Wojciech Ardelt

Crystal and molecular structures of the complex of α-chymotrypsin with its inhibitor Turkey ovomucoid third domain at 1.8 Å resolution

The molecular structure of the complex between bovine pancreatic α-chymotrypsin (EC 3.4.4.5) and the third domain of the Kazal-type ovomucoid from Turkey (OMTKY3) has been determined crystallographically by the molecular replacement method. Restrained-parameter least-squares refinement of the molecular model of the complex has led to a conventional agreement factor R of 0.168 for the 19,466 reflections in the 1.8 A (1 A = 0.1 nm) resolution shell [I ≥ σ(I)]. The reactive site loop of OMTKY3, from Lys131 to Arg211 (I indicates inhibitor), is highly complementary to the surface of α-chymotrypsin in the complex. A total of 13 residues on the inhibitor make 113 contacts of less than 4.0 A with 21 residues of the enzyme. A short contact (2.95 A) from Oγ of Ser195 to the carbonylcarbon atom of the scissile bond between Leu181 and Glu191 is present; in spite of it, this peptide remains planar and undistorted. Analysis of the interactions of the inhibitor with chymotrypsin explains the enhanced specificity that chymotrypsin has for P′3 arginine residues. There is a water-mediated ion pair between the guanidinium group on this residue and the carboxylate of Asp64. Comparison of the structure of the α-chymotrypsin portion of this complex with the several structures of α and γ-chymotrypsin in the uncomplexed form shows a high degree of structural equivalence (root-mean-square deviation of the 234 common α-carbon atoms averages 0.38 A). Significant differences occur mainly in two regions Lys36 to Phe39 and Ser75 to Lys79. Among the 21 residues that are in contact with the ovomucoid domain, only Phe39 and Tyr146 change their conformations significantly as a result of forming the complex. Comparison of the structure of the OMTKY3 domain in this complex to that of the same inhibitor bound to a serine proteinase from Streptomyces griseus (SGPB) shows a central core of 44 amino acids (the central α-helix and flanking small 3-stranded β-sheet) that have α-carbon atoms fitting to within 1.0 A (root-mean-square deviation of 0.45 A) whereas the residues of the reactive-site loop differ in position by up to 1.9 A (Cα of Leu181). The ovomucoid domain has a built-in conformational flexibility that allows it to adapt to the active sites of different enzymes. A comparison of the SGPB and α-chymotrypsin molecules is made and the water molecules bound at the inhibitor-enzyme interface in both complexes are analysed for similarities and differences.

Inhibition of HIV-1 Production and Selective Degradation of Viral RNA by an Amphibian Ribonuclease

Ribonucleases appear to have physiologic roles in host defense against cancer, viruses, and other parasites. Previously it was shown that select ribonucleases added to cells concurrently with virions blocked human immunodeficiency virus, type I (HIV-1) infection of H9 cells. We now report that a ribonuclease homologous to RNase A, named onconase, inhibits virus replication in chronically HIV-1-infected human cells without killing the virally infected cell. Examining the mechanism of this inhibition shows that onconase enters the infected cells and degrades HIV-1 RNA without degrading ribosomal RNA or the three different cellular messenger RNAs analyzed. The homologous human pancreatic RNase lacks anti-viral activity. Comparing recombinant forms of onconase and a onconase-human RNase chimera shows that the N-terminal 9 amino acids and the pyroglutamyl residue of onconase are required for full anti-viral activity. Thus extracellular ribonucleases can enter cells, metabolize select RNAs, and inhibit HIV virion production within viable replicating cells.

Effect of single amino acid replacements on the thermodynamics of the reactive site peptide bond hydrolysis in ovomucoid third domain

We have measured equilibrium constants, Khyd, at pN 6 for the hydrolysis of the reactive site peptide bond (bond between residues 18 and 19) in 42 sequenced variants (39 natural, 3 semisynthetic) of avian ovomucoid third domains. The values range from 0.4 to approximately 35. In 35 cases the effect of a single amino acid replacement on Khyd could be calculated, 13 are without effect and 22 range from a factor of 1.25 to 5.5. Several, but not all, of the effects can be rationalized in terms of residue-residue interactions that are affected by the reactive site hydrolysis. As the measurements are very precise it appears that additional measurements on designed rather than natural variants should allow for the precise measurement of side-chain--side-chain interaction energies.

Cytotoxic Ribonucleases and RNA Interference (RNAi)

Several cytotoxic ribonucleases (CRs), homologs of the pancreatic RNase A, have been isolated from amphibian oocytes or embryos. Of them, onconase (Onc), the CR that shows antitumor properties and is in phase III clinical trials, was the most extensively researched. Degradation of tRNA by Onc internalized into cells that leads to inhibition of protein synthesis is considered the mechanism of its cytotoxicity. Several findings, however, cannot not be explained by nonspecific decline in protein synthesis alone and suggest additional or alternative mechanism(s). We postulate therefore that miRNAs and/or RNA interference (RNAi) may also be targets of CRs. The following arguments support this postulate: (A) miRNAs and siRNAs appear to be unprotected by proteins and therefore, as tRNA, accessible and degradable by CRs; (B) Onc has preferred cleavage sites on tRNAs: their cleavage may generate segments of dsRNA that interfere with translation. Analogous to Dicer, thus, small RNAs with interfering properties may be generated by CRs within the cell; (c) CRs are abundant in oocytes and during embryonic development; their role there is unknown. Since cells undergo perpetual differentiation during embryogenesis it is likely that the function of CRs is to provide additional level of regulation of gene expression via the mechanisms listed in (A) and/or (B).

The cytotoxic ribonuclease onconase targets RNA interference (siRNA).

Onconase (Onc), a ribonuclease from oocytes of Northern Leopard frogs (Rana pipiens) is cytostatic and cytotoxic to a variety of tumor lines in vitro, inhibits growth of tumors in animal in vivo models and enhances sensitivity of tumor cells to a number of other cytotoxic agents with diverse mechanism of action. In Phase III clinical trials Onc demonstrated significant efficacy in patients with malignant mesothelioma that failed prior chemotherapy. We previously postulated that the antitumor activity of Onc and the observed synergisms with other antitumor modalities at least in part may be mediated by targeting RNA interference (RNAi). In the present study we observed that the silencing of the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene in human lung adenocarcinoma A549 cells by siRNA was effectively prevented by Onc. While transfection of cells with GAPDH siRNA reduced expression of this protein by nearly 70%, the expression was restored in the cells exposed to 0.8 µM Onc for 48 or 72 h. The data thus provide evidence that one of the targets of Onc is siRNA, likely within the RNA-induced silencing complex (RISC). In light of the findings that microRNAs are involved in tumor pathogenesis as well as in enhancing cell resistance to anticancer therapy the present data may provide explanation for both, the antitumor Onc activity and its propensity to enhance effectiveness of cytotoxic drugs.

ONCONASE® and Its Therapeutic Potential

Early work by Shogen and Yoon1 demonstrated an anti-tumor activity in extracts of Northern leopard frog (Rana pipiens) embryos. More than a decade later, in 1987, the main active component of those extracts was isolated and purified by Alfacell M. It turned out to be a small (approximately 12 Kd) basic protein of maternal origin (present also in large amounts in unfertilized oocytes). Its complete amino acid sequence was determined in our laboratory and was found to be unique.2 Surprisingly, the sequence was similar to those of pancreatic ribonuclease A (RNase A, EC 3.1.27.5) and other members of the RNase A superfamily. All 3 catalytic residues of RNase A were conserved as were some of the other residues forming the active site and/or the hydrophobic core.2,3 Thus, the protein seemed to be fully equipped to exert ribonucleolytic activity, and indeed was found capable of degrading highly polymerized RNA from yeast and wheat germ, although the reaction rates were distinctly lower that those of other pancreatic-type ribonucleases.2 It was also cytostatic and cytotoxic to several cancer cell lines in vitro including human submaxillary carcinoma A-253,2,4 and significantly increased the survival of mice bearing M109 Madison Carcinoma5. As we discuss later in this article, the protein also posses strong anti viral activity. We provisionally named the molecule P-30 Protein and later changed the name to Onconase (ONC). In addition to ONC, extracts of Rana pipiens oocytes, contain its natural variant, different by 3 amino acid residues6 and at least 4 variants of a novel cytotoxic ribonuclease, amphinase, recently discovered and sequenced in our laboratory.7 In this article, we discuss the structure and function of ONC as well as therapeutic potential of this enzyme with particular emphasis on its anti viral activity.

The interdependence between catalytic activity, conformational stability, and cytotoxicity of onconase.

Onconase (ONC) is a cytotoxic ribonuclease of the pancreatic RNase A superfamily isolated from oocytes or early embryos of the Northern leopard frog (Rana pipiens). It shows anticancer activity and currently is in Phase IIIb clinical trial for unresectable malignant mesothelioma. We generated several variants of ONC possessing mutations in selected structural regions of the molecule that have altered ribonucleolytic activity and/or conformational stability. The relationship between the stability and ribonucleolytic activity of these variants and their cytostatic and cytotoxic properties was investigated on several tumor cell lines. Similar as ONC, all variants were inducing reproductive cell death detected by reduced clonogenicity. The surviving cells proliferated at reduced rates as reflected by diminished size of colonies and prolongation of G0/1 phase of the cell cycle. Some cells were undergoing apoptosis. The cytotoxic and cytostatic effects of ONC and its variants were predominantly determined by their catalytic activity rather than by conformational stability.

Cytostatic and Cytotoxic Properties of Amphinase: A Novel Cytotoxic Ribonuclease from Rana pipiens Oocytes

Onconase (Onc), is a novel amphibian cytotoxic ribonuclease with antitumor activity, and is currently in a confirmatory phase III clinical trial for the treatment of malignant mesothelioma. It was recently reported that Rana pipiens oocytes contain still another ribonuclease, named Amphinase (Amph). Amph shows 38 – 40 % amino acid sequence identity with Onc; presents as four variants varying between themselves from 87 to 99 % in amino acid sequence identity and has a molecular mass ~ 13,000. In the present study we describe the effects of Amph on growth of several tumor cell lines. All four variants demonstrated cytostatic and cytotoxic activity against human promyelocytic HL-60-, Jurkat T-cell- and U-937 monocytic leukemia cells. The pattern of Amph activity to certain extent resembled that of Onc. Thus, cell proliferation was suppressed at 0.5 – 10.0 µg/ml (40 – 80 nM) Amph concentration with distinct accumulation of cells in G1 phase of the cell cycle. In addition, the cells were undergoing apoptosis, which manifested by DNA fragmentation (presence of “sub-G1” cells, TUNEL-positivity), caspases and serine proteases activation as well as activation of transglutaminase. The cytotostatic and cytotoxic effects of Amph required its ribonuclease activity: the enzymatically inactive Amph-2 having histidine at the active site alkylated was ineffective. The effectiveness and cell cycle specificity was generally similar for all four Amph variants and at the equimolar concentrations was somewhat more pronounced than that of Onc. The observed cytostatic and cytotoxic activity of Amph against tumor cell lines suggests that similar to Onc this cytotoxic ribonuclease may have antitumor activity and find an application in clinical oncology.

Analytical ion exchange chromatography of proteins.

A low-pressure system for analytical ion exchange chromatography of proteins is described. Elution of proteins is performed by salt gradient and protein concentration is monitored at 206 nm. Protein mixtures consisting of microgram amounts of each component can be quantitatively resolved in 40 min. Quantitation of results is done by integration of the peak areas using a digital recorder with a data processing system. The method was successfully used for separation of proteins different by 1 unit charge only.

Cytotoxic activity of the amphibian ribonucleases onconase and r-amphinase on tumor cells from B cell lymphoproliferative disorders

Although major advancements in antitumor treatment have been observed, several B cell-derived malignancies still remain incurable. A promising approach that involves targeting RNA either by the use of specific antisense oligonucleotides or cytostatic/cytotoxic ribonucleases (RNases) is being promoted. Two amphibian RNases, onconase (ONC; ranpirnase) and, more recently, r-amphinase (r-Amph), have already been tested, but thus far, mostly on solid tumors. In this study, for the first time we provide comprehensive data on ex vivo and in vivo cytotoxic activity of ONC or r-Amph against cancer cells from different B cell lymphoid malignancies, together with their detailed mode of antitumor action. Our data revealed strong pro-apoptotic activity of ONC and r-Amph in both chronic lymphocytic leukemia and aggressive B cell lymphomas, with less impact on acute lymphoblastic leukemia or multiple myeloma cells. Moreover, the antitumor action of ONC and r-Amph was markedly selective against neoplastic cells sparing normal, healthy control‑derived lymphocytes.