New Dual Inhibitors of Tyrosyl-DNA Phosphodiesterase 1 and 2 Based on Deoxycholic Acid: Design, Synthesis, Cytotoxicity, and Molecular Modeling

Deoxycholic acid derivatives containing various heterocyclic functional groups at C-3 on the steroid scaffold were designed and synthesized as promising dual tyrosyl-DNA phosphodiesterase 1 and 2 (TDP1 and TDP2) inhibitors, which are potential targets to potentiate topoisomerase poison antitumor therapy. The methyl esters of DCA derivatives with benzothiazole or benzimidazole moieties at C-3 demonstrated promising inhibitory activity in vitro against TDP1 with IC50 values in the submicromolar range. Furthermore, methyl esters 4d-e, as well as their acid counterparts 3d-e, inhibited the phosphodiesterase activity of both TDP1 and TDP2. The combinations of compounds 3d-e and 4d-e with low-toxic concentrations of antitumor drugs topotecan and etoposide showed significantly greater cytotoxicity than the compounds alone. The docking of the derivatives into the binding sites of TDP1 and TDP2 predicted plausible binding modes of the DCA derivatives.

Synthesis and In Vitro Study of Antiviral Activity of Glycyrrhizin Nicotinate Derivatives against HIV-1 Pseudoviruses and SARS-CoV-2 Viruses

When developing drugs against SARS-CoV-2, it is important to consider the characteristics of patients with different co-morbidities. People infected with HIV-1 are a particularly vulnerable group, as they may be at a higher risk than the general population of contracting COVID-19 with clinical complications. For such patients, drugs with a broad spectrum of antiviral activity are of paramount importance. Glycyrrhizinic acid (Glyc) and its derivatives are promising biologically active compounds for the development of such broad-spectrum antiviral agents. In this work, derivatives of Glyc obtained by acylation with nicotinic acid were investigated. The resulting preparation, Glycyvir, is a multi-component mixture containing mainly mono-, di-, tri- and tetranicotinates. The composition of Glycyvir was characterized by HPLC-MS/MS and its toxicity assessed in cell culture. Antiviral activity against three strains of SARS-CoV-2 was tested in vitro on Vero E6 cells by MTT assay. Glycyvir was shown to inhibit SARS-CoV-2 replication in vitro (IC502-8 μM) with an antiviral activity comparable to the control drug Remdesivir. In addition, Glycyvir exhibited marked inhibitory activity against HIV pseudoviruses of subtypes B, A6 and the recombinant form CRF63_02A (IC50 range 3.9-27.5 µM). The time-dependence of Glycyvir inhibitory activity on HIV pseudovirus infection of TZM-bl cells suggested that the compound interfered with virus entry into the target cell. Glycyvir is a promising candidate as an agent with low toxicity and a broad spectrum of antiviral action.

New Deoxycholic Acid Derived Tyrosyl-DNA Phosphodiesterase 1 Inhibitors Also Inhibit Tyrosyl-DNA Phosphodiesterase 2

A series of deoxycholic acid (DCA) amides containing benzyl ether groups on the steroid core were tested against the tyrosyl-DNA phosphodiesterase 1 (TDP1) and 2 (TDP2) enzymes. In addition, 1,2,4- and 1,3,4-oxadiazole derivatives were synthesized to study the linker influence between a para-bromophenyl moiety and the steroid scaffold. The DCA derivatives demonstrated promising inhibitory activity against TDP1 with IC₅₀ in the submicromolar range. Furthermore, the amides and the 1,3,4-oxadiazole derivatives inhibited the TDP2 enzyme but at substantially higher concentration. Tryptamide 5 and para-bromoanilide 8 derivatives containing benzyloxy substituent at the C-3 position and non-substituted hydroxy group at C-12 on the DCA scaffold inhibited both TDP1 and TDP2 as well as enhanced the cytotoxicity of topotecan in non-toxic concentration in vitro. According to molecular modeling, ligand 5 is anchored into the catalytic pocket of TDP1 by one hydrogen bond to the backbone of Gly458 as well as by π–π stacking between the indolyl rings of the ligand and Tyr590, resulting in excellent activity. It can therefore be concluded that these derivatives contribute to the development of specific TDP1 and TDP2 inhibitors for adjuvant therapy against cancer in combination with topoisomerase poisons.

Deoxycholic acid as a molecular scaffold for tyrosyl-DNA phosphodiesterase 1 inhibition: A synthesis, structure-activity relationship and molecular modeling study

Para-Bromoanilides of deoxycholic acid with various functional groups on the steroid scaffold were designed as promising tyrosyl-DNA phosphodiesterase 1 (Tdp1) inhibitors. Tdp1 is a DNA repair enzyme, involved in removing DNA damage caused by topoisomerase I poisons; an important class of anticancer drugs. Thus, reducing the activity of Tdp1 can increase the efficacy of anticancer drugs in current use. Inhibitory activity in the low micromolar and submicromolar concentrations was observed with 3,12-dimethoxy para-bromoanilide 17 being the most active with an IC₅₀ value of 0.27 μM. The activity of N-methyl para-bromoanilides was 3-4.8 times lower than of the corresponding para-bromoanilides. Increased potency of the ligands was seen with higher molecular weight and log P values. The ligands were evaluated for their cytotoxic potential in a panel of tumor cell lines; all were nontoxic to the A549 pulmonary adenocarcinoma cell line. However, derivatives containing a hydroxyl group at the 12th position were more toxic than their 12-hydroxyl group counterparts (acetoxy-, oxo- and methoxy- group) against HCT-116 human colon and HepG2 hepatocellular carcinomas. In addition, an N-methyl substitution led to an increase in toxicity for the HCT-116 and HepG2 cell lines. The excellent activity as well as low cytotoxicity, derivative 17 can be considered as a lead compound for further development.

New type of anti-influenza agents based on benzo[d][1,3]dithiol core

We synthesized a series of amides with a benzo[d][1,3]dithiol core. The chemical library of compounds was tested for their cytotoxicity and inhibiting activity against influenza virus A/California/07/09 (H1N1)pdm09 in MDCK cells. For each compound, values of CC₅₀, IC₅₀ and selectivity index (SI) were determined. Compounds of this structure type were for the first time found to exhibit anti-influenza activity. The structure of an amide substituent in the tested compounds was demonstrated to have a significant effect on their activity against the H1N1 influenza virus and cytotoxicity. Compound 4d has a high selectivity index of about 30. 4d was shown to be most potent at early stages of viral cycle. In direct fusogenic assay it demonstrated dose-dependent activity against fusogenic activity of hemagglutinin of influenza virus. Based on molecular docking and regression analysis data, viral hemagglutinin was suggested as possible target for these new antiviral agents.

Novel 3'-Substituted-1',2',4'-Oxadiazole Derivatives of 18βH-Glycyrrhetinic Acid and Their O-Acylated Amidoximes: Synthesis and Evaluation of Antitumor and Anti-Inflammatory Potential In Vitro and In Vivo

A series of novel 18βH-glycyrrhetinic acid (GA) derivatives containing 3'-(alkyl/phenyl/pyridin(-2″, -3″, and -4″)-yl)-1',2',4'-oxadiazole moieties at the C-30 position were synthesized by condensation of triterpenoid's carboxyl group with corresponding amidoximes and further cyclization. Screening of the cytotoxicity of novel GA derivatives on a panel of tumor cell lines showed that the 3-acetoxy triterpenoid intermediates-O-acylated amidoxime 3a-h-display better solubility under bioassay conditions and more pronounced cytotoxicity compared to their 1',2',4'-oxadiazole analogs 4f-h (median IC50 = 7.0 and 49.7 µM, respectively). Subsequent replacement of the 3-acetoxy group by the hydroxyl group of pyridin(-2″, 3″, and -4″)-yl-1',2',4'-oxadiazole-bearing GA derivatives produced compounds 5f-h, showing the most pronounced selective toxicity toward tumor cells (median selectivity index (SI) > 12.1). Further detailed analysis of the antitumor activity of hit derivative 5f revealed its marked proapoptotic activity and inhibitory effects on clonogenicity and motility of HeLa cervical carcinoma cells in vitro, and the metastatic growth of B16 melanoma in vivo. Additionally, the comprehensive in silico study revealed intermediate 3d, bearing the tert-butyl moiety in O-acylated amidoxime, as a potent anti-inflammatory candidate, which was able to effectively inhibit inflammatory response induced by IFNγ in macrophages in vitro and carrageenan in murine models in vivo, probably by primary interactions with active sites of MMP9, neutrophil elastase, and thrombin. Taken together, our findings provide a basis for a better understanding of the structure-activity relationship of 1',2',4'-oxadiazole-containing triterpenoids and reveal two hit molecules with pronounced antitumor (5f) and anti-inflammatory (3d) activities.

Novel Semisynthetic Derivatives of Bile Acids as Effective Tyrosyl-DNA Phosphodiesterase 1 Inhibitors

An Important task in the treatment of oncological and neurodegenerative diseases is the search for new inhibitors of DNA repair system enzymes. Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is one of the DNA repair system enzymes involved in the removal of DNA damages caused by topoisomerase I inhibitors. Thus, reducing the activity of Tdp1 can increase the effectiveness of currently used anticancer drugs. We describe here a new class of semisynthetic small molecule Tdp1 inhibitors based on the bile acid scaffold that were originally identified by virtual screening. The influence of functional groups of bile acids (hydroxy and acetoxy groups in the steroid framework and amide fragment in the side chain) on inhibitory activity was investigated. In vitro studies demonstrate the ability of the semisynthetic derivatives to effectively inhibit Tdp1 with IC₅₀ up to 0.29 µM. Furthermore, an excellent fit is realized for the ligands when docked into the active site of the Tdp1 enzyme.

Cardioprotective effect of resveratrol and resveratroloside

Cardioprotective effect of resveratrol and resveratroloside was determined in ischemia-reperfusion experiments on rats. It was found that single intraperitoneal administration of any compound (10 mg/kg) followed by 30-min ischemia and 120-min reperfusion resulted in statistically significant decrease of myocardial infarct area (55.0±4.0% for control group; 40.7±4.4% for the group 1 received resveratrol; 41.6±4.8% for the group 2 received resveratroloside). The cardioprotective effect of resveratroloside was detected for the first time.

Anti-viral activity of (-)- and (+)-usnic acids and their derivatives against influenza virus A(H1N1)2009

Influenza is a widespread respiratory infection. Every year it causes epidemics, quickly spreading from country to country, or even pandemics, involving a significant part of the human population of the earth. Being a highly variable infection, influenza easy accumulates the resistance mutations to many antivirals. Usnic acid, a dibenzofuran originally isolated from lichens belongs to the secondary metabolites and has a broad spectrum of biological activity. In humans, it can act as an anti-inflammatory, antimitotic, antineoplasic, antibacterial, and antimycotic agent. In this work we studied for the first time the antiviral activity of usnic acid and its derivatives against the pandemic influenza virus A(H1N1)pdm09. A total of 26 compounds representing (+) and (-) isomers of usnic acid and their derivates were tested for cytotoxicity and anti-viral activity in MDCK cells by microtetrazolium test and virus yield assay, respectively. Based on the results obtained, 50% cytotoxic dose (CTD(50)) and 50% effective dose (ED(50)) and selectivity index (SI) were calculated for each compound. Eleven of them were found to have SI higher than 10 (highest value 37.3). Absolute configuration was shown to have critical significance for the anti-viral activity. With minor exceptions, in the pair of enantiomers, (-)-usnic acid was more active comparing to (+)-isomer, but its biological activity was reversed after the usnic acid was chemically modified. Based on the obtained results, derivatives of usnic acid should be considered as prospective compounds for further optimization as anti-influenza substances.

Cholesterol-induced stimulation of postinflammatory liver fibrosis

We studied the effect of high-cholesterol diet and factors inhibiting 3-hydroxy-3-methylglutaryl coenzyme A reductase on the development of liver fibrosis in C57Bl/6 mice with CCl4- or zymosan-induced hepatitis. Feeding a high-cholesterol diet led to a sharp increase in collagen content in the liver tissue of animals with CCl4-induced or zymosan-induced hepatitis. Atorvastatin and calcitriol produced less pronounced fibrogenic effects. Mevalonate partially prevented the development of cholesterol-induced fibrogenesis. High-cholesterol diet led to accumulation of oxysterols, cholesterol esters, and triglycerides and increased the expression of transforming growth factor-beta1 mRNA in liver tissue. Cholesterol-induced potentiation of the fibrogenic response is probably associated with transforming growth factor-beta1 induction due to accumulation of lipids and oxysterols in the liver.

Long-lived reactive intermediate photogenerated from N-(5-azido-2-nitrobenzoyl)-N'-(D-biotinyl)-1,2-diaminoethane as an affinity reagent to streptavidin

Irradiation of a complex between N-(5-azido-2-nitrobenzoyl)-N'-(D-biotinyl)-1,2-diaminoethane (I) and streptavidin with light of 313 nm led to the covalent attachment of the photobiotin analogue I to the protein. Streptavidin could also be labelled in the dark with prephotolyzed I. These results indicate that a long-lived reactive intermediate was formed upon irradiation. Moreover, after cleavage of labelled streptavidin with proteinase K this intermediate appears to be covalently attached to the same peptide as the one obtained by direct photoaffinity labelling. An iminosulfurane II derived from the reaction of biotin sulfur atom with aryl nitrene is responsible for the dark-labelling reaction. The photoproduct II converts in an aqueous solution almost completely into N-(5-amino-2-nitrobenzoyl)-N'-(D-(S-oxo)biotinyl)-1,2-diaminoethane (the half-life of II is 10 days).

PAcM-AN: poly (N-acryloylmorpholine)-conjugated antisense oligonucleotides

A new amphiphilic, high-molecular weight poly (N-acryloylmorpholine) (PAcM) polymer has been used to be linked to oligonucleotide chains through a liquid-phase stepwise synthesis. This new conjugate has been investigated for its melting property, nuclease stability and capacity to elicit RNase H activity. Its antisense activity against an HIV-1 target has been also evaluated.

Solid-phase synthesis of oligoribonucleotides using T4 RNA ligase and T4 polynucleotide kinase

The concept of solid-phase synthesis of oligoribonucleotides using T4 RNA ligase and T4 polynucleotide kinase has been proposed and tested with model homo-oligoribonucleotides. The method consists of the immobilization of the first oligomer block at the 3'-terminus on a solid support followed by a chain elongation in the 5'-direction with trinucleoside diphosphates using T4 RNA-ligase and phosphorylation using polynucleotide kinase. Hydrazides of Biogel P-300, Sepharose 4B and cellulose were tested as solid supports for immobilization of initial oligomers. The properties of supports were rated on reactivities of immobilized 5'-phosphorylated oligomers as phosphate donors in the solid phase reactions, hydrodynamical properties and capacity to eliminate donor molecules spontaneously during reactions. Hydrazide of Sepharose 4B appeared to be a more suitable support because of better hydrodynamic properties and highest reactivities of immobilized donors. Saturated concentrations of RNA ligase and polynucleotide kinase and optimal time of joining reaction were determined. In a model experiment ApApA was twice attached to the immobilized hydrazide of Sepharose 4B donor (pA)6pAox. The yield of (Ap)12 was 25%.

[Porphyrin derivatives of oligonucleotides. I. Synthesis of oligonucleotide derivatives bearing 2,4-di(alpha-(2-hydroxyethoxy)ethyl)- deuteroporphyrin IX or a metal complex of it and study of the oxidative modification of DNA by these derivatives]

A method for coupling 2,4-di[alpha-(2-hydroxyethoxy)ethyl] deuteroporphyrin dimethyl ether (IX), DDPOH and its complexes with metals to the 5'- or 3'-end of oligonucleotides was elaborated. In the presence of an oxidizing agent (H2O2), Fe(III)DDP-derivatives of oligonucleotides modified single-stranded DNA. The reaction was strictly site-specific and occurred at two neighbouring guanosine residues. A few types of modification were observed: cross-linking, modification leading to DNA cleavage upon piperidine treatment, and direct chain scission. The total modification yield reached 90%. Covalent attachment of Fe(III)DDP-group to oligonucleotides increased the efficiency of their uptake and the melting temperature of their complementary complexes.

[Interaction of Escherichia coli RNA polymerase with oligoribonucleotides, homologous to "10"- and "35"- segments of the SPC promotor of bacterial genes]

It was shown previously that E. coli RNA polymerase in a highly selective manner recognizes and binds 11-14-mere oligodeoxyribonucleotides related to the "-10" region of the nontranscribed DNA strand of bacterial gene promoters. The oligodeoxyribonucleotides cover the Pribnow box with flanking nucleotides up to the transcription start. These affinity oligodeoxyribonucleotides inhibit competitively the transcription of bacterial DNA carried out by E. coli RNA polymerase. The present work has demonstrated that E. coli RNA polymerase is not capable of binding the oligoribonucleotides homologous to the affinity oligodeoxyribonucleotides related to the "-10" area of the spc promoter, but binds the oligoribonucleotides which are complementary to the latter. The oligoribonucleotides with a high affinity for the E. coli RNA polymerase strongly inhibit transcription of the bacterial DNA. Attachment of alkylating groups to the 5'-ends of the affinity oligodeoxy- and oligoribonucleotides provides their covalent binding to the E. coli RNA polymerase subunits. It was shown that the modified affinity 32P-labelled oligodeoxyribonucleotide is covalently bound to the sigma-subunit while the modified affinity 32P-labelled oligoribonucleotide is covalently bound to the beta'beta-subunits of the E. coli RNA polymerase. It is suggested that the affinity oligoribonucleotides can be transcribed from the non-transcribed DNA strand in the region of the open complex and functions presumably as a primer which is splitted later from the nascent RNA or as a regulator of transcription.

[Effective complementarily-addressed photomodification of nucleic acids by oligonucleotide derivatives, containing aromatic azido groups]

Highly effective site-specific photomodification of a DNA-target was carried out with oligonucleotide reagents carrying aromatic azido groups. Oligonucleotide derivatives with a photoactive function R on the 5'-terminal phosphate and at C-5 atom of deoxyuridine were synthesized: R1NH(CH2)3NHpd(TCCACTT) and d(ULNHRCCACTT), where R1 is p-azidotetrafluorobenzoyl, R2 is 2-nitro, 5-azidobenzoyl, R3 is p-azidobenzoyl; LNH = -CH2NH-, -CH2OCH2CH2NH- or -CH2NHCOCH2CH2NH-. The prepared compounds form stable complementary complexes and effect site-specific photomodification of the target DNA. The modification of pentadecanucleotide d(TAAGTGGAGTTTGGC) with the reagents was investigated. Maximum extent of modification strongly depended on the reagent's type, the photoreagent with R1 being the most effective. Whatever the binding site was, this agent provided a 65-70% modification in all cases except LNH = -CH2NH-, when the yield was twice lower. For the reagents bearing R1 the modification sites were identified. Selective modification at the G9 residue was detected in the case of LNH = -CH2OCH2CH2NH- and when a photoactive group was linked to the terminal phosphate.

[Diastereomers of nonionic oligonucleotide analogs. VI. Isolation of diastereomers of ethyl phosphotriesters of the octanucleotide d(GCCAAACA) by high performance affinity chromatography]

Diastereomers of oligonucleotide ethyl phosphotriesters were separated by high-performance complementary (affinity) chromatography on a column with the immobilized complementary oligonucleotide. The elution buffer contained 0.18 M K2HPO4, pH 7.5, and 30% acetonitrile. The temperature of the separation was a few degrees lower than Tm of corresponding oligonucleotide complexes. The diastereomers separated completely or partially were: d[GCC(Et)AAACA], d[GCCA(Et)AACA], d[GCAA(Et)ACA], d[GCC(Et)A(Et)AACA], d[GCC(Et)AA(Et)ACA], d[GCCA(Et)A(Et)ACA], d[GCC(Et)A(Et)A(Et)ACA].

[The determination of ampicillin in the blood and urine of patients by microcolumn high-performance liquid chromatography]

The method of the quantitative determination of ampicillin in the blood serum and urine on the Soviet-made chromatograph "Milichrom" with an ultraviolet detector and 2 x 62 cm column is described. The conditions of chromatography were as follows: wavelength-210 nm; elution rate-100 microliters/min; analysis time-12 min. The conditions of chromatographic analysis were selected on sorbents Lichrosorb RP-18, Nucleosil S-18 and Silosorb S-18. The given method of ampicillin determination--is characterized by a high specificity, accuracy, the use of small volumes of the blood taken from a finger, the rapidity of making analyses and may be recommended for introduction in the clinical practice for optimization of treating patients with ampicillin.

[Chloroquine metabolism in the mono-oxygenase system of mouse liver microsomes]

Metabolism of chloroquine in microsomes of mice liver tissue was studied in vitro by means of thin-layer and microcolumn liquid chromatographies. Chloroquine was metabolized in the system with liver microsomal monooxygenases. The products of its oxidation, involving side chain and aminoquinoline nucleus, were studied. As the enzymatic system is principally similar in various species, analogous metabolites of chloroquine appear to be produced after oxidation of the substance in the plasmodium microsomal monooxygenase system. Thus, this metabolic pathway is responsible for chloroquine resistance of the malarial parasite.

Oligonucleotides complementary to a promoter over the region -8...+2 as transcription primers for E. coli RNA polymerase

Primer-dependent transcription by E. coli RNA polymerase on T7 promoter A2 has been studied. Synthetic deoxyribonucleotides complementary to the promoter over the region -8...+2 were taken as primers. A ribonucleoside residue was present at the 3'-end of some of these oligonucleotides. The octanucleotide complementary to the region -8...-1 appeared to be an active primer. Oligonucleotides having lengths from 3 to 6 nucleotide residues complementary to the promoter over the region -4...+2 also exhibited primer activity. The latter was some 5-10 times greater in the case of oligonucleotides having a ribonucleoside residue at the 3'-end. Oligonucleotides which on complementary binding do not reach the center of phosphodiester bond synthesis, as well as the decanucleotides (-8...+2) and octanucleotides (-6...+2) of both the ribo- and deoxyribo-series were inactive as primers.

[Glycogen content in the DNA-synthesizing and nonsynthesizing hepatocytes of rats of different ages]

The glycogen content in DNA synthesizing and non-synthesizing hepatocytes has been conducted cytochemically during the rat postnatal development. Within all the periods of investigation, the average glycogen content in DNA synthesizing hepatocytes (phase S) are shown to be lower than that in hepatocytes being in phases G0 and G1. The absolute value of reduction of the glycogen content with diploid mononucleate hepatocytes in S-phase is almost the same for rats of all the age groups examined. The absolute value of reduction of the glycogen content in diploid binucleate hapatocytes in S-phase is twice as much as that in diploid mononucleate hepatocytes being at the same stage of the cell cycle. Regardless of the postnatal development stage and of the total glycogen content in the liver, the glycogen content in DNA non-synthesizing hepatocytes of different ploidy is in conformity with the genome number.

[Glycogen concentration in DNA-synthesizing and non-DNA-synthesizing hepatocytes of week-old rats]

Using the combined cytochemistry, that allows to determine glycogen and DNA contents, and to localize 3H-thymidine label in one and the same cell, glycogen content was measured in both 3H-TdR-marked and 3H-TdR-non-marked hepatocytes of week-old rats. The vast majority of hepatocytes in a liver population of such rats are mononuclear 3H-TdR-non-marked cells with a 2C DNA content, which corresponds to the diploid chromosome set. The ratio of binuclear hepatocytes with diploid nuclei is in average 0.6%. At one injection of 3H-TdR, 6.6% of hepatocytes are marked in average which are almost exclusively mononuclear cells with 2c to 4c DNA content. In binuclear hepatocytes with two diploid nuclei (2c X 2), the label was seen only in single instances. The average glycogen content in S-phase hepatocytes is aproximately one third of that in hepatocytes that did not start DNA synthesis (G1 and G2 phases). The glycogen content in hepatocytes is seen reducing during S-phase. The glycogen content in G2-phase hepatocytes does not differ from that of hepatocytes before they start DNA synthesis. The availability of glycogen is not necessary for the beginning of S-phase: DNA synthesis in hepatocytes of week-old rats can start and proceed irrespective of the presence of glycogen in these. The glycogen content in binuclear hepatocytes with diploid nuclei that did not start DNA-synthesis is twice as much as in mononuclear hepatocytes before they started DNA synthesis.