Sandbox 645
From Proteopedia
HIV-1 Protease
IntroductionHIV -1 protease (HIV PR ) is a retroviral aspartyl protease that is derived from HIV-1, a lentivirus that is best characterized for its ability to lower host immunity by infecting CD4+ T lymphocytes, macrophages, and dendritic cells.[1] Aspartyl proteases are protease enzymes that utilize aspartate residue(s) for the catalysis of peptide substrates. Eukaryotic forms of these proteases include the , cathepsins and renins. While they have a two-domain structure, the retroviral aspartyl proteases are much smaller and homologous to a single domain of the eukaryotic aspartic proteases. HIV-1 protease is essential for the life cycle of HIV. The protease takes newly synthesized polyproteins and cleaves them by means of a hydrolysis reaction into the smaller mature protein components of the HIV virion.[2] These proteins are used to form the virion capsid that encases the viral genome. Effectively inhibiting HIV-1 protease will result in the inability for HIV to propagate as it will no longer have the ability to form complete virion units to infect new cells. The HIV PR, together with single stranded RNA (ssRNA), reverse transcriptase, integrase, and other viral factors, is found inside the HIV-1 virion.[3] 
Structure & FunctionStructure of HIV-1 Protease In the mid 1980's, the structure of HIV-1 Protease was hypothesized by Lawrence Pearl and William Taylor to consist of a single domain of the eukaryotic aspartic protease and function in the dimeric form.[5] As NMR was not yet in use at this time, x-ray crystallography was implored but required a large quantity of large crystals. This was problematic as heavy atom derivatives had to be used to overcome the phase problems with this new structure and a considerable amount of protein was needed. Eventually these problems were overcome and the first images of HIV-1 protease where announced by the Merck group, who were most successful at large-scale protein purification and crystallization. Unlike most members of the aspartyl protease class, which generally exist as two domain monomers, HIV protease is a dimmer with two identical that are comprised of 99 amino acids. These two subunits come together to form a very narrow 7.46 angstrom diameter for the ligand to navigate; enclosing the active site in the middle. Instead of one flap (a long flexible β-hairpin loop from the N-terminal domain) closing over the active site like in pepsins, the homodimeric retroviral enzyme has two poorly ordered flaps.[6]The polyprotein is capable of making it to the active site not by squeezing through the narrow tunnel but rather by having the flaps . Each subunit donates the catalytic triad, Asp-Thr-Gly, to the highly conserved active site, which also closely resembles that of monomeric proteases like pepsin. The residues are Asp25, Thr26 and Gly27 on each of the subunits. The active site is highly conserved in the retroviral aspartyl protease just as in the eukaryotic aspartyl proteases. As will be seen in the mechanism, the two will hydrolytically cleave the polyprotein that comes into the active site.
Mechanism
The mechanism most commonly accepted for the aspartyl proteases is a general acid-base mechanism involving the coordination of a water molecule between the two highly conserved aspartate residues which leads to hydrolysis. One of the aspartate residues induces activation of the water molecule by removing one of the protons. This allows the nucleophilic oxygen to attack the carbonyl carbon of the peptide and form a tetrahedral oxyanion intermediate. Rearrangement leads to the protonation of the scissile amide and thus cleavage. Applications & ResearchCurrently there is no cure for HIV. However after some extensive research, some drugs were to be designed in order to pause the HIV affects. This happens by the ability of the drugs to mimic the tetrahedral intermediates in the active site and prevent the polypeptide from binding the Asp residues. When the HIV infects an organism it tends to multiply within the body’s cells. The virus is then released to infect other cells. In this manner, the infection of HIV infects the newly made cells of the body. While the viruses are produced, proteins and enzymes used to manufacture the DNA in addition to other components of the virus are made. In this case, is that enzyme that is needed to bring the structural and enzymes of the virus together. Protease drugs are what could inhibit this virus.
Based on the crystal structure data and protein receptor ligand complexes studied, interatomic interactions that work on burying atoms and find the statistical preference for amino acid pairs. A free energy model of the receptor-ligand is formulated and helps in showing the interfacial interactions. The interaction strength of this model has a reliability of ±1.5 kcal/mol, which reveals the importance of atomic interaction to stabilize the receptor-ligand interface. The analysis of a binding motif of HIV-1 protease inhibitor complex shows the important contacts instead of the set of atoms.
1) Saquinavir (Invirase) is known to be one of the first FDA approved protease inhibitor for HIV treatment. This usually occurs by HIV protease binding an active site , which will prevent polyproteins from also binding. Saquniavir's chemical structure has the ability to intermediate of the hydrolytic reaction to interact . 
2) Indinavir (Crixivan) this protease inhibitor is an oral medication that blocks the protease activity and leads to defect the viruses. Once these viruses are unable to reach the body’s cells, it will decrease in number.  This inhibitor doesn’t have the ability to prevent the HIV transmission among individuals, nor does it cure AIDS or HIV infection. (Crixivan)is approved by the FDA in March 1995. [8]
 Ritonavir is soluble in isopropanol and practically insoluble in water.
 Nelfinavir is slightly soluble in water at pH ≤ 4 and completely soluble in methanol.
References
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