Neutron Studies Reveal New Areas for Improvement in Drug Design of HIV Inhibitors

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A team of scientists recently reported on the first study of interactions between the antiretroviral drug, amprenavir, and the HIV-1 protease enzyme.

A team of scientists recently reported on the first study of interactions between the antiretroviral drug, amprenavir, and the HIV-1 protease enzyme. The findings provide the first true picture of how the protease inhibitor blocks viral replication. More importantly, the study reveal how drug design can be improved to enhance performance, combat resistance and reduce dosage of antiretroviral medications to treat HIV.

The study was carried out using neutrons at the Institut Laue-Langevin in Grenoble, France, with results reported in the Journal for Medicinal Chemistry. A joint X-ray/neutron structure of the HIV-1 protease enzyme in complex with amprenavir was determined. According to Professor Irene Weber from the Department of Chemistry and Biology, Georgia State University, the neutron crystal structure provides important new insights into the chemistry of how drugs bind HIV protease.

The HIV-1 protease enzyme plays a key role in the lifecycle of a virus and is one of the most-studied enzymes. It breaks polypeptide chains to create proteins used for replication and production of new infectious virus particles. Scientists have been using X-rays to investigate how to target and block the protease’s action in spreading the virus. X-ray analysis, however, has limitations because it cannot detect the hydrogen bonds between the enzyme and the inhibitor, which is the antiretroviral drug. Hydrogen atoms are virtually invisible to X-ray analysis and scientists are often left to speculate how this binding takes place.

Scientists from Georgia State University, Purdue University and Oak Ridge National Laboratory in the USA and Harwell Oxford in Great Britain found a solution to this problem through the use of neutrons. Neutrons are highly sensitive to lighter elements and the team were able to identify the positions of every hydrogen atom involved in the enzyme-inhibitor complex for the first time and see which were involved in bonding.

The neutron studies revealed a different picture to that inferred from X-ray studies, which had overplayed the importance of many of the hydrogen bonds. The team found only two really strong hydrogen bonds between the drug and the HIV enzyme. This discovery now presents drug designers with a set of new potential sites for the improvement of the drug’s surface chemistry to significantly strengthen the binding and hence increase drug efficacy and reduce dosage requirements.


The findings may also help address drug resistance, which is one of the biggest issues in combating HIV infection. Virus can evolve over time with binding between enzyme and inhibitor becoming weaker. One solution is to improve the binding of the inhibitor with the main-chain atoms of the virus’ protease rather that to target the side chains.

This research has changed the landscape of drug design of protease inhibitors. Advances in antiretroviral therapeutics were once thought to be limited by the strong hydrogen bond interactions with the main-chain atoms of the HIV-1 protease enzyme. However, this study has shown that it is possible to create new avenues for HIV medications that are much less affected by virus evolution and resistance.

“This study perfectly illustrates the benefits of neutrons in drug design due to their unique sensitivity to hydrogen atoms. Until recently high-resolution neutron studies of large biological systems were restricted due to the size of crystals that needed to be grown and the length of time it took for the results to be collected. However, significant technical developments, led by pioneering work here at the ILL, have greatly extended the range of experiments that can be performed providing the pharma industry with a powerful new tool to improve the performance of their products,” commented Dr Matthew Blakeley from Institut Laue-Langevin in a press statement.

Dr Andrey Kovalevsky from Oak Ridge National Laboratory said in the same release, “X-ray crystallography has been playing a crucial role in the structure-guided drug design for over two decades.  It provides us with a picture of how a drug molecule binds to its macromolecular target, which is usually achieved through non-covalent interactions between these two molecules.  The majority of such weak intermolecular interactions involve hydrogen atoms that normally remain invisible in X-ray structures.  If one knows where hydrogen atoms are located it gives a researcher a much better idea about the nature and strength of the interactions.  By applying neutron crystallography we have effectively increased the clarity of this picture, because hydrogen atoms become visible in the neutron structures.  It is fair to say that by using neutrons we are now able to see every atom in a protein/drug complex, all the way to the smallest atom in nature.  We are confident that by combining the two crystallographic techniques it will be possible to significantly improve the method of structure-guided drug design, which will provide patients with newer more effective medicines to not only battle HIV infection, but for other diseases as well.”