Conquering Infinity with  Chemical Genetics

By Malorye Branca

Good chemistry: Stuart Schreiber's passion for designing small molecules to probe cellular function is spreading fast. 
February 10, 2003 | At the precise point where a drug touches a protein inside a cell, lies the intersection of two dramatically different fields. On one side, biologists try to understand what is happening to the cell and its constituents. On the other side, chemists try to understand why something is happening. These two disciplines are represented by different laboratories, different traditions, vocabularies, and experimental tools.

But over the past decade, Stuart Schreiber, the chairman of Harvard University's Department of Chemistry and Chemical Biology (the suffix was his idea), has been on a mission to unite these two sciences in one lab, exploring new research vistas and changing the way drugs are found.

Drug developers are starting to agree.

To make effective drugs, they need to bring the borders of chemistry and biology together very precisely. Having the genome is one thing, but the chemome (if there is such a thing) would surpass any other "-ome" in terms of size and complexity. "Chemical space is virtually infinite," says Brent Stockwell, a fellow at the Whitehead Institute and Schreiber protege. "It's been said that there are more possible small molecules than there are atoms in the universe."

The unmapped and unexplored spaces leave giant holes in our understanding. "The great unanswered question today is, which compounds do we screen?" Stockwell says. Meanwhile, biologists wonder how to identify the most physiologically relevant targets.

Data are amassing faster than people can use them, putting a premium on sharper tools to tease out the viable targets and better "rules" to craft the compounds against them.

His Chemical Genetic Kingdom 
Stuart Schreiber has a knack for getting scientists from different disciplines to work together.

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Schreiber's neat approach essentially does both. Chemical genetics provides information about gene function using small molecules (the largest category of existing drugs). By using small molecules to "interrupt" cellular activities, Schreiber can piece together complicated cellular pathways and identify the key proteins, such as those responsible for apoptosis (cell death).

This approach beats pure genetics because it's not hardwired — plugged into the organism from birth — the way mutations are. Changes in cellular response are observed as it happens. Chemical probes also provide information about function and chemistry simultaneously. Studying how compounds affect cells should divulge what kind of chemical structures elicit certain effects.

"Chemical genetics is becoming a major innovation," says Paul Caron, head of bioinformatics at Vertex Pharmaceuticals Inc. "The industry has spent a lot of time doing high-throughput screening and combinatorial chemistry, and they have come up with a lot of potent selective probes." As a result, he says, "The major companies are now thinking about using chemistry to validate targets."

Twists and Turns 
Other scientists are excitedly building on Schreiber's approach, rapidly expanding chemical genetics in academia and industry.

Well-stocked: Whitehead Institute researcher Brent Stockwell's new database of known compounds and their effects provides a new way to explore the interface of targets and compounds. 
At the Whitehead Institute, Stockwell is creating a database of chemical effects. Traditionally, chemical geneticists screen random compounds, but Stockwell is studying chemicals whose activities are known, including approved drugs and natural products. He's already up to 2,000 compounds and counting. "When we find a compound in that collection that causes a specific effect, we already know a lot about how it acts within the cell," he says. "So this is a rapid method for linking specific molecular mechanisms to cellular processes."

Stockwell is building an annotated compound library, which will be the first large-scale public database of small molecules. Researchers will be able to enter the names of specific compounds and retrieve a ranked set of the cellular mechanisms those compounds affect.

Much time has been spent structuring and organizing the biological information. "Traditionally, if you have a molecule that is a kinase inhibitor, you would refer to it exactly that way," Stockwell says. "But when you inhibit one protein, you cause all kinds of other changes, too."

The approach, called vector annotation, ranks all the changes induced by a compound — a list of some 13,000 biological mechanisms, linked to gene names and some protein names. Stockwell aims to publish these details soon and will then open the database to the public. (The database will be available at

Stockwell's group can now examine many compounds with similar effects, at one time. "If we do a screen with 2,000 compounds, we may find 80 that have a certain property, such as inhibiting growth of tumor cells," he says. Stockwell will expand the collection to 5,000 compounds over the next couple of years. "I think other people are starting to adopt my approach," he says. "We will see these kinds of collections starting to be used widely."

Cancer Connection 
Stockwell's project is already fueling new research. His Whitehead colleague Todd Golub (also a pediatric oncologist at the Dana-Farber Cancer Institute) is using Stockwell's probes and genomewide gene expression studies to study cancer cells.

"The community has gotten pretty good at getting gene expression patterns," Golub says, "but we don't yet have a clear handle on how to manipulate those patterns."

Golub is looking for small molecules to elicit big changes, coaxing leukemia cells back into normal-looking blood cells, and monitoring the transformation via gene expression patterns. "A traditional chemical biology screen would say, 'Can we find compounds that can reverse the phenotype?'" he notes. "The twist here is to convert the phenotype into a gene expression pattern and do the screen against that signature."

The work, as yet unpublished, is being spearheaded by Kimberly Stegmaier and features Affymetrix GeneChips to capture the gene expression profiles of normal and cancerous cell types. As it's technically and financially prohibitive to do a whole-genome scan for every compound, they reduce the expression signatures to a "handful" of candidate genes and validate them using TaqMan, a real-time quantitative PCR (polymerase chain reaction). This approach cuts costs but still gives them an accurate signature.

Golub's group is concentrating on known compounds, but, he says, "It would be a big mistake to focus on cancer drugs. That strategy would preclude the possibility of discovering the unexpected effects of other compounds."

Tox Screen 
Chemical genetics is also being applied to toxicogenomics — the study of what characteristics make compounds toxic. Many groups, including CuraGen Corp., Gene Logic Inc., and PHASE-1 Molecular Toxicology Inc., are banking gene expression signatures of toxicity. That kind of data can be even more valuable, according to Pfizer Inc.'s Anton Fliri, if researchers can cull information about the nature of the chemical structures associated with toxicity.

"Chemical space is so huge, we have barely any clues about how to relate it to function," Fliri said at a recent Marcus Evans conference on data analysis. Different chemicals can have similar side effects, such as inhibiting potassium channels. Gene expression data from compounds with toxic effects, he suggests, can be combined with information about chemical structure, and mined for useful relationships. This would tell chemists at least what parts of chemical space not to explore. With today's tools, tens of thousands of compounds can be screened simultaneously, making it feasible, though costly and time-consuming, to create such databases. "We need to get more sophisticated in how we design chemicals," Fliri said.

Cellular Genomics Inc. (CGI) has morphed chemical genetics into another intriguing tool.

Using chemical probes to target individual proteins can be more specific than mutagenesis, antisense, or RNAi. Typically, however, compounds react with more than one protein, and proteins perform multiple functions in the cell. As Vertex' Caron points out, "If you remove that protein entirely from the system, you don't know which of its subfunctions was most important."

That leaves a maze of pathways and net- works to analyze in search of good targets — and good chemicals.

ASKA and ye shall receive: Cellular Genomics' reengineered "ASKA" kinases respond only to a tailored molecule, making it possible to study very specific effects.
While at Princeton University, Kevan Shokat, now a professor at the University of California at San Francisco and a member of CGI's scientific advisory board, developed a pair of tools for studying one piece of the cellular machinery at a time. First, he genetically re-engineered the active site of a protein kinase (an enzyme that adds phosphate groups to proteins) so only specifically shaped chemicals could bind. Next, he designed and developed such compounds.

The setup enables Shokat to judge how good a target is before creating the optimal chemical against it. "The pharmaceutical industry is always looking for reference compounds," says Mark Velleca, vice president of research and preclinical development at CGI. "Our system functions as a modular reference system; it establishes a benchmark of optimal functionality for each target."

The re-engineered molecules are called analog sensitive kinase allele (ASKA) proteins. The kinase family represents a rich source of about 1,000 drug targets. "They are the largest druggable target class in the genome," Velleca says. CGI is using ASKAs both for internal drug discovery and in collaborations (including Serono S.A. and Schering AG). Using genetically engineered ASKA mice, Vellaca says, "You can not only validate a target before you start lead optimization, but you can actually do it in parallel."

Vertex Pharmaceuticals, meanwhile, is developing its own brand of technology. "We are using chemical genetics and finding potent and very selective compounds through a combination of screening, designing focused libraries around known kinases, and doing standard structure-based design," Caron says. "You do whatever it takes to get that compound, but once you have a reagent, these molecules are in a direct path to the clinic."

According to Caron, Vertex is seeing success with this approach. "Chemical genetics gives you the opportunity to get a quick answer," he says.

Infinite Wisdom 
Even the most jaded venture capitalist would have to sit up and take notice of the Infinity Pharmaceuticals advisory board.

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Schreiber is not leaving the commercialization of chemical genetics entirely to others. He is now a co-founder of Infinity Pharmaceuticals Inc., in Waltham, Mass., one of the few startups to generate much excitement during the past couple of years. Part of Infinity's appeal is a pre-eminent management team and scientific advisory board (see "Infinite Wisdom," right), but the company has an equally compelling platform, which sprang largely from Schreiber's work at Harvard's Institute for Chemistry and Cell Biology (ICCB).

Infinity Intrigue 
Having been a scientific advisor for two other biotech companies — Vertex and Ariad Pharmaceuticals — Schreiber had some opinions about how to commercialize his own technology. "When a biotech is about three years old, things get difficult," he says. "Because of financial forces, there becomes enormous pressure to reach milestones."

This is a critical point because, he says, "Scientists may get frustrated if these new forces prevent them from realizing their creative potential." Hoping to insulate Infinity from that effect, Schreiber bided his time to ensure the technology platform was mature before sending it out into the commercial world.

Split synthesis: The infinite possibilities of diversity-oriented synthesis, for the production of "druggable" compounds.
Finally, others prodded him to action. By 2001, he says, "many of my trainees at the ICCB were champing at the bit to industrialize the process. Several of my trusted colleagues and friends, particularly Eric [Lander] and Rick [Klausner], agreed the platform was ripe."

With those kinds of advisers, it's understandable why Schreiber is sanguine about the company's launch at the beginning of what is now refered to as "the nuclear winter of genomic financing." "We really can't credit ourselves for the timing," he says, wryly. "That's just when it was ready."

The company leverages four major technologies: diversity-oriented synthesis, virtual screening, chemical genomics (also called chemogenomics), and chemical genetics. It's a mouthful of cutting-edge science, but the gist is using new tools to guide drug discovery and development, as follows:

  • Diversity-oriented synthesis provides complex, specific, but "druggable" compounds in a few simple steps. The goal is to generate a broader range of compound types than is tested by most pharmas and to see if some of these can succeed where others have failed.

  • Computer programs "populate small molecules in multidimensional chemical space," Schreiber says. Infinity builds models of these new chemicals, testing them virtually before taking them into the lab.

  • Compounds are designed that are "biased" toward the most important classes of potential targets (e.g., kinases, proteases). This chemo- genomics, target-class approach takes advantage of each family's specific characteristics and allows the company to tackle multiple targets in the same family at once.

  • Chemical genetics helps Infinity understand the rules about how these compounds work in cells. Their sophisticated screens are designed to help them find better targets faster.

If the chemicals are the picks and shovels, then the assays are the ground that Infinity mines. "Where Eric Lander is playing such a key role is helping to apply the principles of genomics to using phenotypic screens," Schreiber explains. "The slow step in screening has been actually identifying the protein to which the small molecule binds." New tools emerging from genomics, particularly Lander's lab, will let Infinity pinpoint those proteins more easily.

Informatics at Infinity 
It's a brand-new company, with brand-new technologies and a totally new way of doing things.

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Infinity is an atypical pharmaceutical company in almost every way, including the targets it is going after. "In the next year or two, the focus will be on applying the platform broadly, to select clinical candidates in a number of areas, including what are viewed as intractable targets," Schreiber says. An impressive informatics system wraps it all together, so they can move quickly from screens to drugs (see "Informatics at Infinity," right).

Investors like Infinity, largely because it plays up the idea of doing drug lead development (chemistry) earlier, in parallel with target validation (biology). Pundits such as those at the Boston Consulting Group have published reports predicting that chemogenomics alone might save $200 million in development costs per drug.

Chemical diversity is either one of the more controversial or cutting-edge aspects of Infinity's platform, depending on how one looks at it. Infinity contends its compounds will be complex enough to be highly specific but devoid of the drawbacks associated with traditional natural compounds. Others are not so sure.

"[Pharma] people tend to shy away from complex, because it often means more difficult," says John Montana, CEO of Cambridge, England's Amedis Pharmaceuticals Ltd., a chemistry-based company developing new silicon-based drugs. "Natural molecules have their place, but the more complex they are, the more difficult they are to work with." Vertex' Caron agrees: "Pharmas want the compounds to be in the drug-like space. They want small, soluble compounds."

For Infinity to succeed, it's not enough for one of these tools to work — they all have to work together.

Schreiber is confident that he's done his homework: "It took us five years just to develop highly accurate, reproducible, and quantitative imaging technologies that would let us capture the information from the phenotypic screens and protein-binding experiments, and make that retrievable from multiple federated databases," he says. More importantly, he's not letting the technology drive the science. "There is a huge amount of work that goes into quality control and vetting our results."

But some big problems remain. "Two big steps are left that can't be solved at the ICCB," Schreiber says. "These compounds need to be rapidly optimized for pharmacokinetics and ADME/Tox [absorption, distribution, metabolism, excretion, and toxicology]." According to Schreiber, the Institute has figured out how to design chemical probes for this task; it's up to Infinity to refine them.

If Infinity can use chemical genetics to improve ADME/Tox studies, it will be one of the most important and valuable contributions the field has made, at least from a drug development standpoint. It will also mean Schreiber has done just about everything feasible to set his own company on the path to success. *