Knowledge of the tertiary structure of the proteinase from human immunodeficiency virus HIV-1 is important to the design of inhibitors that might possess antiviral activity and thus be useful in the treatment of AIDS. The conserved Asp-Thr/Ser-Gly sequence in retroviral proteinases suggests that they exist as dimers similar to the ancestor proposed for the pepsins. Although this has been confirmed by X-ray analyses of Rous sarcoma virus and HIV-1 proteinases, these structures have overall folds that are similar to each other only where they are also similar to the pepsins. We now report a further X-ray analysis of a recombinant HIV-1 proteinase at 2.7 A resolution. The polypeptide chain adopts a fold in which the N- and C-terminal strands are organized together in a four-stranded beta-sheet. A helix precedes the single C-terminal strand, as in the Rous sarcoma virus proteinase and also in a synthetic HIV-1 proteinase, in which the cysteines have been replaced by alpha-aminobuytric acid. The structure reported here provides an explanation for the amino acid invariance amongst retroviral proteinases, but differs from that reported earlier in some residues that are candidates for substrate interactions at P3, and in the mode of intramolecular cleavage during processing of the polyprotein.
"The major substrate specificity signature features of HIV PR involve (i) a preference for Glu in the P2 0 position; (ii) a certain preference for large aliphatic and Fig. 2. Three-dimensional structures of selected retroviral PRs. (A) Crystal structures of HIV-1 PR in three conformations: the apo-form of the HIV-1 PR with flaps in open conformation (PDB code 3PHV (Lapatto et al., 1989)), HIV-1 PR with flaps in closed conformation (PDB code 4LL3 (Kozisek et al., 2014)) with inhibitor (DRV) bound in the enzyme active site shown in sticks (with carbon atoms colored green, oxygen atoms red, nitrogens blue and sulfur yellow), HIV-1 PR with flaps in semi-open conformation (PDB code 1ZTZ (Cigler et al., 2005). Inhibitor bound in the enzyme active site (metallacarborane) is shown in sticks (with carbon atoms colored yellow, boron atoms cyan, and cobalt atom maroon). "
"The flexibility and the flap switch in the active site on some aspartic proteases (e.g. HIV-1 protease, renin, BACE1 and plasmepsin II) upon ligands/inhibitors binding were analysed by several experimental and computational studies (Hong & Tang, 2004; Hornak, Okur, Rizzo & Simmerling, 2006; Lapatto et al., 1989; Pietrucci, Marinelli, Carloni, & Laio, 2009; Politi et al., 2011; Sadiq & De Fabritiis, 2010; Steiner et al., 2011; Tzoupis et al., 2012; Xu et al., 2012). Specific MD simulations on HIV-1 protease reveal a reversible transition between open and closed flap conformations (Shang & Simmerling, 2012). "
[Show abstract][Hide abstract] ABSTRACT: The aspartic protease renin (REN) catalyses the rate-limiting step in the Renin-Angiotensin-Aldosterone System (RAAS), which regulates cardiovascular and renal homoeostasis in living organisms. Renin blockage is therefore an attractive therapeutic strategy for the treatment of hypertension. Herein, computational approaches were used to provide a structural characterization of the binding site, flap opening and dynamic rearrangements of REN in the key conserved residues and water molecules, with the binding of a dodecapeptide substrate or different inhibitors. All these structural insights during catalysis may assist future studies in developing novel strategies for REN inactivation. Our molecular dynamics simulations of several unbound-REN and bound-REN systems indicate similar flexible-segments plasticity with larger fluctuations in those belonging to the C-domain (exposed to the solvent). These segments are thought to assist the flap opening and closure to allow the binding of the substrate and catalytic water molecules. The unbound-REN simulation suggests that the flap can acquire three different conformations: closed, semi-open and open. Our results indicate that the semi-open conformation is already sufficient and appropriate for the binding of the angiotensinogen (Ang) tail, thus contributing to the high specificity of REN, and that both semi-open and open flap conformations are present in free and complexed enzymes. We additionally observed that the Tyr75-Trp39 H-bond has an important role in assisting flap movement, and we highlight several conserved water molecules and amino acids that are essential for the proper catalytic activity of REN.
"The core of the active site is hydrophobic and contains two aspartic acid residues contributed by both subunits. Flexible anti-parallel β-sheets from both monomers form two flaps that cover the active site thereby restricting access to it
[5,21,24-26]. In the free enzyme state, the flaps assume a semi-open conformation
[21,22,27,28] and with a ligand in the active site, they assume a closed conformation
[Show abstract][Hide abstract] ABSTRACT: Human Immunodeficiency Virus Type 1 (HIV-1) protease inhibitors (PIs) are the most potent class of drugs in antiretroviral therapies. However, viral drug resistance to PIs could emerge rapidly thus reducing the effectiveness of those drugs. Of note, all current FDA-approved PIs are competitive inhibitors, i.e., inhibitors that compete with substrates for the active enzymatic site. This common inhibitory approach increases the likelihood of developing drug resistant HIV-1 strains that are resistant to many or all current PIs. Hence, new PIs that move away from the current target of the active enzymatic site are needed. Specifically, allosteric inhibitors, inhibitors that block HIV-1 protease active site, should be sought. Another common feature of current PIs is they were all developed based on the structure-based design. Drugs derived from a structure-based strategy may generate target specific and potent inhibitors. However, this type of drug design can only target one site at a time and drugs discovered by this method are often associated with strong side effects such as cellular toxicity, limiting its number of target choices, efficacy, and applicability. In contrast, a cell-based system may provide a useful alternative strategy that can overcome many of the inherited shortcomings associated with structure-based drug designs. For example, allosteric PIs can be sought using a cell-based system without considering the site or mechanism of inhibition. In addition, a cell-based system can eliminate those PIs that have strong cytotoxic effect. Most importantly, a simple, economical, and easy-to-maintained eukaryotic cellular system such as yeast will allow us to search for potential PIs in a large-scaled high throughput screening (HTS) system, thus increasing the chance of success. Based on our many years of experience in using fission yeast as a model system to study HIV-1 Vpr, we propose the use of fission yeast as a possible surrogate system to study the effects of HIV-1 protease on cellular functions and to explore its utility as a HTS system to search for new PIs to battle HIV-1 strains resistant to the current PI drugs.
Cell and Bioscience 09/2012; 2(1):32. DOI:10.1186/2045-3701-2-32 · 3.63 Impact Factor
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