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The Molecular Maturation Mechanism of HIV-1 Protease

Final Report Summary - HIVPROTMOLMECH (The Molecular Maturation Mechanism of HIV-1 Protease)

Since the discovery of HIV three decades ago, an enormous worldwide research effort has been conducted to understand the basic biology of the pathogen. This has resulted in the development of sophisticated anti-retroviral therapies that markedly increase the lifespan of infected individuals. Many of the inhibitors corresponding to such therapies are examples of “structure aided drug design”, where an atomic level knowledge of a key viral enzyme target provides the basis for discovering suitable drug candidates.

However, such advances are plagued by the emergence of multi-drug resistance mutations that render treatment ineffective over a period of time. Furthermore, whilst much of the general lifecycle of the virus is now understood, there are critical aspects that still remain a mystery and that could form effective targets for therapy, were they understood at an atomic level of detail.

One key example is the activation of the enzyme that leads to viral maturation, the HIV-1 protease. This enzyme self-activates from within an array of linked proteins that it is meant to process, a critical event that enables all subsequent maturation events. Despite state-of the-art experimental methods that have provided insight into the mechanism, a full atomic-level understanding of the mechanism remained unknown. The main objective of HIVProtMolMech was to discover the mechanism by which this critical process occurs at the atomic level.
The research employed the use of a state-of-the-art volunteer distributed computational infrastructure developed by the host, called GPUGrid ( This enabled the problem to be investigated via the use of high throughput all-atom molecular dynamics simulations.

An initial study on the dynamics of the mature enzyme resulted in the discovery of a network of molecular conformations accessible that are involved in enzyme function and that are exhibited even in the absence of substrate. The energetics and kinetics of these conformational transitions were described, agreeing well with experiment (Ref 1). A subsequent investigation provided a complete quantitative description of the kinetics of transitions across all catalytically relevant conformations (Ref 2).

The principal study involved the design and simulation of a model system that represented the immature protease. It was discovered that the immature enzyme is capable of associating its upstream distal linkage region to its own active site and does so using the same ensemble of conformations that it exhibits in the mature protease (Figure 1). A complete kinetic treatment of the transitions involved was developed allowing for the rate of such a process to be calculated for the first time. The discovery provides the atomic-level basis for a new branch of inhibitor therapy that targets the immature protease rather than the mature one (Ref 3).

This was supported by a general theoretical development that accounted for the complete processing of polymer chains by a catalyst (Ref 4). This successfully described the in vitro kinetics of viral maturation (Ref 5) and provides a proof of concept for a multiscale research strategy that will enable the dynamics of HIV maturation itself to be predicted from an understanding of the molecular components that constitute the process.

During the project, it emerged that additional studies would be beneficial to the final outcome of the project. One study optimized a strategy to calculate protein-ligand binding affinities from high throughput simulation (Ref 6), a key feature of describing macromolecular interactions. Molecular simulation research was also conducted on other targets, specifically the reverse transcriptase of HIV, for which a novel allosteric mechanism of inhibition was discovered (Ref 7) and on the first dimerized crystal structure of a key signaling protein that belongs to the largest superfamily (GPCRs) of proteins. This enabled the key aspects of how such proteins bind to each other in the membrane to be reviewed (Ref 8). A final study investigated the conformational plasticity of the fusion peptide of HIV, a protein that acts as a molecular harpoon through which the virus gains entry to cells. It was possible to characterize the conformational transitions by which this protein transiently folds into structures that may be used in viral entry (Ref 9).

In conclusion, the research conducted within HIVProtMolMech has successfully met its principal objectives as well as additional objectives that emerged during the project. This has led to 3 publications within the time frame of the project and a further 6 envisioned soon (2 currently under review and 4 awaiting submission). It also led to dissemination of the findings at several international scientific conferences. The project has significant potential socioeconomic implications, especially for the pharmaceutical sector, through which an effective and potentially resistance proof therapy against HIV can be developed. It has also made important contributions towards understanding the basic mechanism of key aspects of the retroviral lifecycle. This may furnish a translatable body of research that may be applicable to other disease domains in the near future and has direct ramifications for improved health led by the European socioeconomic area.

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