Ben M. Dunn

Effective blocking of HIV-1 proteinase activity by characteristic inhibitors of aspartic proteinases.

Inhibitory constants (K i) between 5 and 35 nM were derived (under different conditions of pH and ionic strength) for the interaction of HIV‐1 proteinase with acetyl‐pepstatin and H‐261, two characteristic inhibitors of aspartic proteinases. Thus this enzyme, essential for replication of the AIDS virus, may be classified unequivocally as belonging to this proteinase family.

Sequence, expression and modeled structure of an aspartic proteinase from the human malaria parasite Plasmodium falciparum

A clone encoding the aspartic proteinase (PFAPD) from Plasmodium falciparum strain HB3 was obtained during the course of a project designed to sequence and identify the protein coding regions of the parasites genome. The protein encoded by the clone contains a sequence identical to the N-terminal sequence determined for an aspartic proteinase isolated from the digestive vacuole of P. falciparum and demonstrated to participate in the hemoglobin digestive pathway (D. Goldberg, personal communication). The translated polypeptide sequence encompasses a number of features characteristic of aspartic proteinases, having > 30% identity and > 50% similarity overall to human cathepsin D, cathepsin E and renin. A model of the three-dimensional structure of PFAPD was constructed using rule-based procedures. This confirms that the primary sequence may be folded as a single chain into a three dimensional structure closely resembling those of other known aspartic proteinases. It includes a lengthy prosegment, two typical-hydrophobic-hydrophobic-Asp-Thr/Ser-Gly motifs and a tyrosine residue positioned in a beta-hairpin loop. The distribution of hydrophobic residues throughout the active site cleft is indicative of a likely preference for hydrophobic polypeptide substrates. The recombinant form of this enzyme expressed using the pGEX2T vector in Escherichia coli is active in digesting hemoglobin at acidic pH and in hydrolyzing a synthetic peptide corresponding to the putative initial cleavage site in hemoglobin. Activity is inhibited completely by pepstatin, confirming the identity of PFAPD as a member of the aspartic proteinase family. Specific mRNA for PFAPD is expressed in the erythrocytic stages of the life cycle.

High level expression and characterisation of Plasmepsin II, an aspartic proteinase from Plasmodium falciparum

DNA encoding the last 48 residues of the propart and the whole mature sequence of Plasmepsin II was inserted into the T7 dependent vector pET 3a for expression in E. coli. The resultant product was insoluble but accumulated at ∼20 mg/l of cell culture. Following solubilisation with urea, the zymogen was refolded and, after purification by ion‐exchange chromatography, was autoactivated to generate mature Plasmepsin II. The ability of this enzyme to hydrolyse several chromogenic peptide substrates was examined; despite an overall identity of ∼35% to human renin, Plasmepsin II was not inhibited significantly by renin inhibitors.

Aspartic Peptidase Inhibitors: Implications in Drug Development

The last decade has witnessed an effervescence of research interest in the development of potent inhibitors of various aspartic peptidases. As an enzyme family, aspartic peptidases are relatively a small group that has received enormous interest because of their significant roles in human diseases like involvement of renin in hypertension, cathepsin D in metastasis of breast cancer, β-Secretase in Alzheimers Disease, plasmepsins in malaria, HIV-1 peptidase in acquired immune deficiency syndrome, and secreted aspartic peptidases in candidal infections. There have been developments on clinically active inhibitors of HIV-1 peptidase, which have been licensed for the treatment of AIDS. The inhibitors of plasmepsins and renin are considered a viable therapeutic strategy for the treatment of malaria and hypertension. Relatively few inhibitors of cathepsin D have been reported, partly because of its uncertain role as a viable target for therapeutic intervention. The β-secretase inhibitors OM99-2 and OM003 were designed based on the substrate specificity information. The present article is a comprehensive state-of-the-art review describing the aspartic peptidase inhibitors illustrating the recent developments in the area. In addition, the homologies between the reported inhibitor sequences have been analyzed. The understanding of the structurefunction relationships of aspartic peptidases and inhibitors will have a direct impact on the design of new inhibitor drugs.

Initial Cleavage of the Human Immunodeficiency Virus Type 1 GagPol Precursor by Its Activated Protease Occurs by an Intramolecular Mechanism

ABSTRACT Processing of the GagPol polyprotein precursor of human immunodeficiency virus type 1 (HIV-1) is a critical step in viral assembly and replication. The HIV-1 protease (PR) is translated as part of GagPol and is both necessary and sufficient for precursor processing. The PR is active only as a dimer; enzyme activation is initiated when the PR domains in two GagPol precursors dimerize. The precise mechanism by which the PR becomes activated and the subsequent initial steps in precursor processing are not well understood. However, it is clear that processing is initiated by the PR domain that is embedded within the precursor itself. We have examined the earliest events in precursor processing using an in vitro assay in which full-length GagPol is cleaved by its embedded PR. We demonstrate that the embedded, immature PR is as much as 10,000-fold less sensitive to inhibition by an active-site PR inhibitor than is the mature, free enzyme. Further, we find that different concentrations of the active-site inhibitor are required to inhibit the processing of different cleavage sites within GagPol. Finally, our results indicate that the first cleavages carried out by the activated PR within GagPol are intramolecular. Overall, our data support a model of virus assembly in which the first cleavages occur in GagPol upstream of the PR. These intramolecular cleavages produce an extended form of PR that completes the final processing steps accompanying the final stages of particle assembly by an intermolecular mechanism.

The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix.

Aspartic proteinase A from yeast is specifically and potently inhibited by a small protein called IA3 from Saccharomyces cerevisiae . Although this inhibitor consists of 68 residues, we show that the inhibitory activity resides within the N-terminal half of the molecule. Structures solved at 2.2 and 1.8 Å, respectively, for complexes of proteinase A with full-length IA3 and with a truncated form consisting only of residues 2–34, reveal an unprecedented mode of inhibitor–enzyme interactions. Neither form of the free inhibitor has detectable intrinsic secondary structure in solution. However, upon contact with the enzyme, residues 2–32 become ordered and adopt a near-perfect α-helical conformation. Thus, the proteinase acts as a folding template, stabilizing the helical conformation in the inhibitor, which results in the potent and specific blockage of the proteolytic activity.

Separation and characterization of four different amino acid sequence variants of a sea anemone (Stichodactyla helianthus) protein cytolysin.

A basic protein cytolysin previously isolated from the Caribbean sea anemone Stichodactyla helianthus was shown by CM cellulose chromatography to consist of four isotoxins possessing different N-terminal amino acid sequences. These are designated as toxins I-IV in order of increasing isoelectric point. The estimated molecular sizes (17,400-18,200) of toxins I-III were very similar; toxins I and II posses one additional amino acid at their amino terminus relative to toxin III. Under denaturing conditions, toxin IV behaved as a significantly larger (19,600) polypeptide; Edman sequencing established that it possesses a seven residue extension at the N-terminal end relative to toxin III. None of the variants contained half-cystines or reducing sugars. Toxin III contributed 83% of the total purified cytolytic (hemolytic) activity, toxin II 14%, and the relatively insoluble toxins I and IV together only contributed about 3% of the total cytolytic activity. Cytolysin III lysed Ehrlich ascitic tumour cells, but when administered intraperitoneally in nonlethal doses to mice already inoculated with this tumour, it failed to protect the mice against the tumour. Comparison of the partial amino acid sequence of equinatoxin, another sea anemone protein cytolysin, with that of Stichodactyla cytolysin III indicates they are highly homologous. Many other cytolytic proteins isolated from sea anemones share these properties with Stichodactyla cytolysins: (1) selective inhibition of hemolytic activity by preincubation with sphingomyelin, (2) a molecular size of 10,000-20,000, and (3) an isoelectric point of 9 or above.

Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes.

The crystal structure of a pepstatin-insensitive carboxyl proteinase from Pseudomonas sp. 101 (PSCP) has been solved by single-wavelength anomalous diffraction using the absorption peak of bromide anions. Structures of the uninhibited enzyme and of complexes with an inhibitor that was either covalently or noncovalently bound were refined at 1.0–1.4 Å resolution. The structure of PSCP comprises a single compact domain with a diameter of ∼55 Å, consisting of a seven-stranded parallel β-sheet flanked on both sides by a number of helices. The fold of PSCP is a superset of the subtilisin fold, and the covalently bound inhibitor is linked to the enzyme through a serine residue. Thus, the structure of PSCP defines a novel family of serine-carboxyl proteinases (defined as MEROPS S53) with a unique catalytic triad consisting of Glu 80, Asp 84 and Ser 287.

Comparing the accumulation of active- and nonactive-site mutations in the HIV-1 protease.

Protease inhibitor resistance still poses one of the greatest challenges in treating HIV. To better design inhibitors able to target resistant proteases, a deeper understanding is needed of the effects of accumulating mutations and the contributions of active- and nonactive-site mutations to the resistance. We have engineered a series of variants containing the nonactive-site mutations M46I and I54V and the active-site mutation I84V. These mutations were added to a protease clone (V6) isolated from a pediatric patient on ritonavir therapy. This variant possessed the ritonavir-resistance-associated mutations in the active-site (V32I and V82A) and nonactive-site mutations (K20R, L33F, M36I, L63P, A71V, and L90M). The I84V mutation had the greatest effect on decreasing catalytic efficiency, 10-fold when compared to the pretherapy clone LAI. The decrease in catalytic efficiency was partially recovered by the addition of mutations M46I and I54V. The M46I and I54V were just as effective at decreasing inhibitor binding as the I84V mutation when compared to V6 and LAI. The V6(54/84) variant showed over 1000-fold decrease in inhibitor-binding strength to ritonavir, indinavir, and nelfinavir when compared to LAI and V6. Crystal-structure analysis of the V6(54/84) variant bound to ritonavir and indinavir shows structural changes in the 80s loops and active site, which lead to an enlarged binding cavity when compared to pretherapy structures in the Protein Data Bank. Structural changes are also seen in the 10s and 30s loops, which suggest possible changes in the dynamics of flap opening and closing.

[14]Subsite preferences of retroviral proteinases

Publisher Summary This chapter describes the methodology that has been deployed in the quest for information to facilitate an understanding of the considerable specificity that is exhibited by proteases from different retroviruses. This is followed by an analysis of data from a number of seminal studies. The examples presented in the chapter illustrates several points in which substitution of amino acid side chains leads to the alteration of efficiency in peptide bond cleavage by retroviral proteases. It also emphasizes on the significant role of hydrogen bonding of backbone atoms of the bound substrate to the correct positioning within the active site. The chapter concludes with a discussion on all substrate and inhibitor molecules that form the maximal number of hydrogen bonds, making compromises with the positions of the side chains of the ligand to achieve this.