Model may aid cancer drug discovery
The researchers reported these findings in Pharmacology Research & Perspectives.
Creating the model
To build the P-gp model, Dr Wise and his colleagues used static structures from the US Protein Data Bank repository. They used structures showing various stages of transport to simulate 4 points of reference.
From there, the team fed a supercomputer parameters and characteristics of the protein, as well as how it should behave physically, including when kinetic energy was added to bring the protein and its surrounding membrane and water up to body temperature.
The animated model resulted from calculating differences between 2 structures and using targeted molecular dynamics programs to slightly nudge the model to the next step.
“You do that several million times and make several trillion calculations, and you arrive at the next structure,” Dr Wise said. “In this way, we can nudge P-gp through a full catalytic transport cycle.”
Finally, using a docking program, the researchers individually introduced daunorubicin and other drugs into the protein and watched the drugs move through P-gp’s catalytic cycle.
“What happened was: the drugs moved,” Dr Wise said. “And they moved the way they should move, clinically, biochemically, physiologically, to pump the compounds out of the cell.”
Challenging the model
The researchers ran a critical control to further test if the model worked.
“We thought maybe anything you put in the protein, relevant or not, would get pumped through,” Dr Wise said. “So we put in something that is not a transport substrate of P-gp, something that, biochemically, would never be transported by P-gp.”
“We put it in, starting where daunorubicin is effectively pumped out, and, very quickly, the compound left the protein. But it left the opposite way, back into the cell. This experiment gave us more confidence that what we are seeing in these models is reflecting what happens in the cell.”
Dr Wise admitted that, until he saw it for himself, he had doubts the virtual P-gp model would behave like real-life P-gp.
“It’s a crude approximation of a complex, sophisticated human protein, but it’s so much better than the static images available now,” Dr Wise said.
“I’ve got to emphasize for all the disbelievers, for the ‘culture of doubters’ out there, that this model works. It moves the drugs through the membrane. That speaks for itself. What P-gp does in the cell, cancerous or normal, it does in our simulations.” 
