New algorithm helps decipher how drugs work inside body

Researchers, including one of Indian-origin, have developed a computer algorithm that can help scientists for the first time see how drugs produce pharmacological effects inside the body.
The algorithm, developed by researchers at Columbia University Medical Center (CUMC), could help create drugs that are more efficient and less prone to side effects, suggest ways to regulate a drug's activity, and identify novel therapeutic uses for new and existing compounds.
"For the first time we can perform a genome-wide search to identify the entire set of proteins that play a role in a drug's activity," said study co-author Dr Andrea Califano, the Clyde and Helen Wu Professor of Chemical Systems Biology and chair of the department of Systems Biology at CUMC.

Scientists design drugs to pinpoint molecular targets in the cell. However, when a drug enters the human body, it becomes part of an incredibly complex system, and can interact with other molecules in ways that are hard to predict.
This unanticipated cross-talk causes side effects and stops many promising drug candidates from being used in clinical care.
Califano's lab has devised a new approach called DeMAND (Detecting Mechanism of Action by Network Dysregulation) to characterise a drug's effects more precisely.

The method involves creating a computational model of the network of protein interactions that occur in a diseased cell. Experiments are then performed to track gene expression changes in diseased cells as they are exposed to a drug of interest.

The DeMAND algorithm combines data from the model with data from the experiments to identify the complement of proteins most affected by the drug.
DeMAND improves on more labour intensive and less efficient methods, which are only capable of identifying targets to which a compound binds most strongly.
This provides a more comprehensive picture, because DeMAND identifies many molecules that are affected in addition to the drug's direct target.
So far, DeMAND's predictions are proving to be accurate when tested with follow-up experiments. The researchers said that when they exposed human diffuse B-cell lymphoma cells to a panel of drugs, the algorithm identified 70 per cent of previously documented targets.

Using DeMAND, the researchers showed that a similar subset of proteins is affected by the unrelated drugs sulfasalazine and altretamine.
Altretamine is currently used to treat ovarian cancer, but these results suggest that, like sulfasalazine, it could be used for bowel inflammation or rheumatoid arthritis too.
"DeMAND could accelerate the drug discovery process and reduce the cost of drug development by unravelling how new compounds work in the body," said co-senior author Mukesh Bansal.
"Our findings on altretamine also show that it can determine novel therapeutic applications for existing FDA- approved drugs," Bansal said.
The study was published in the journal Cell.