NAD<sup>+</sup>‐Dependent DNA Ligase: A novel target waiting for the right inhibitor

Dwivedi, Namrata; Dube, Divya; Pandey, Jyoti; Singh, Biswajit K.; Kukshal, Vandna; Ramachandran, Ravishankar; Tripathi, Rama Pati

doi:10.1002/med.20114

Cited by 42 publications

(36 citation statements)

References 64 publications

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“…We previously evaluated NAD ϩ -dependent DNA ligase (LigA), which appeared to be essential for mycobacterial viability, as a putative drug target (34). LigA inhibitors that do not affect ATP-dependent ligases were also identified (35,36). Unexpectedly, depletion of LigA did not significantly affect the growth of mycobacteria (34), largely precluding LigA as a target for new anti-TB drugs.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of DNA Primase DnaG as a Potential Target for Antibiotics

Kuron

Korycka-Machała

Brzostek

et al. 2014

Antimicrob Agents Chemother

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c Mycobacteria contain genes for several DNA-dependent RNA primases, including dnaG, which encodes an essential replication enzyme that has been proposed as a target for antituberculosis compounds. An in silico analysis revealed that mycobacteria also possess archaeo-eukaryotic superfamily primases (AEPs) of unknown function. Using a homologous recombination system, we obtained direct evidence that wild-type dnaG cannot be deleted from the chromosome of Mycobacterium smegmatis without disrupting viability, even in backgrounds in which mycobacterial AEPs are overexpressed. In contrast, single-deletion AEP mutants or mutants defective for all four identified M. smegmatis AEP genes did not exhibit growth defects under standard laboratory conditions. Deletion of native dnaG in M. smegmatis was tolerated only after the integration of an extra intact copy of the M. smegmatis or Mycobacterium tuberculosis dnaG gene, under the control of chemically inducible promoters, into the attB site of the chromosome. M. tuberculosis and M. smegmatis DnaG proteins were overproduced and purified, and their primase activities were confirmed using radioactive RNA synthesis assays. The enzymes appeared to be sensitive to known inhibitors (suramin and doxorubicin) of DnaG. Notably, M. smegmatis bacilli appeared to be sensitive to doxorubicin and resistant to suramin. The growth and survival of conditional mutant mycobacterial strains in which DnaG was significantly depleted were only slightly affected under standard laboratory conditions. Thus, although DnaG is essential for mycobacterial viability, only low levels of protein are required for growth. This suggests that very efficient inhibition of enzyme activity would be required for mycobacterial DnaG to be useful as an antibiotic target. Mycobacterium tuberculosis is a deadly pathogen that claims nearly 2 million lives annually and infects an estimated 2 billion people, who serve as a reservoir of latently infected individuals (1). Most tuberculosis (TB) cases are not the result of new infections but are caused by the reactivation of dormant M. tuberculosis (2). TB caused by drug-sensitive strains is fully treatable, but patients must take three or four drugs for approximately Ն6 months. Premature termination of drug therapy results in the emergence of resistant strains. The World Health Organization estimates that 50 million individuals harbor multidrug-resistant (MDR) M. tuberculosis, which is resistant to at least rifampin and isoniazid. Treating these MDR strains requires second-line drugs, which are expensive, have side effects, and take longer to work (up to 2 years). More disturbing is that strains of untreatable extensively drug-resistant (XDR) TB, which are additionally resistant to any fluoroquinolone and at least one of three injectable secondline drugs (capreomycin, kanamycin, or amikacin), have already been identified in 58 countries. This XDR form, together with totally drug-resistant (TDR) TB, seems to represent the greatest health threat (3). The options for treating ...

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Section: Discussionmentioning

confidence: 99%

Evaluation of DNA Primase DnaG as a Potential Target for Antibiotics

Kuron

Korycka-Machała

Brzostek

et al. 2014

Antimicrob Agents Chemother

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“…All bacteria encode a highly conserved NAD-dependent ligase (LigA), which is essential for cell growth being a key player in DNA replication, repair and recombination. This makes it a very promising target for the development of new antibacterial drugs [21,22].…”

Section: Nad-dependent Dna Ligasementioning

confidence: 99%

NAD homeostasis in the bacterial response to DNA/RNA damage

2014

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“…A diverse range of inhibitors of NAD + -dependent DNA ligase have been identified (Dwivedi et al, 2008). Two classes of inhibitors, pyridochromanones and glycosyl derivatives, inhibit NAD + -dependent DNA ligases by competing with NAD + binding and do not interact with DNA.…”

Section: Dna Ligasesmentioning

confidence: 99%

Structure of the adenylation domain of NAD⁺-dependent DNA ligase fromStaphylococcus aureus

2009

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PDB References: SauLigA, 3jsl, r3jslsf; 3jsn, r3jsnsf.DNA ligase catalyzes phosphodiester-bond formation between immediately adjacent 5 0 -phosphate and 3 0 -hydroxyl groups in double-stranded DNA and plays a central role in many cellular and biochemical processes, including DNA replication, repair and recombination. Bacterial NAD + -dependent DNA ligases have been extensively characterized as potential antibacterial targets because of their essentiality and their structural distinction from human ATP-dependent DNA ligases. The high-resolution structure of the adenylation domain of Staphylococcus aureus NAD + -dependent DNA ligase establishes the conserved domain architecture with other bacterial adenylation domains. Two apo crystal structures revealed that the active site possesses the preformed NAD + -binding pocket and the 'C2 tunnel' lined with hydrophobic residues: Leu80, Phe224, Leu287, Phe295 and Trp302. The C2 tunnel is unique to bacterial DNA ligases and the Leu80 side chain at the mouth of the tunnel points inside the tunnel and forms a narrow funnel in the S. aureus DNA ligase structure. Taken together with other DNA ligase structures, the S. aureus DNA ligase structure provides a basis for a more integrated understanding of substrate recognition and catalysis and will be also be of help in the development of small-molecule inhibitors.

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NAD⁺‐Dependent DNA Ligase: A novel target waiting for the right inhibitor

Cited by 42 publications

References 64 publications

Evaluation of DNA Primase DnaG as a Potential Target for Antibiotics

Evaluation of DNA Primase DnaG as a Potential Target for Antibiotics

NAD homeostasis in the bacterial response to DNA/RNA damage

Structure of the adenylation domain of NAD⁺-dependent DNA ligase fromStaphylococcus aureus

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NAD+‐Dependent DNA Ligase: A novel target waiting for the right inhibitor

Cited by 42 publications

References 64 publications

Evaluation of DNA Primase DnaG as a Potential Target for Antibiotics

Evaluation of DNA Primase DnaG as a Potential Target for Antibiotics

NAD homeostasis in the bacterial response to DNA/RNA damage

Structure of the adenylation domain of NAD+-dependent DNA ligase fromStaphylococcus aureus

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Product

Resources

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NAD⁺‐Dependent DNA Ligase: A novel target waiting for the right inhibitor

Structure of the adenylation domain of NAD⁺-dependent DNA ligase fromStaphylococcus aureus