HIV Protease

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Introduction

After the US Center for Diseases Control (CDC) first reported acquired immunodeficiency syndrome (AIDS), scientists discovered that human immunodeficiency virus (HIV) is the causative agent in AIDS. AIDS spreads fast, spreading all over the world in a short period. Scientists have never slowed down the research on AIDS, and there has been great progress, especially the development of antiretroviral therapy specifically for HIV-1 (HIV-1). The identification of HIV retrovirus and the in-depth understanding of the role of different elements in its life cycle have prompted researchers around the world to develop inhibitors that target different steps in the virus life cycle. An attractive target is the HIV-1 protease (HIV PR), which plays an important role in the proper assembly and maturation of the virion. Understanding the chemical mechanism of this enzyme has always been a basic requirement for the development of highly effective inhibitors.

HIV is a type of retrovirus, which carries genetic information in the form of RNA. The fusion of virus and cell membrane is a prerequisite for infection. This process is mediated by viral envelope glycoproteins (gp120, gp41) and receptors (CD4 and co-receptors) on target cells. When the virus enters the cell, its RNA is reverse-transcribed into DNA. The viral DNA then enters the nucleus of the host cell, where the DNA is integrated into the cell's genetic material through integrase. The activation of the host cell results in the transcription of viral DNA into messenger RNA, which is ultimately translated into viral protein. HIV protease is the third virus-encoded enzyme in this process, which is responsible for cleaving the virus polyprotein precursor into single mature proteins. The viral protein and viral RNA are reassembled into new virions, which bud from the cell and are released to infect another cell.

HIV protease: a logical target for AIDS therapy

Unless the HIV life cycle is blocked by specific treatments, the virus will quickly spread throughout the body after infection, causing the body's immune system to function impaired or even destroyed. Through the analysis of the HIV life cycle, several steps that may prevent virus replication are summarized. For example, there are several commercially available drugs that can inhibit reverse transcriptase (RT), such as the nucleoside analogs AZT, ddI, ddC, and d4T. Their participation will cause the production of DNA to be stopped. The second category is non-nucleoside inhibitors (NNIs), such as nevirapine, efavirenz, and delavirdine. These inhibitors can cause a conformational change in the active site of the enzyme, thereby inhibiting its action. Another key step in the HIV life cycle is the proteolytic cleavage of polypeptide precursors into mature enzymes and structural proteins through the catalysis of HIV PR. It has been shown that immature viral particles cannot undergo maturation to an infective form. The necessity of this enzyme in the virus life cycle makes it a promising target for the treatment of HIV infection.

Structure of HIV protease

HIV PR is an aspartyl protease composed of 99 amino acids, which acts as a homodimer. The National Cancer Institute has created a database dedicated to providing information on the structure of HIV PR. So far, more than 140 types of HIV-1 PR, its mutants, and enzymes complexed with various inhibitors have been reported. The enzyme homodimer complexed with TL-3 is shown in fig. 1 (PDB ID: 3TLH).

Figure 1. Structure of HIV PR complexed with TL-3 (PDB: 3TLH) (Brik, A.; Wong, C.H. 2003)

Each monomer contains a glycine-rich β-sheet region called the flap, part of which constitutes the substrate-binding site and one of the two necessary aspartyl residues Asp-25 and Asp-25' are located in the cavity bottom. The interaction between the substrate and amino acid side chains determines the specificity of the enzyme. Using standard nomenclature (Fig. 2), the S1 and S'1 (S2 and S'2, etc.) subsites are structurally equivalent. Both S1 subsites have strong hydrophobic properties, and most of the S2 subsites except Asp-29, Asp-29', Asp-30 and Asp-30' are hydrophobic. The S3 subsites are adjacent to the S1 subsites and are also mostly hydrophobic.

Figure 2. Standard nomenclature P1⋯Pn, P1′⋯Pn′ is used to designate amino acid residues of peptide substrates (Brik, A.; Wong, C.H. 2003)