Structural Biochemistry/Enzyme/HIV-1 Proteases

HIV-1 ProteasesEdit

HIV, Human immunodeficiency virus is commonly known to be responsible for causing AIDS. The HIV-1 Proteases, which also known as HIV PR is vital for HIV. HIV PR is an aspartic protease, meaning aspartate residues are used in the process of peptide substrates catalysis. Without HIV PR, HIV could not achieve maturation and it remains uninfected. Its importance in HIV survival has made HIV PR inhibitors the new widely studied agents to hope to become to key to find a cure for AIDS.


X-ray crystallography has been used for understand the structure of HIV PR and helped on new drug design. It shows the precise picture and help characterize HIV PR at atomic level. There have been over 160 structures discovered and many researchers have been testing for new available drugs. The main structure of HIV PR follows a specific sequence: Asp-Thr-Gly, a sequence commonly found in aspartic proteases. . Its structure is made with two identical subunits, possibly resulted from gene duplication, a structure.HIV-1 PR do demonstrate the characteristic of retroviruses and aspartic proteases. The molecule is confirmed as a homodimer with an active site similar to those of the aspartic protease. The difference between the aspartic proteases and HIV-1PR monomer is HIV-1PR’s dimer interface has 4 short strands, but aspartic proteases have 6 long strands in pepsins. Due to the structure difference its MW is only about 1/3 of pepsin. It’s active site triplet at c β strand, and the active site loop is d β chain with residues 30-35. Active site is found at Asp25, Thr26, Gly27 located on the loop. HIV PR is symmetric with the identical subunits but its substrate/inhibitor (Polypeptide) is asymmetric.

Mechanism of HIV ProteaseEdit

Protease are enzyme catalyst with high specificity for the hydrolysis of peptide bonds. The mechanism was discovered using kinetics, affinity labeling and X-ray crystallography. The most agreed mechanism is the acid-base mechanism. A water molecule is activated by acid-base role of the active site of aspartate residues and the water molecule attacks the carbonyl carbon of the scissile bond as a nucleophile. The other proposed and widely accepted mechanism is described by Suguan which is based on the crystal structure of the aspartic protease complexes. The reduced peptide inhibitor of these aspartic protease complexes is crucial. At the active pH range, only 1 of the 2 active site of aspartic acids is unprotonated. Asp group with the negative charge and nucleophilic H2O is activated by the negatively charged Asp and then attacks the carbonyl group in the substrate scissile bond. It resulted in an oxyanion tetrahedral intermediate, and the protonated amide(nitrogen atom) rearrange and turn the tetrahedeal intermediate into hydrolysis products.

HIV PR Inhibitor DesignEdit

There have been numerous research done on HIV PR inhibitor to hope for finding the cure to AIDS, and most researches were focusing on designing HIV PR inhibitors based on classical substrates or transition-state analogs. From strategies on aspartic protease, the design of peptidomimetic inhibitors-renin inhibitors has been successful at the first level. The mechanism of these renin inhibitors was studied but there was limited contribution in relation to HIV PR inhibitors. Another strategy based on synthesis of peptide substrates analog. The nonhdrolyzable isostere, has a tetrahedral geometry is replacing the scissile P1-P11’ amide bond. This gives potent HIV PR inhibitors effective in virus replication in vitro. From X-ray crystallography the structure of the HIV PR was discovered and new inhibitors were designed according the structure. The HIV PR has symmetric active site, and a design two-fold (C2) symmetric or pseudo- C2 symmetric inhibitors. It was design to mimic the symmetry at the active site so the C2 axes of the enzyme and inhibitor were nearly superimpose for effective binding.

Drug ResistanceEdit

Although many new drugs design are developed, the effectiveness of these drugs are significantly decreasing due to drug-resistant and cross-resistant mutants. This is due to a HIV viruses high rate of replication and the high error rate of reverse transcriptase during the rapid butation. The drug resistance of HIV is what made the drug design difficult. The mutations affecting the binding sites and inhibitors and resulted in drug resistance, and there is at least 6 mutated residues found in HIV PR.


PudMed Web of Science STRUCTURE-BASED INHIBITORS OF HIV-1 PROTEASE Author(s): WLODAWER, A (WLODAWER, A); ERICKSON, JW (ERICKSON, JW) Source: ANNUAL REVIEW OF BIOCHEMISTRY Volume: 62 Pages: 543-585 DOI: 10.1146/annurev.biochem.62.1.543 Published: 1993

Ashraf Brik and Chi-Huey Wong, Org. Biomol. Chem., 2003, 1, 5 Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA