HIV-1 protease or PR is a

retroviral aspartyl protease Retroviral aspartyl proteases or retropepsins are single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger pol or gag polyprotein. Retrovira ...

(retropepsin), an

enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...

involved with

peptide bond In organic chemistry, a peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along a peptide or protein cha ...

hydrolysis in retroviruses, that is essential for the life-cycle of HIV, the

retrovirus A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. After invading a host cell's cytoplasm, the virus uses its own reverse transcriptase e ...

that causes

AIDS The HIV, human immunodeficiency virus (HIV) is a retrovirus that attacks the immune system. Without treatment, it can lead to a spectrum of conditions including acquired immunodeficiency syndrome (AIDS). It is a Preventive healthcare, pr ...

. HIV-1 PR cleaves newly synthesized polyproteins (namely, Gag and Gag- Pol) at nine cleavage sites to create the mature protein components of an HIV

virion A virion (plural, ''viria'' or ''virions'') is an inert virus particle capable of invading a Cell (biology), cell. Upon entering the cell, the virion disassembles and the genetic material from the virus takes control of the cell infrastructure, t ...

, the infectious form of a virus outside of the host cell. Without effective HIV-1 PR, HIV virions remain uninfectious.

Structure

Mature HIV protease exists as a 22 kDa

homodimer In biochemistry, a protein dimer is a macromolecular complex or protein multimer, multimer formed by two protein monomers, or single proteins, which are usually Non-covalent interaction, non-covalently bound. Many macromolecules, such as proteins ...

, with each subunit made up of 99 amino acids. A single active site lies between the identical subunits and has the characteristic Asp- Thr- Gly (Asp25, Thr26 and Gly27)

catalytic triad A catalytic triad is a set of three coordinated amino acid residues that can be found in the active site of some enzymes. Catalytic triads are most commonly found in hydrolase and transferase enzymes (e.g. proteases, amidases, esterases, aminoac ...

sequence common to aspartic proteases. As HIV-1 PR can only function as a dimer, the mature protease contains two Asp25 amino acids, one from each monomer, that act in conjunction with each other as the catalytic residues. Additionally, HIV protease has two molecular "flaps" which move a distance of up to 7 Å when the enzyme becomes associated with a substrate. This can be visualized with animations of the flaps opening and closing.

Biosynthesis

Precursor

The Gag-Pol polyprotein, which contains premature coding proteins, including HIV-1 PR. PR is located between the reverse transcriptase (which is at the C-terminus of PR) and the p6^pol (which is at the N-terminus of PR) of the transframe region (TFR). In order for this precursor to become a functional protein, each monomer must associate with another HIV-1 PR monomer to form a functional catalytic active site by each contributing the Asp25 of their respective catalytic triads.

Synthesis Mechanism

When viral HIV-RNA enters the cell, it is accompanied by a

reverse transcriptase A reverse transcriptase (RT) is an enzyme used to convert RNA genome to DNA, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genomes, by retrotransposon mobi ...

, an

integrase Retroviral integrase (IN) is an enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme ...

, and a mature HIV-1 PR. The reverse transcriptase converts viral RNA into DNA, facilitating the integrase's role in incorporating viral genetic information with the host cell DNA. The viral DNA can either remain dormant in the nucleus or be transcribed into mRNA and translated by the host cell into the Gag-Pol polyprotein, which would then be cleaved into individual functional proteins (including a newly synthesized HIV-1 PR) by the mature HIV-1 PR. The HIV-1 PR precursor catalyzes its own production by facilitating its cleavage from the Gag-Pol polyprotein in a mechanism known as auto-processing. Auto-processing of HIV-1 PR is characterized by two sequential steps: (1) the intramolecular cleavage of the N-terminus at the p6^pol-protease cleavage site, which serves to finalize PR processing and increase enzymatic activity with the newly formed PR-reverse transcriptase intermediate, and (2) the intermolecular cleavage of the C-terminus at the protease-reverse transcriptase cleavage site, leading to the assembly of two PR subunits into mature dimers. Dimerization of the two subunits allows for fully functional, combined active site, characterized by two Asp25 catalytic residues (one from each monomer), to form.

Function

HIV-1 PR serves a dual purpose. Precursor HIV-1 PR is responsible for catalyzing its own production into mature PR enzymes via PR auto-processing. Mature protease is able to hydrolyze peptide bonds on the Gag-Pol polyproteins at nine specific sites, processing the resulting subunits into mature, fully functional proteins. These cleaved proteins, including reverse transcriptase, integrase, and RNaseH, are encoded by the coding region components necessary for viral replication.

Mechanism

As an aspartic protease, the dimerized HIV-1 PR functions through the aspartyl group complex, in order to perform hydrolysis. Of the two Asp25 residues on the combined catalytic active site of HIV-1 PR, one is deprotonated while the other is protonated, due to pKa differences from the micro-environment. In a general aspartic protease mechanism, once the substrate is properly bound to the active site of the enzyme, the deprotonated Asp25 catalytic amino acid undergoes base catalysis, rendering the incoming water molecule a better nucleophile by deprotonating it. The resulting hydroxyl ion attacks the carbonyl carbon of the peptide bond, forming an intermediate with a transient oxyanion, which is stabilized by the initially protonated Asp25. The oxyanion re-forms a double bond, leading to the cleavage of the peptide bond between the two amino acids, while the initially deprotonated Asp25 undergoes acid catalysis to donate its proton to the amino group, making the amino group a better leaving group for complete peptide bond cleavage and returning to its original deprotonated state. While HIV-1 PR shares many of the same characteristics as a non-viral aspartic protease, some evidence has shown that HIV-1 PR catalyzes hydrolysis in a concerted manner; in other words, the nucleophilic water molecule and the protonated Asp25 simultaneously attack the scissile peptide bond during catalysis. Aspartyl protease mechanism

As a drug target

With its integral role in HIV replication, HIV protease has been a prime target for drug therapy. HIV protease inhibitors work by specifically binding to the active site by mimicking the tetrahedral intermediate of its substrate and essentially becoming “stuck,” disabling the enzyme. After assembly and budding, viral particles lacking active protease cannot mature into infectious virions. Several

protease inhibitors Protease inhibitors (PIs) are medications that act by interfering with protease, enzymes that cleave proteins. Some of the most well known are antiviral drugs widely used to treat HIV/AIDS, hepatitis C and COVID-19. These protease inhibitors pre ...

have been licensed for HIV therapy. There are ten HIV-1 PR inhibitors that are currently approved by the

Food and Drug Administration The United States Food and Drug Administration (FDA or US FDA) is a List of United States federal agencies, federal agency of the United States Department of Health and Human Services, Department of Health and Human Services. The FDA is respo ...

: indinavir, saquinavir,

ritonavir Ritonavir, sold under the brand name Norvir, is an antiretroviral medication used along with other medications to treat HIV/AIDS. This combination treatment is known as highly active antiretroviral therapy (HAART). Ritonavir is a protease inhi ...

nelfinavir Nelfinavir, sold under the brand name Viracept, is an antiretroviral medication used in the treatment of HIV/AIDS. Nelfinavir belongs to the class of drugs known as protease inhibitor (pharmacology), protease inhibitors (PIs) and like other PIs ...

, lopinavir, amprenavir, fosamprenevir, atazanavir, tipranavir, and

darunavir Darunavir (DRV), sold under the brand name Prezista among others, is an antiretroviral medication used to treat and prevent HIV/AIDS. It is generally recommended for use with other antiretrovirals. It is often used with low doses of ritonavir ...

. Many of the inhibitors have different molecular components and thus different mechanistic actions, such as blocking the active site. Their functional roles also extend to influencing circulation concentrations of other inhibitor drugs (ritonavir) and being used only for certain circumstances in which the virus exhibits tolerance of other inhibitors (tipranavir).

Evolution and resistance

Due to the high

mutation rate In genetics, the mutation rate is the frequency of new mutations in a single gene, nucleotide sequence, or organism over time. Mutation rates are not constant and are not limited to a single type of mutation; there are many different types of mu ...

s of retroviruses, especially due to mutationally sensitive regions (notably the region containing the catalytic triad sequence), and considering that changes to a few amino acids within HIV protease can render it much less visible to an inhibitor, the active site of this enzyme can change rapidly when under the selective pressure of replication-inhibiting drugs. Despite most of known resistant mutations can affect the stability of the HIV-1 PR, this protein could still perform its catalytic activity, sometimes facilitated by compensatory mutations. Two types of mutations are generally associated with increasing drug resistance: "major" mutations and "secondary" mutations. Major mutations involve a mutation on the active site of HIV-1 PR, preventing the selective inhibitors from binding it. Secondary mutations refer to molecular changes on the periphery of the enzyme due to prolonged exposure of similar chemicals, potentially affecting inhibitor specificity for HIV-1 PR. One approach to minimizing the development of drug-resistance in HIV is to administer a combination of drugs which inhibit several key aspects of the HIV replication cycle simultaneously, rather than one drug at a time. Other drug therapy targets include

, virus attachment, membrane fusion, cDNA integration and virion assembly.

External links

* The MEROPS online database for peptidases and their inhibitors
A02.001
* - the HIV-1 protease structure in interactive 3D. * - Animation of the flaps opening and closing based on X-ray crystal structures. *

References

{{Portal bar, Biology, border=no HIV/AIDS EC 3.4.23 Proteases Enzymes of known structure