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Small Molecule Drug Discovery Patent Issued

U.S. Patent and Trademark Office

U.S. Patent and Trademark Office in Alexandria, Virginia (A. Kotok)

30 August 2016. A company developing small-molecule treatments for biological targets considered difficult to address is receiving a patent for its core drug identification technology. The U.S. Patent and Trademark Office today awarded patent number 9,428,845 to 7 inventors including Gregory Verdine, a founder of Warp Drive Bio Inc., a biotechnology company in Cambridge, Massachusetts, which owns the patent.

Warp Drive Bio discovers small molecule or low molecular weight drugs directed at disease-causing proteins considered difficult to address with other small molecule drugs or protein biologics alone. These protein targets, says the company, are either inside cells making them inaccessible to biologics, or do not have particular hydrophobic, or water-repelling, binding pockets needed by small molecule drugs. Warp Drive Bio’s technology, known as Small Molecule-Assisted Receptor Targeting, or Smart, combines properties of both small molecule drugs and biologics to penetrate and thus operate inside cells, and create binding surfaces suitable for small molecule drugs.

The patent covers methods and processes for screening compounds for these properties and identifying drug candidates meeting specified criteria. Among the criteria are biological activities of presenter and target proteins interacting with a test compound. The interactions include direct contacts between the test compound and the presenter or target proteins, as well as binding sites on the presenter or target proteins.

The patent also covers contingencies for interactions among test compound and presenter and target proteins, such as when one of the entities is missing, as well as situations where a test compound has a greater affinity for a presenter or target protein, or more complex interactions where a test compound has selective activity with the presenter or target protein.

The Smart technology is based on biochemical research by Verdine and colleagues at Harvard University on synthetic biologics that address processes underlying growth and proliferation of human cancer cells, control of gene expression, and preservation of genomic integrity. Verdine’s lab studies epigenetics, external influences on genetic activity, resulting in changes to DNA that repress activities of genes for transcribing their codes into proteins.

Among the projects of Warp Drive Bio, as reported in Science & Enterprise, is treatments targeting the Ras oncogene, a gene that turns normal function cells into a wide range of tumor cells. Mutations in Ras oncogenes produce proteins that send signals encouraging cell proliferation and inhibit normal cell death resulting in the formation and growth of tumors. These mutations are associated with about 30 percent of human cancers including, non-small cell lung, colorectal, pancreatic, bladder, kidney, thyroid, melanoma, and liver tumors, as well as blood-related cancers.

Verdine founded Warp Drive Bio in 2012 with Harvard University geneticist George Church and protein biochemist James Wells at University of California in San Francisco. The company is a joint project of the French pharmaceutical company Sanofi and venture capital firm Third Rock Ventures, with additional start-up funding from Greylock Ventures.

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