User:Kerry Frattarola/Sandbox 1

Structure

Indinavir is an antiviral compound that acts as a protease inhibiter. Figure 2 below depicts Indinavir’s structure. The drug has a molecular weight of 711.875 g/mol and is very soluble in water and ethanol ^[1]. Indinavir works by specifically binding to the HIV-1 protease active site by mimicking a target substrate protein and essentially becoming “stuck” in the enzyme active site, disabling the enzyme. Indinavir’s pyridine attracts protease Arg8 to hold it in place. Its ketone interacts with the protease Asp25 to perform initiate aspartic catalysis. The bond between the ketone and amine doesn't lyse due to the nature of the inhibitor.

Function

Indinavir functions as a competitive inhibitor affecting the HIV protease protein. Indinavir essentially mimics the target substrate of HIV protease and binds to the protease active site. The HIV protease enzyme is essential to the reproduction of the HIV virus and further infection. HIV protease performs post-translational cleavage of polyproteins, such as Gag, that serve as important factors in virus development. HIV protease is released from the virus soon after the cell is infected and immediately beings lysing polyproteins into vital proteins such as reverse transcriptase, integrase, and protease. The virus will halt development if the polyproteins are not lysed and the resulting particles from the virus will be non-infective. The hydrophobic phenyl functional groups located on the terminal ends of Indinavir increased the potency of the drug compared to earlier protease inhibiters.

Mechanism

The active site of HIV-1 protease is inhibited by Indinavir when the molecule interacts with the specific sites that a Gag protein peptide would normally interact with. The active site contains Asp25, which is involved in peptide cleavage, Thr26, which is involved in stabilizing the active site conformation, and Gly27, which is involved in the binding of a protein in a position that gives Asp25 access to its cleavage site. (Don't know how to reference this) Arg8 also plays a role in holding a substrate in place in the enzyme active site. When the Indinavir molecule enters the protease active site it imitates the transition state of Gag protein peptides. The virus' peptide bonds [-NH-CO-] can be cleaved via aspartic catalysis. Indinavir contains a hydroxyethylene [-CH2-CH(OH)-] site instead that cannot be cleaved by Asp25. The molecule becomes stuck inside the active site because of the hydrogen bonds between Arg8 and Indinavir's pyridine ring and the interactions between Gly27 and Indinavir's aromatic rings. This blocks all further cleavage of viral peptides by the protease molecule.

Indinavir acts with the Asp25, Thr26 and Gly27 subunits in the HIV-1 protease enzyme.^[2]

Cellular Effects

Indinavir blocks the cleavage of the Gag polyprotein. This inhibition does not allow for the maturation of new viral particles produced from infected cells. Viral particles that do not mature will not be able to infect new cells, lowering the viral load. Protease inhibitors do not have any effect on already infected cells but they do prevent further cell to cell transmission of the virus.