B target

with an inhibitor exhibiting in vivo

activity has been revealed at the 3-D

structural level for this important class

of potential diabetes therapeutics,” says

Edward Maggio, Ph.D., CEO.

Inherent conformational flexibility of

PTB-1B allows it to exist in both closed

and open forms, creating significant but

common drug-design challenges, which

the firm’s “dynamic pharmacophore”

technology, DynaPharm®, was success-

fully able to circumvent, Dr. Maggio

notes. And because the structure of

PTP-1B is similar to many other phos-

phatase-binding compounds, the firm

expects the knowledge to accelerate the

design of other potent, selective, phar -

m a ceu t i c a l l y re l e v a n t inhibitors.

Genes to Leads Technology

Employed for this diabetes research

was Cengent’s Genes to Leads® technol-

ogy, designed for rapid generation of

nonpeptide, small molecule drug leads,

Reprint from

D a i l y B i o t e c h U p d a t e s . . . w w w . g e n e n g n e w s . c o m

Volume 23, Number 12June 15, 2003

Structural Proteomics Extends its Contributions

The three-dimensional structure of PTP-1B is used to search Cengent’s StructureBank® database of thou-sands of proprietary drug target structures to identify and rank the most structurally similar proteins.Because such proteins are most likely to cause nonselective binding to a new drug, Cengent dubs theseantitargets.

based on differential structure informa-

tion derived from dynamic conforma-

tions of protein targets and of struc-

turally complementary proteins, or

antitargets.

“Starting from a target se-quence,

Genes to Leads yields initial drug leads,

that have good selectivity, within 2 to 4

months, reducing the number of com-

pounds that actually need to be tested

from hundreds of thousands to just two or

three hundred,” according to Dr. Maggio.

The technology is applied along with

Cengent’s experimental and in silico

tools and methods, with the aim of

maximizing efficiency across the drug

discovery and development timeline.

Given that standard x-ray crystallogra-

phy methods prove effective for only

about 5% of all targets, according to

expert estimation, and that the number of

available protein targets is increasing from

the current industry-wide estimate of 500,

to a predicted 3,000 to 10,000 within the

next few years, throughput without com-

promise of accuracy is paramount.

Addressing this, Cengent claims

its technologies “provide rapid 3-D

structure-based assignments of bio-

chemical functions to novel protein

sequences with substantially greater

accuracy than that achieved using stan-

dard sequence-based methods.

“Multidimensional comparative 3-D

structural analysis of drug targets and

structurally related antitargets is accel-

erating the discovery and optimization

of highly selective drug leads, while sig-

nificantly cutting the time and cost of

chemical synthesis and purification,”

says Dr. Maggio, summarizing the con-

tributions of current-day structural

proteomics, “as well as improving the

selection of the most informative coun-

terscreens and most relevant animal

models, and expanding the intellectual

property portfolio surrounding newly

discovered drugs and drug targets.”

Cengent Therapeutics was officially

launched a few weeks ago, following the

merger announced earlier this year of

Structural Bioinformatics (SBI) and

Gene-Formatics, two heavyweights in

the relatively small circumscribed

group of self-identifying structural pro-

teomics firms.

SBI provided drug discovery pro-

grams and structural content, having

developed several proprietary databases

toward the goal of “generating as many

high-quality drug-target protein struc-

tures as possible,” notes Kal Ram-

narayan, Ph.D., former vp and CSO of

SBI who now holds the same positions

at Cengent.

GeneFormatics brought to the merg-

er its in silico screening and optimiza-

tion technologies for determining pro-

tein function, and the combined firm

now offers one of the most comprehen-

sive suite of structural proteomics ser-

vices and tools in the industry.

Among its offerings are Genes to

Leads, which incorporates Cengent’s

DynaPharm and CombiLib in silico

screening tools (that integrate “molecu-

lar movies” that provide dynamic 3-D

molecular characterization of protein

active sites); structure determination

services, including x-ray crystallogra-

phy, Cengent’s proprietary ProMax™

augmented homol-ogy modeling, and

high-field NMR; and StructureBank®,

for large-scale, multidimensional com-

parative analysis of protein targets and

antitargets.

As are most structural proteomics

firms these days, Cengent positions itself

as a collaborator, in addition to offering

enabling services and drug discovery

tools, “all of which have been designed

to be synergistic with the needs and in-

house activities of our pharma/discov-

ery R&D clients,” notes Dr. Maggio, with

many options customizable.

Ongoing collaborations include deals

with several large pharmas, such as

Johnson & Johnson (New Brunswick,

NJ) and Pfizer (New York City), as well

as several smaller pharmas in the U.S.,

Europe, and Japan. Recently the Genes to

Leads platform was applied to the rapid

discovery of patented an-thrax lethal-

factor inhibitors (U.S. patent 6,436,933),

the firm notes.

Like other structure-guided pro-

teomics firms, Cengent is also advanc-

ing in-house discovery and optimiza-

tion R&D. Pipelines include asthma and

cancer (with patents pending for novel

HER-2 inhibitors for breast cancer), in

addition to diabetes. Cengent Thera-

peutics is also building on GeneFormat-

ics’ IP covering application of structure-

based technologies for rapid production

of chemically synthesizable anthrax vac-

cine immunogens.

The efforts over the last several years of

structural proteomics companies to

establish themselves as integrated

providers of discovery, validation, opti-

mization, and development firms are now

bearing fruit, as evinced by Big Pharma’s

increasing adoption of these technologies

and by facilities expansions at a time

when other biofirms are struggling.

Focus Spurs Expansion

In the last few weeks, Astex Technol-

ogy (London) expanded with a new

36,000-sq-ft facility at Cambridge Sci-

ence Park. Curren-tly housing 94 staff,

the facility has about a 150-person

capacity. Astex is now recruiting medic-

inal chemists and biologists, to add to its

current count of 22 and 8, re-spectively,

which points to the firm’s strong focus in

drug discovery.

Harren Jhoti, Ph.D., founder and

CSO, describes a benefit common for

structural proteomics firms in doing in-

house R&D, namely the inherent valida-

tion aspect that augments the attractive-

ness of the technologies to potential

partnering pharmas.

Astex’ high throughput x-ray crystal-

lography HTX® platform incorporates

its Pyramid™ fragment-based x-ray

crystallographic screening, in which the

firm’s proprietary fragment libraries are

mined for novel, low-affinity fragments.

Astex then optimizes these using its

chemistry expertise to develop “potent,

nanomolar lead compounds with good

druglike properties and which are active

in cells,” Dr. Jhoti explains.

Schering (Berlin) recently agreed to

apply the Pyramid technology in a four-

year multitarget discovery alliance

focused on orally available small mole-

cule drugs against solid tumors. Scher-

ing funds Astex’ relevant research pro-

grams and assumes preclinical and com-

mercial development responsibilities.

With worldwide commercialization

rights, Schering will offer Astex mile-

stone payments and royalties on eventu-

al product sales.

A recent collaboration with

AstraZeneca (AZ; London) fo-cused on

a key Alzheimer’s disease target was

established after AZ had found lead gen-

eration intractable to conventional HTS

approaches, according to Dr. Jhoti. Astex

had solved a novel crystal structure of

the target and was thus called upon to

advance the program, with terms simi-

lar to those in the Schering deal.

In a collaboration with the Institute

of Cancer Research and Cancer

Research Technology (ICR; Cambridge,

U.K.), Astex retains commercialization

rights to therapeutics stemming from

application of the firm’s technology to

identification of novel drugs against

protein kinase B, for which ICR holds

certain intellectual rights.

Astex’ internal therapeutic focus is

in oncology and inflammation. Having

reportedly solved the first crystal

structures of human cytochrome P450,

the enzymes associated with drug

metabolism, the firm is now applying

this information to develop novel in

silico ADMET tools to reduce later-

stage attrition.

Overcoming Intractabilities

Much more confounding than DNA

research, work with proteins, especially

structure-function biology, poses sig-

nificant challenges in addition to its

notable benefits for discovery projects.

A frequently cited example is the col-

lective refusal of the highly pharmaceu-

tically relevant membrane proteins to

yield to traditional analytical methods.

As are the other established structural

biology firms, in a multi-pronged

approach to overcome these challenges

and other bottlenecks in structure-guid-

ed discovery, Affinium Pharmaceuti-

cals (Toronto) has devised numerous

technologies ranging from proprietary

cell lines to automation solutions.

Affinium’s aim is a true industrialized

interrogation of protein target structure

and function. New this year is its “nude

screening” approach, designed to screen

“naked” proteins, as described by John

Mendlein, Ph.D., J.D.; that is, proteins

unlabeled with radioactivity or fluo-

rescence markers, to rapidly assess lig-

ands that stabilize targets for structure

determination of specific protein-ligand

binding events.

This approach has been incorporated

into Affinium’s established, integrated,

automated ProteoChem™ Discovery

Process, which subsumes the Proteo-

Works™ System (including multiple

proprietary expression and purification

methods reportedly rendering more-

than-95%-pure milligram quantities of

concentrated target proteins, 100% of

which are active); the mass spec-based

ProteoActive™ System for elucidating

protein-protein interactions; and the

ProteoVision™ System of proprietary

NMR and x-ray crystallography meth-

ods for accelerating protein-structure

determination for small molecule

design and libraries. A ProteoTrack™

database tracks all resulting data.

The firm’s focus on results-genera-

tion has enabled Affinium “to go from

informatics to novel 3-D structures in

less than three weeks,” Dr. Mendlein

reports. Such gains have been noticed by

GlaxoSmithKline (GSK; Middle-sex,

U.K.), which earlier this year granted

Affinium worldwide discovery, develop-

ment, marketing, and distribution

Crystal structure of human cytochrome P450 discovered by Astex Technology. Astex has advanced developments in the field of human cytochrome P450 structural biology, including the recent announcement that it has solved the first structures of human isoforms 3A4 and 2C9. Astex is using the crystal structures to detect the ways in which compounds bind to these key metabolizing enzymes as part of its drug optimization and drug rescue programs.

rights to compounds generated from a

GSK antibacterial research program, in

exchange for a significant equity posi-

tion in Affinium.

The acquisition includes late-stage

leads and IP on high-resolution struc-

tures related to a novel target, as well as

several compounds resulting from

GSK’s lead optimization efforts to date.

“These lead agents have the potential

to treat antibiotic-resistant Staphylococ-

cus infections, such as serious methi-

cillin-resistant Staph, in the near term,

and other species of gram-positive and

gram-negative bacteria, in the long

term,” Dr. Mendlein says. “Results of

these potent, novel-acting agents thus

far suggest possibilities for both oral and

IV administration.”

Tech Adopted by Big Pharma

Being summoned by Big Pharma

to install one’s technologies in a new

facility for the pharma’s in-house

research represents a significant validat-

ing milestone. Structural Genomix’

(SGX; San Diego) Gene-to-Structure

platform is the subject of one such col-

laboration.

SGX is implementing its Gene-to-

Structure technology in a high throughput

structural biology facility to allow Eli Lilly

& Co. (Indianapolis) to bring the platform

in-house, to be applied to “as many of

Lilly’s internal programs as possible,”

according to Stephen Burley, M.D., D.Phil,

CSO and senior vp of research at SGX.

The platform incorporates SGX’

Gene-to-Protein, Protein-to-Crystal,

and Crystal-to-Struc-ture components,

each of which blends SGX’ in-house

technologies and customized robotic

instrumentation from third-party sup-

pliers. Eli Lilly’s facility will include

modular, automated systems and SGX’

process technology for protein engi-

neering, crystallization, and structure

determination, with access to SGX’

expertise and proprietary beamline

facility at the Advanced Photon Source

at Argonne National Laboratories.

In another collaboration with Boeh-

ringer Ingelheim (Ingelheim, Germany),

SGX’ technologies are being applied

early in the discovery process—“imme-

diately after high throughput screen-

ing,” Dr. Burley notes, to garner ligand-

binding information to inform choices

about lead design and to maximize

application of chemistry resources.

SGX has developed specific expertise in

selected protein families, including kinases,

nuclear receptors, and proteases, and

combines these with its integrated platform

for use by collaborators and for applica-

tion in its own oncology program.

Scaffolds

Plexxikon (Berkeley, CA) recently

announced a discovery collaboration

with Genentech (S. San Francisco) to

develop a series of small molecule

inhibitors against a protein kinase target

with implications in oncology. Genen-

tech retains commercialization and

marketing options under worldwide

license and is responsible for develop-

ment, including clinical testing and

manufacturing.

P l e x x i k o n w i l l a p p l y i t s Scaf-

fold-Based Drug Discovery™, which

creates low molecular weight com-

pounds that target conserved regions

among multiple protein-family members.

The firm then applies structure-directed

chemistry involving co-crystallography,

parallel biochemical assays, and screen-

ing of a proprietary, focused, 25,000-

compound library, to render optimized

leads. Plexxikon ex-pects to deliver the

first chemical leads to Genentech with-

in three to six months.

The platform can reportedly screen

co-complexed proteins in approximate-

ly 100 different crystallization condi-

tions at various temperatures in an

automated manner, enabling simulta-

neous testing of up to 500 compounds.

Michael Milburn, Ph.D., senior vp of

research, says the platform differs from

other fragment-based technologies in

that leads are more efficiently derived

from this scaffold approach.

“Our current capacity is 40 co-crystal

structures a month, with approximately

two structures completed per work-

day,” Dr. Milburn says, “a capacity that

will likely double within the next six

months.”

The firm plans soon to publish the

first co-crystal structures of phosphodi-

esterase-5 (PDE5), the target of Pfizer’s

Viagra®, as well as structures of a num-

ber of PDE5 compounds.

Development of novel scaffolds for

kinase, PDE, and nuclear receptor families

is ongoing, with three in-house discovery

projects either in or due to enter animal

studies—a significant accomplishment,

Dr. Milburn notes, for a company that

opened its labs for operation just 20

months ago. GEN