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Affinium Aims to Hook Deals By Better Integrating Proteomics, Discovery Process


In John Mendlein’s PowerPoint animation, a white coated scientist in a small silo works furiously to generate protein targets, represented as bright yellow balls, then hurls the balls up over the high walls of the silo to a scientist trapped in the cylinder next door. Other scientists in informatics and screening silos are also processing and producing yellow balls, tossing them up over the walls as fast as they can, but despite these efforts, some scientists soon begin to drown in yellow balls — representing bottlenecks — while the others wait patiently for incoming projectiles.

This scenario, which Mendlein, CEO of Affinium Pharmaceuticals, showed at a recent drug discovery conference in Stuttgart, Germany, illustrates what he said is the current predicament of pharma: high-throughput generation of targets and information has created bottlenecks at multiple stages of drug discovery.

The answer to this problem is not better technology at one stage of the process, Mendlein said, but a better way to integrate the different stages of the process.

Enter Affinium, which has remade itself from a structural proteomics company into a structure-guided drug discovery company with not only x-ray crystallography and NMR but also capabilities in proteomics informatics, lead generation, and ADME-TOX. The company offers pharma partners not just best-of-breed technology but best-of-breed integration, Mendlein told ProteoMonitor in a recent interview.

The Toronto-based company landed a $30 million, three-year partnership with Pfizer last May, but so far, other big pharma deals have eluded it (Lilly last week chose rival Structural Genomix for a technolgy deal - see article p.1.)

Perhaps this slowness in attracting pharma deals derives from Affinium’s novel strategy: Traditionally, pharma has partnered with different companies at different stages of the drug discovery process, hand-picking the best technology in each area, then weaving them into its own proprietary process.

But using multiple companies creates challenges for pharma, including the administrative burden of closing multiple deals and managing the collaborations, as well as integrating data between different platforms, Mendlein said.

Pfizer chose Affinium, he said, because the company’s ability to link these different stages of drug discovery increases the overall speed of the process.

“Speed is more important than cost because speed ultimately allows you to market products for a longer period of time,” said Mendlein. “And you can’t easily reduce time in the clinic, so it’s preferable to work on getting targets and leads to the product stage faster, so you can ultimately have more in clinical trials and get more shots on goal.”

But the fully integrated process, where the white coats happily abandon their silos for a communal table that allows them to smoothly exchange the yellow balls of data, targets, and leads, is still not a complete reality, Mendlein admitted. In the real world, it takes work to develop the integration mindset, and, he said, “you can spend an inordinate amount of research on developing technologies vs. putting [them] to work.”

Affinium is currently trying to work around the technological sinkhole, and has even jumped further down the pipeline, buying an antibacterial project from GlaxoSmithKline in February.

The project is an antibiotic specific for staphylococcus, which was generated through structure-guided discovery fitting in with Affinium’s structure-based discovery approach. The company thinks there is a possibility for $200 million in annual sales for this drug. While pharma is mostly interested in the billion-dollar blockbusters, a small company like Affinium, Mendlein said, can make money on a smaller-market compound with a “focused, targeted marketing effort” Additionally, the company is going to take advantage of Canada’s national healthcare system, and the abundance of centralized clinical records to conduct clinical trials there.

Meanwhile, Mendlein is hitting the road to work on the company’s next big pharma deal. And despite the recent slump in the market, he remains optimistic.

“The hesitance on the part of large pharma to engage in large-scale discovery deals is based on their [negative] experience with large-scale genomics deals,” he said. “But once they see that these small companies can help them integrate multiple steps of the discovery process and save them time, they will jump on the bandwagon again.”


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