Neutron studies reveal HIV drug mechanism weaker than assumed

Neutron studies of an HIV enzyme and its inhibitor have revealed new areas for improvement in drug design to enhance performance, combat resistance and reduce dosage of antiretroviral treatments.

An international team used neutrons at the Institut Laue-Langevin to analyse the binding between HIV-1 protease and amprenavir.

“HIV protease acts at the stage of virus maturation when it hydrolyses large poly-protein chains in order to liberate functional and structural proteins. If the protease is inhibited the viral particles do not mature and remain non-infectious,” Andrey Kovalevsky from Oak Ridge National Laboratory told Laboratory News.

For the past two decades scientists have used highly intense X-rays to investigate the best way to target and block the protease’s role in spreading the virus. However, X-ray analysis has its drawbacks. The strongest bonds between the enzyme and an inhibitor are usually hydrogen bonds. Hydrogen bonds are actually invisible to X-ray analysis, so it’s been difficult for scientists to speculate as to how this binding takes place.

“X-ray crystallography gives information on the locations of heavy atoms, such carbon, nitrogen, oxygen, sulphur, that are common in protein molecules, but with X-rays it is almost impossible to detect hydrogen atoms that constitute about half of the atoms in any given protein molecule,” explained Kovalevsky.

Because neutrons scatter well from hydrogen, but even better from its isotope deuterium, the team produced a recombinant HIV-1 protease in which most hydrogen atoms were substituted with deuterium atoms. They then used protein crystallisation to obtain crystals of the protease-amprenavir complex for neutron crystallographic analysis.

The neutron studies revealed a very different picture to that inferred from the X-ray studies which had indicated a far greater role for hydrogen bonding in the interaction between enzyme and inhibitor. The researchers actually found only two really strong hydrogen bonds between the drug and the HIV enzyme.

While concerning, the new information does provide drug designers with a set of new potential sites for the improvement of the drug’s surface chemistry to significantly strengthen the binding and increased the effectiveness of HIV drugs.

The team have proposed a number of future steps for better drug design of HIV therapies in the future:

“The two strong hydrogen bonds between amprenavir and the catalytic residues of the protease can be made even stronger if a functional group is added to the amprenavir structure near the location of the hydroxyl making these bonds. Also, we found that there were three missing hydrogen bonds that were considered strong using X-ray structures. The chemistry of amprenavir can also be modified with functional groups in those places in order to make new hydrogen bonds that would improve the inhibitor’s binding,” said Kovalevsky