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Radford HM, Toft CJ, Sorenson AE, Schaeffer PM. Inhibition of Replication Fork Formation and Progression: Targeting the Replication Initiation and Primosomal Proteins. Int J Mol Sci 2023; 24:ijms24108802. [PMID: 37240152 DOI: 10.3390/ijms24108802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Over 1.2 million deaths are attributed to multi-drug-resistant (MDR) bacteria each year. Persistence of MDR bacteria is primarily due to the molecular mechanisms that permit fast replication and rapid evolution. As many pathogens continue to build resistance genes, current antibiotic treatments are being rendered useless and the pool of reliable treatments for many MDR-associated diseases is thus shrinking at an alarming rate. In the development of novel antibiotics, DNA replication is still a largely underexplored target. This review summarises critical literature and synthesises our current understanding of DNA replication initiation in bacteria with a particular focus on the utility and applicability of essential initiation proteins as emerging drug targets. A critical evaluation of the specific methods available to examine and screen the most promising replication initiation proteins is provided.
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Affiliation(s)
- Holly M Radford
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Casey J Toft
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Alanna E Sorenson
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Patrick M Schaeffer
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
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Lata K, Vishwakarma J, Kumar S, Khanam T, Ramachandran R. Mycobacterium tuberculosis Endonuclease VIII 2 (Nei2) forms a prereplicative BER complex with DnaN: Identification, characterization, and disruption of complex formation. Mol Microbiol 2021; 117:320-333. [PMID: 34820919 DOI: 10.1111/mmi.14848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022]
Abstract
Mycobacterium tuberculosis Nei2 (Rv3297) is a BER glycosylase that removes oxidized base lesions from ssDNA and replication fork-mimicking substrates. We show that Endonuclease VIII 2 (Nei2) forms a BER complex with the β-clamp (DnaN, Rv0002) with a KD of 170 nM. The Nei2-β-clamp interactions enhance Nei2's activities up to several folds. SEC analysis shows that one molecule of Nei2 binds to a single β-clamp dimer. Nei2 interacts with subsites I and II of the β-clamp via a noncanonical 223 QGCRRCGTLIAY239 Clamp Interacting Protein (CIP) motif in the C-terminal zinc-finger domain, which was previously shown by us to be dispensable for intrinsic Nei2 activity. The 12-mer peptide alone exhibited a KD of 10.28 nM, suggesting that the motif is a key mediator of Nei2-β-clamp interactions. Finally, we identified inhibitors of Nei2-β-clamp interactions using rational methods, in vitro disruption, and SPR assays after querying a database of natural products. We found that Tubulosine, Fumitremorgin C, Toyocamycin, and Aleuritic acid exhibit IC50 values of 94.47, 83.49, 109.7, and 71.49 µM, respectively. They act by disrupting Nei2-β-clamp interactions and do not affect intrinsic Nei2 activity. Among other things, the present study gives insights into the role of Nei2 in bacterial prereplicative BER.
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Affiliation(s)
- Kiran Lata
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Jyoti Vishwakarma
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanjay Kumar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Taran Khanam
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Abstract
A range of enzymes in DNA replication and repair bind to DNA-clamps: torus-shaped proteins that encircle double-stranded DNA and act as mobile tethers. Clamps from viruses (such as gp45 from the T4 bacteriophage) and eukaryotes (PCNAs) are homotrimers, each protomer containing two repeats of the DNA-clamp motif, while bacterial clamps (pol III β) are homodimers, each protomer containing three DNA-clamp motifs. Clamps need to be flexible enough to allow opening and loading onto primed DNA by clamp loader complexes. Equilibrium and steered molecular dynamics simulations have been used to study DNA-clamp conformation in open and closed forms. The E. coli and PCNA clamps appear to prefer closed, planar conformations. Remarkably, gp45 appears to prefer an open right-handed spiral conformation in solution, in agreement with previously reported biophysical data. The structural preferences of DNA clamps in solution have implications for understanding the duty cycle of clamp-loaders.
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Yin Z, Whittell LR, Wang Y, Jergic S, Ma C, Lewis PJ, Dixon NE, Beck JL, Kelso MJ, Oakley AJ. Bacterial Sliding Clamp Inhibitors that Mimic the Sequential Binding Mechanism of Endogenous Linear Motifs. J Med Chem 2015; 58:4693-702. [PMID: 25970224 DOI: 10.1021/acs.jmedchem.5b00232] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The bacterial DNA replication machinery presents new targets for the development of antibiotics acting via novel mechanisms. One such target is the protein-protein interaction between the DNA sliding clamp and the conserved peptide linear motifs in DNA polymerases. We previously established that binding of linear motifs to the Escherichia coli sliding clamp occurs via a sequential mechanism that involves two subsites (I and II). Here, we report the development of small-molecule inhibitors that mimic this mechanism. The compounds contain tetrahydrocarbazole moieties as "anchors" to occupy subsite I. Functional groups appended at the tetrahydrocarbazole nitrogen bind to a channel gated by the side chain of M362 and lie at the edge of subsite II. One derivative induced the formation of a new binding pocket, termed subsite III, by rearrangement of a loop adjacent to subsite I. Discovery of the extended binding area will guide further inhibitor development.
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Affiliation(s)
- Zhou Yin
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Louise R Whittell
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Yao Wang
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Slobodan Jergic
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Cong Ma
- ‡School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Peter J Lewis
- ‡School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Nicholas E Dixon
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Jennifer L Beck
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Michael J Kelso
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Aaron J Oakley
- †School of Chemistry and Centre for Medical and Molecular Bioscience, The University of Wollongong and The Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
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Yin Z, Wang Y, Whittell L, Jergic S, Liu M, Harry E, Dixon N, Kelso M, Beck J, Oakley A. DNA Replication Is the Target for the Antibacterial Effects of Nonsteroidal Anti-Inflammatory Drugs. ACTA ACUST UNITED AC 2014; 21:481-487. [DOI: 10.1016/j.chembiol.2014.02.009] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/03/2014] [Accepted: 02/13/2014] [Indexed: 12/11/2022]
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Yin Z, Whittell LR, Wang Y, Jergic S, Liu M, Harry EJ, Dixon NE, Beck JL, Kelso MJ, Oakley AJ. Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach. J Med Chem 2014; 57:2799-806. [PMID: 24592885 DOI: 10.1021/jm500122r] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bacterial sliding clamp (SC), also known as the DNA polymerase III β subunit, is an emerging antibacterial target that plays a central role in DNA replication, serving as a protein-protein interaction hub with a common binding pocket to recognize linear motifs in the partner proteins. Here, fragment-based screening using X-ray crystallography produced four hits bound in the linear-motif-binding pocket of the Escherichia coli SC. Compounds structurally related to the hits were identified that inhibited the E. coli SC and SC-mediated DNA replication in vitro. A tetrahydrocarbazole derivative emerged as a promising lead whose methyl and ethyl ester prodrug forms showed minimum inhibitory concentrations in the range of 21-43 μg/mL against representative Gram-negative and Gram-positive bacteria species. The work demonstrates the utility of a fragment-based approach for identifying bacterial sliding clamp inhibitors as lead compounds with broad-spectrum antibacterial activity.
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Affiliation(s)
- Zhou Yin
- School of Chemistry and Centre for Medical and Molecular Bioscience, University of Wollongong , Wollongong, New South Wales 2522, Australia
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Park B, Kim Y. Exogenous JH and ecdysteroid applications alter initiation of polydnaviral replication in an endoparasitoid wasp, Cotesia plutellae (Braconidae: Hymenoptera). BMB Rep 2011; 44:393-8. [PMID: 21699752 DOI: 10.5483/bmbrep.2011.44.6.393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polydnaviruses are a group of double-stranded DNA viruses and are symbiotically associated with some ichneumonoid wasps. As proviruses, the replication of polydnaviruses occurs in the female reproductive organ at the pupal stage. This study analyzed the effects of two developmental hormones, juvenile hormone (JH) and ecdysteroid, on the viral replication of Cotesia plutellae bracovirus (CpBV). All 23 CpBV segments identified contained a conserved excision/rejoining site ('AGCTTT') from their proviral segments. Using quantitative real-time PCR based on this excision/rejoining site marker, initiation of CpBV replication was determined to have occurred on day 4 on the pupal stage. Pyriproxyfen, a JH agonist, significantly inhibited adult emergence of C. plutellae, whereas RH5992, an ecdysteroid agonist, had no inhibitory effect. Although RH5992 had no effect dose on adult development, it significantly accelerated viral replication. The results of immunoblotting assays against viral coat proteins support the effects of the hormone agonists on viral replication.
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Affiliation(s)
- Bokri Park
- Department of Bioresource Sciences, Andong National University, Andong 760-749, Korea
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Beck JL. Developments in Electrospray Ionization Mass Spectrometry of Non-Covalent DNA–Ligand Complexes. Aust J Chem 2011. [DOI: 10.1071/ch11046] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many anti-cancer drugs function by binding non-covalently to double-stranded (ds) DNA. Electrospray ionization mass spectrometry (ESI-MS) has emerged over the past decade as a sensitive technique for the determination of stoichiometries and relative binding affinities of DNA–ligand interactions. The chromosome contains nucleotide sequences, for example, guanosine-rich regions, that predispose them to the formation of higher order structures such as quadruplex DNA (qDNA). Sequences that form qDNA are found in the telomeres. The proposal that ligands that stabilize qDNA might interfere with the activity of telomerase in cancer cells has stimulated the search for ligands that are selective for qDNA over dsDNA. The insights gained from the development of ESI-MS methods for analysis of non-covalent dsDNA–ligand complexes are now being applied in the search for qDNA-selective ligands. ESI-MS is a useful first-pass screening technique for qDNA-binding ligands. This short review describes some experimental considerations for ESI-MS analysis of DNA–ligand complexes, briefly addresses the question of whether non-covalent DNA–ligand complexes are faithfully transferred from solution to the gas phase, discusses ion mobility mass spectrometry as a technique for probing this issue, and highlights some recent ESI-MS studies of qDNA-selective ligands.
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Essential biological processes of an emerging pathogen: DNA replication, transcription, and cell division in Acinetobacter spp. Microbiol Mol Biol Rev 2010; 74:273-97. [PMID: 20508250 DOI: 10.1128/mmbr.00048-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Within the last 15 years, members of the bacterial genus Acinetobacter have risen from relative obscurity to be among the most important sources of hospital-acquired infections. The driving force for this has been the remarkable ability of these organisms to acquire antibiotic resistance determinants, with some strains now showing resistance to every antibiotic in clinical use. There is an urgent need for new antibacterial compounds to combat the threat imposed by Acinetobacter spp. and other intractable bacterial pathogens. The essential processes of chromosomal DNA replication, transcription, and cell division are attractive targets for the rational design of antimicrobial drugs. The goal of this review is to examine the wealth of genome sequence and gene knockout data now available for Acinetobacter spp., highlighting those aspects of essential systems that are most suitable as drug targets. Acinetobacter spp. show several key differences from other pathogenic gammaproteobacteria, particularly in global stress response pathways. The involvement of these pathways in short- and long-term antibiotic survival suggests that Acinetobacter spp. cope with antibiotic-induced stress differently from other microorganisms.
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Watt SJ, Urathamakul T, Schaeffer PM, Williams NK, Sheil MM, Dixon NE, Beck JL. Multiple oligomeric forms of Escherichia coli DnaB helicase revealed by electrospray ionisation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:132-40. [PMID: 17154355 DOI: 10.1002/rcm.2818] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The Escherichia coli DnaB protein (DnaB(6)) is the hexameric helicase that unwinds genomic DNA so it can be copied by the DNA replication machinery. Loading of the helicase onto DNA requires interactions of DnaB(6) with six molecules of its loading partner protein, DnaC. Nano-electrospray ionisation mass spectrometry (nanoESI-MS) of mutant proteins was used to examine the roles of the residues Phe102 (F102) and Asp82 (D82) in the N-terminal domain of DnaB in the assembly of the hexamer. When the proteins were prepared in 1 M ammonium acetate containing magnesium and adenosine triphosphate (ATP) at pH 7.6, both hexameric and heptameric forms of wild-type and F102W, F102E and D82N mutant DnaBs were observed in mass spectra. The spectra of the D82N mutant also showed substantial amounts of a decameric species and small amounts of a dodecamer. In contrast, the F102H DnaB mutant was incapable of forming oligomers of order higher than the hexamer. Thus, although Phe102 is not the only determinant of hexamer assembly, this residue has a role in oligomerisation. NanoESI mass spectra were obtained of mixtures of DnaB(6) with DnaC. The DnaB(6)(DnaC)(6) complex (calculated M(r) 481 164) was observed only when the two proteins were present in equimolar amounts. The data are consistent with cooperative assembly of the complex. ESI mass spectra of mixtures containing DnaC and ATP showed that DnaC slowly hydrolysed ATP to ADP as indicated by ions corresponding to DnaC/ATP and DnaC/ADP complexes. These experiments show that E. coli DnaB can form a heptameric complex and that nanoESI-MS can be used to probe assembly of large (>0.5 MDa) macromolecular complexes.
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Affiliation(s)
- Stephen J Watt
- Department of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
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