N. S. Dyrkheeva

Multifunctional human apurinic/apyrimidinic endonuclease 1: Role of additional functions

Human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is a multifunctional enzyme involved in base excision repair (BER). APE1 cleaves DNA 5′ of an AP site to produce a single-strand break with 5′-OH and 3′-deoxyribose phosphate. In addition to its AP-endonucleolytic function, APE1 possesses 3′-phosphodiesterase, 3′–5′ exonuclease, and 3′-phosphatase activities. Independently of its function as a repair protein, APE1 was identified as a redox factor (Ref-1). The review summarizes the published and original data on the role of the additional functions of APE1 in DNA repair and apoptosis and regulation of the BER system via APE1 interaction with DNA and other repair proteins.

AP endonuclease 1 as a key enzyme in repair of apurinic/apyrimidinic sites

Human apurinic/apyrimidinic endonuclease 1 (APE1) is one of the key participants in the DNA base excision repair system. APE1 hydrolyzes DNA adjacent to the 5′-end of an apurinic/apyrimidinic (AP) site to produce a nick with a 3′-hydroxyl group and a 5′-deoxyribose phosphate moiety. APE1 exhibits 3′-phosphodiesterase, 3′-5′-exonuclease, and 3-phosphatase activities. APE1 was also identified as a redox factor (Ref-1). In this review, data on the role of APE1 in the DNA repair process and in other metabolic processes occurring in cells are analyzed as well as the interaction of this enzyme with DNA and other proteins participating in the repair system.

Usnic acid derivatives are effective inhibitors of tyrosyl-DNA phosphodiesterase 1

The synthesis of (+)-usnic acid derivatives is described. The derivatives contain one or two cyano groups, connected to the acetophenone fragment of dibenzofuran core by linkers of different length and character, or some other modifications. The influence of these compounds on the activity of recombinant human tyrosyl-DNA phosphodiesterase 1 and MCF-7 tumor cells’ viability has been estimated. The data indicate a distinct dependence of functional characteristics of the compounds on their structure.

Interaction of APE1 and other repair proteins with DNA duplexes imitating intermediates of DNA repair and replication

Interactions of APE1 (human apurinic/apyrimidinic endonuclease 1) and DNA polymerase β with various DNA structures imitating intermediates of DNA repair and replication were investigated by gel retardation and photoaffinity labeling. Photoaffinity labeling of APE1 and DNA polymerase β was accomplished by DNA containing photoreactive group at the 3′-end in mouse embryonic fibroblast (MEF) cell extract or for purified proteins. On the whole, modification efficiency was the same for MEF-extract proteins and for purified APE1 and DNA polymerase β depending on the nature of the 5′-group of a nick/gap in the DNA substrate. Some of DNA duplexes used in this work can be considered as short-patch (DNA with the 5′-phosphate group in the nick/gap) or long-patch (DNA containing 5′-sugar phosphate or 5′-flap) base excision repair (BER) intermediates. Other DNA duplexes (3′-recessed DNA and DNA with the 5′-hydroxyl group in the nick/gap) have no relation to intermediates forming in the course of BER. As shown by both methods, APE1 binds with the highest efficiency to DNA substrate containing 5′-sugar phosphate group in the nick/gap, whereas DNA polymerase β binds to DNA duplex with a mononucleotide gap flanked by the 5′-p group. When APE1 and DNA polymerase β are both present, a ternary complex APE1-DNA polymerase β-DNA is formed with the highest efficiency with DNA product of APE1 endonuclease activity and with DNA containing 5′-flap or mononucleotide-gapped DNA with 5′-p group. It was found that APE1 stimulates DNA synthesis catalyzed by DNA polymerase β, and a human X-ray repair cross-complementing group 1 protein (XRCC1) stimulates APE1 3′–5′ exonuclease activity on 3′-recessed DNA duplex.

Pre-steady state kinetics of DNA binding and abasic site hydrolysis by tyrosyl-DNA phosphodiesterase 1

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) processes DNA 3′-end-blocking modifications, possesses DNA and RNA 3′-nucleosidase activity and is also able to hydrolyze an internal apurinic/apyrimidinic (AP) site and its synthetic analogs. The mechanism of Tdp1 interaction with DNA was analyzed using pre-steady state stopped-flow kinetics with tryptophan, 2-aminopurine and Förster resonance energy transfer fluorescence detection. Phosphorothioate or tetramethyl phosphoryl guanidine groups at the 3′-end of DNA have been used to prevent 3′-nucleosidase digestion by Tdp1. DNA binding and catalytic properties of Tdp1 and its mutants H493R (Tdp1 mutant SCAN1) and H263A have been compared. The data indicate that the initial step of Tdp1 interaction with DNA includes binding of Tdp1 to the DNA ends followed by the 3′-nucleosidase reaction. In the case of DNA containing AP site, three steps of fluorescence variation were detected that characterize (i) initial binding the enzyme to the termini of DNA, (ii) the conformational transitions of Tdp1 and (iii) search for and recognition of the AP-site in DNA, which leads to the formation of the catalytically active complex and to the AP-site cleavage reaction. Analysis of Tdp1 interaction with single- and double-stranded DNA substrates shows that the rates of the 3′-nucleosidase and AP-site cleavage reactions have similar values in the case of single-stranded DNA, whereas in double-stranded DNA, the cleavage of the AP-site proceeds two times faster than 3′-nucleosidase digestion. Therefore, the data show that the AP-site cleavage reaction is an essential function of Tdp1 which may comprise an independent of AP endonuclease 1 AP-site repair pathway.

Inhibitory Effect of New Semisynthetic Usnic Acid Derivatives on Human Tyrosyl-DNA Phosphodiesterase 1

Usnic acid, a lichen secondary metabolite produced by a whole number of lichens, has attracted the interest of researchers owing to its broad range of biological activity, including antiviral, antibiotic, anticancer properties, and it possessing a certain toxicity. The synthesis of new usnic acid derivatives and the investigation of their biological activity may lead to the discovery of compounds with better pharmacological and toxicity profiles. In this context, a series of new usnic acid derivatives comprising a terpenoid moiety were synthesized, and their ability to inhibit the catalytic activity of the human DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 was investigated. The most potent compounds (15A, 15B, 15G: , and 16A, 16B, 16G: ) had IC50 values in the range of 0.33 - 2.7 µM. The inhibitory properties were mainly dependent on the flexibility and length of the terpenoid moiety, but not strongly dependent on the configuration of the asymmetric centers. The synthesized derivatives showed low cytotoxicity against human cell lines in an MTT assay. They could be used as a basis for the development of more effective anticancer therapies when combined with topoisomerase 1 inhibitors.

Novel group of tyrosyl-DNA-phosphodiesterase 1 inhibitors based on disaccharide nucleosides as drug prototypes for anti-cancer therapy

Abstract A new class of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors based on disaccharide nucleosides was identified. TDP1 plays an essential role in the resistance of cancer cells to currently used antitumour drugs based on Top1 inhibitors such as topotecan and irinotecan. The most effective inhibitors investigated in this study have IC50 values (half-maximal inhibitory concentration) in 0.4–18.5 µM range and demonstrate relatively low own cytotoxicity along with significant synergistic effect in combination with anti-cancer drug topotecan. Moreover, kinetic parameters of the enzymatic reaction and fluorescence anisotropy were measured using different types of DNA-biosensors to give a sufficient insight into the mechanism of inhibitor’s action.

Quantitative parameters of the 3′–5′ exonuclease reaction of human apurinic/apyrimidinic endonuclease 1 with nicked DNA containing dYMP or a modified dCMP analogue

Human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is a multifunctional enzyme. In addition to its main AP endonuclease activity, that incises DNA 5′ to the AP-site, it possesses other weak enzymatic activities. One of them is 3′–5′ exonuclease activity, which is most effectively exhibited for DNA duplexes containing modified or mismatched nucleotides at the 3′-end of the primer chain. There is a presumption that APE1 can correct the DNA synthesis catalyzed by DNA polymerase β through the base excision repair process. We determined the quantitative parameters of the 3′–5′ exonuclease reaction in dependence on the reaction conditions to reveal the detailed mechanism of this process. The kinetic parameters of APE1 exonuclease excision of mismatched dCMP and dTMP from the 3′ terminus of single-strand DNA and of photoreactive dCMP analogues applied for photoaffinity modification of proteins and DNA in recombinant systems and cell/nuclear extracts were determined.