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SBI, Quest Say Novel IT Can Help Predict Resistance to HIV Drugs

NEW YORK, Feb. 27 - Structural Bioinformatics said it has come up with a novel computational method that may help predict patients' resistance to protease inhibitors.

Collaborating with researchers at Quest Diagnostics, with whom SBI has an ongoing partnership, the company said it used its Variome polymorphism database to create 3-D molecular models of highly mutated viral proteins based on genetic data obtained from individuals with HIV.

From this, SBI said it was able to determine the structure of HIV protease, an essential protein for HIV replication, and bind it to seven protease inhibitors currently sold in the US.

The company said it determined the binding affinity of these protease inhibitors by calculating the binding energy of each of them to the active site of the protease. "The scientists were then able to demonstrate with a high degree of confidence that the binding energy directly correlates to drug resistance measured using commercially available cell-based phenotypic resistance assays," SBI said in a statement.

"Rules-based resistance interpretation may not accurately predict the additive or canceling effects of multiple mutations in the protease," Peter Heseltine, medical director for infectious diseases at Quest Diagnostics' Nichols Institute. "With this technology, we will be able to more rapidly predict drug resistance with an accuracy approaching that of lengthy cell-based phenotypic assays."

Researchers presented their findings at the 9th annual Conference on Retroviruses and Opportunistic Infection, held in Seattle, Wash., through Thursday.

The Variome database contains 3-D protein structures derived from DNA polymorphisms. Based on this extensive collection of variants, SBI said, its researchers are able to create a statistical representation of the range of target protein shapes.

Armed with this information, SBI's researchers may predict drug activity and perhaps even "synthesize drug candidates with activity against highly conserved regions of each target's active binding site."


In December 2000, Quest made an equity investment in SBI, extending a relationship that began in 1999.

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