December 1, 2008 (Vol. 28, No. 21)

New Owner Sees Opportunity in Informatics and Enhances Presence with an Acquisition

Tripos International is the newly formed private company that resulted from the break up of the former Tripos, which was spun out of Washington University in 1979. When Vector Capital acquired Tripos in March 2007, it kept the Discovery Informatics business and renamed it Tripos International, and it sold Tripos Discovery Research to Commonwealth Biotech.

Tripos Discovery Research developed drug-like compounds that were designed using software tools invented at Tripos Discovery Informatics. The current focus on computational chemistry software at Tripos International “brings us right back to our roots and the delivery of high-quality software,” says Patrick Flanagan, COO.

When Vector Capital purchased Tripos, it also looked for other companies that would add value to its portfolio of molecular modeling and drug discovery tools. It found a match in Pharsight, which Tripos International acquired last month. Pharsight also provides software products and services for optimizing drug development, such as tools for preclinical and clinical pharmacokinetic and pharmacodynamic modeling and analysis, product profile visualization, regulatory reporting, biostatistics, and clinical trial simulation.

Whereas Tripos’ products are centered on the modeling and chemoinformatics needs of early-stage drug discovery, the purchase of Pharsight extends the company’s reach into the clinical trials space. “By having a strong footprint in numerous stages of the R&D chain for biotechnology and drug development, we can help our customers make better and faster decisions,” remarks Flanagan.

A catalytic complex of HIV-1 reverse transcriptase rendered using new core functionality in the SYBYL Molecular Modeling suite.

Suites of Tools

Among the informatics products offered by Tripos are SYBYL®, a molecular modeling platform that provides fundamental components for investigating molecular structure and properties, with a focus on producing and optimizing lead candidates. SYBYL enables basic and advanced modeling operations for researchers in the life sciences, according to Flanagan. More advanced utilities and workflows allow customers to perform much more complicated interactions with molecules. These include tools for protein structure prediction, new ligand design, virtual screening, and pharmacophore perception.

Tripos continues to develop suites of tools to meet the changing and complex needs of molecular modelers in biotechnology, pharmaceutical, and consumer goods companies. New products include Topomer Search and Topomer CoMFA®.

Tripos’ Topomer platform speeds processes that chemists use to accurately predict the chemical activity and properties of compounds in drug discovery, Flanagan reports. Scientists can create quantitative, predictive 3-D QSAR models in minutes with Topomer CoMFA, then use Topomer Search to identify new substituents and reactive groups that are predicted to improve biological activity. Millions of structures can reportedly be searched overnight on a single processor. Topomer CoMFA also considers the synthetic costs and therapeutic benefits during each lead discovery and optimization decision.

Benchware® Discovery 360 (D360) is an enterprise application that supports chemical synthesis and testing decisions, stores searches, retrieves research information, and shares experimental results with project team members. Recently, Benchmark D360 was installed at Wyeth Discovery Research, where the system helps scientists access, analyze, and share data from different repositories of biological and chemical information.

Tripos worked closely with Wyeth scientists to set up workflows to reduce the time spent analyzing and joining data collected from multiple sources. Rather than taking hours, the process now can be performed in minutes, Flanagan says.

Benchware D360 combines chemical and biological data with analytical and inventory data. Overall research efficiency increases because scientists can spend more time working in the laboratory and deciphering data. A similar platform was set up at Bristol-Myers Squibb. “We have a history of doing large collaborative projects with our pharmaceutical clients,” continues Flanagan.

Tripos is expected to release Pantheon™ for beta testing this month. This flexible software platform runs on desktop computers and addresses the computer-assisted drug design and informatics needs of medicinal chemists and molecular modelers. Pantheon includes a robust set of basic chemoinformatics and modeling components, such as 3-D visualization, a sketcher, and chemically aware spreadsheets. Results can be shared with others in an organization. Additional workflows can be added to gain more complex capabilities.

For instance, Muse™, a new workflow for de novo design, is being tested at AstraZeneca. The Tripos/AstraZeneca collaboration will incorporate a scoring system developed at AstraZeneca into future releases of the product. Muse allows researchers to build compounds from scratch, while considering multiple parameters for optimization such as biological potency, selectivity, and ADME properties.

In the future, Muse will find structures, scaffolds, and side chains that meet specific design objectives. The commercial release of Pantheon and Muse is tentatively scheduled for early next year.

Benchware Discovery 360 (D360) allows data access and analysis and empowers collaboration among research teams. Multiple different views of a dataset within the D360 application after retrieval from the database are shown.


Tripos’ products and services are not limited to drug discovery. The same software tools can help chemists in other industries to identify and optimize new compounds such as better pesticides or improved flavors or fragrances for food or consumer products.

Tripos International maintains offices around the world to provide personal technical support for its software and regularly schedules training workshops. “It’s challenging to find experts who have backgrounds and expertise in software, chemistry, and pharmacology,” observes Flanagan. “We can provide them.”

Clients can bring problems to Tripos to gain insights regarding their projects. For larger collaborations, Tripos experts regularly visit clients and work shoulder-to-shoulder with company scientists to find solutions. Either way, “we’re a working part of the team,” says Flanagan.

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