Fractionation of aurintricarboxylic acid and effects of its components on nuclear swelling and nucleic acid synthesis

Characterization of Aurintricarboxylic Acid (ATA) Interactions with Plasma Transporter Protein and SARS-CoV-2 Viral Targets: Correlation of Functional Activity and Binding Energetics

In an effort to identify functional-energetic correlations leading to the development of efficient anti-SARS-CoV-2 therapeutic agents, we have designed synthetic analogs of aurintricarboxylic acid (ATA), a heterogeneous polymeric mixture of structurally related linear homologs known to exhibit a host of biological properties, including antiviral activity. These derivatives are evaluated for their ability to interact with a plasma transporter protein (human serum albumin), eukaryotic (yeast) ribosomes, and a SARS-CoV-2 target, the RNA-dependent RNA polymerase (RdRp). The resultant data are critical for characterizing drug distribution, bioavailability, and effective inhibition of host and viral targets. Promising lead compounds are selected on the basis of their binding energetics which have been characterized and correlated with functional activities as assessed by inhibition of RNA replication and protein synthesis. Our results reveal that the activity of heterogeneous ATA is mimicked by linear compounds of defined molecular weight, with a dichlorohexamer salicylic-acid derivative exhibiting the highest potency. These findings are instrumental for optimizing the design of structurally defined ATA analogs that fulfill the requirements of an antiviral drug with respect to bioavailability, homogeneity, and potency, thereby expanding the arsenal of therapeutic regimens that are currently available to address the urgent need for effective SARS-CoV-2 treatment strategies.

In vitro and in vivo activity of aurintricarboxylic acid preparations against Cryptosporidium parvum

Objectives

The aim of this study was to assess the effect of commercial aurintricarboxylic acid (ATA) against Cryptosporidium parvum.

Methods

The anticryptosporidial effect of ATA was evaluated in vitro using cell culture and double fluorogenic staining, and in vivo in experimentally infected neonatal C57BL/6 mice. Mice were orally treated for 9 consecutive days starting on the day of infection with daily ATA doses of 50 and 100 µmol/kg. Paromomycin (100 mg/kg) was used as a positive control.

Results

In both in vitro models, ATA at concentrations of 100 and 10 µmol/L completely inhibited sporozoites within 10 and 60 min, respectively. Viability of oocysts exposed to 100 µmol/L and assessed by flow cytometry and in cell culture was reduced by 65% and 61%, respectively. The treatment of neonatal mice with a daily ATA dose of 100 µmol/kg led to 97–99% inhibition of infection without any observable negative effects on the animals. In comparison, the mean reduction of infection for paromomycin was 79–84%.

Conclusions

ATA exerted high anticryptosporidial activity and should be considered for further study.

Aurine tricarboxylic acid, a potent metal-chelating inhibitor of NFkappaB-DNA binding

The metal-interaction of aurine tricarboxylic acid (ATA) and its inhibitory effect on the DNA binding of NFkappaB were studied. Chemical speciation and spectroscopic studies have shown the strong interaction of ATA with metal ions present in the biological systems. EPR, FTIR and electronic spectral studies indicated the square planar structure of the metal-binding carboxylic and hydroxyl groups of ATA indicating the ground state 2B1g. Electrophoretic mobility shift assay using NFkappaB and 32P labeled DNA has shown that ATA was inhibitory against the DNA-NFkappaB binding at 30 microM. This activity was the strongest among the metal-chelating inhibitors of NFkappaB-DNA binding reported so far.

A method for isolation of nuclei containing undegraded RNA from RNAase-rich plasmodia of Physarum polycephalum

(1) In order to protect the nuclear RNA of Physarum polycephalum plasmodia during cell homogenisation and purification of the nuclei, the following conditions were used: low temperature (-11 degrees C), high pH (8.1-8.9), formaldehyde (2.8%) and spermine (2.3 mM). (2) The efficiency of these RNAase-inhibiting and inactivating conditions is demonstrated by the high molecular weight of the processing products of transcripts from ribosomal genes (11.9, 9.5 and 5.0 kilobases), which were recovered from the isolated nuclei and visualised on agarose gels. (3) Hybridisation experiments with a DNA probe from an actin gene on size-fractionated nuclear RNA (Northern blots) indicate that the transcripts from actin genes are rapidly spliced in P. polycephalum. (4) The nuclear polyadenylated RNA has an average size of about 2.2 kb, which is not significantly larger than the average length of mRNA.

Mechanism of action of polymeric aurintricarboxylic acid, a potent inhibitor of protein--nucleic acid interactions

The mechanism of inhibition of protein--nucleic acid complex formation by polymeric aurintricarboxylic acid (ATA) was investigated by proton magnetic resonance spectroscopy. The approach was the synthesis of totally deuterated ATA, followed by a 100-MHz proton magnetic resonance study of its interaction with bovine pancreatic ribonuclease A (RNase), a model nucleic acid binding protein. The binding of ATA to RNase elicited chemical shift changes and line broadening in the C(2)--H resonances of histidyl residues 12 and 119, both of which are located in the active site, whereas that of histidyl residue 105, which resides on the exterior of the protein structure, is unaffected. (Histidyl residue 48 is not observed under our conditions except at high pH.) The epsilon-methylene protons of the lysyl side chains were also broadened upon the binding of ATA. Polymeric ATA displaces cytidine 2'-monophosphate and cytidine 3'-monophosphate from the active site of the enzyme as revealed by nuclear magnetic resonance spectroscopy. These observations suggest that the mechanism of action of ATA involves competition between the nucleic acid and the polymeric ATA for binding in the active site of the protein. Electron spin resonance spectroscopy reveals that polymeric ATA is a stable free radical, thus accounting for the major line broadening effect upon binding to protein. This finding may provide a powerful means of probing the nucleic acid binding site of proteins by proton magnetic resonance spectroscopy.

Fractionation and structural elucidation of the active components of aurintricarboxylic acid, a potent inhibitor of protein nucleic acid interactions

Commercially available, as well as synthetically prepared, samples of aurintricarboxylic acid (a widely employed potent inhibitor of protein nucleic acid interactions) consist mostly of a heterogeneous collection of polymers, as shown by fractionation schemes utilizing both dialysis and ultrafiltration, and by molecular weight measurements. 13C-NMR studies suggest that the polymeric material is of the phenol-formaldehyde type; inhibitory assays that depend on the formation of a protein-nucleic acid complex revealed that potency varied directly with the molecular weight of the polymer. Fractions of molecular weight 400 were essentially inactive.