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Arı E, Şahin N, Üstün E, Dündar M, Karcı H, Özdemir İ, Koç A, Gürbüz N, Özdemir İ. Synthesis, antimicrobial activity and molecular docking study of benzyl functionalized benzimidazole silver(I) complexes. J Biol Inorg Chem 2023; 28:725-736. [PMID: 37934281 DOI: 10.1007/s00775-023-02024-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/10/2023] [Indexed: 11/08/2023]
Abstract
In this study, a series of N-functionalized benzimidazole silver(I) complexes were prepared and characterized by FT-IR, 1H, 13C{1H} NMR spectroscopy, and elemental analysis. Synthesized N-benzylbenzimidazole silver(I) complexes were evaluated for their antimicrobial activities against bacteria Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and the fungal strains Candida albicans and Candida glabrata. The results indicated that N-alkylbenzimidazole silver(I) complexes exhibited good antimicrobial activity compared to N-alkylbenzimidazole derivatives. Especially, complex 2e presented perfect antimicrobial activity than the other complexes. The characterized molecules were optimized by DFT-based calculation methods and the optimized molecules were analyzed in detail by molecular docking methods against bacterial DNA-gyrase and CYP51. The amino acid residues detected for both target molecules are consistent with expectations, and the calculated binding affinities and inhibition constants are promising for further studies. A series of N-alkylbenzimidazole silver(I) complexes were synthesized and fully characterized by means of 1H NMR, 13C NMR, and FT-IR spectroscopies. Synthesized N-alkylbenzimidazole silver(I) complexes were investigated for their antimicrobial activities against bacteria Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and the fungal strains Candida albicans and Candida glabrata. All complexes showed better activity according to Ampicilin against Pseudomonas aeruginosa. The molecules which were firstly optimized by DFT-based calculation methods were also analyzed by molecular docking methods against DNA gyrase of E. Coli and CYP51. 338 × 190 mm (96 × 96 DPI).
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Affiliation(s)
- Erkan Arı
- Department of Chemistry, Faculty of Science and Art, İnönü University, 44280, Malatya, Turkey
| | - Neslihan Şahin
- Department of Science Education, Faculty of Education, Cumhuriyet University, 58040, Sivas, Turkey
| | - Elvan Üstün
- Department of Chemistry, Faculty of Art and Science, Ordu University, 52200, Ordu, Turkey
| | - Muhammed Dündar
- Department of Molecular Biology and Genetics, Faculty of Science and Art, İnönü University, Malatya, Turkey
- Drug Application and Research Center, İnönü University, 44280, Malatya, Turkey
| | - Hüseyin Karcı
- Department of Chemistry, Faculty of Science and Art, İnönü University, 44280, Malatya, Turkey
- Drug Application and Research Center, İnönü University, 44280, Malatya, Turkey
| | - İlknur Özdemir
- Department of Chemistry, Faculty of Science and Art, İnönü University, 44280, Malatya, Turkey.
- Drug Application and Research Center, İnönü University, 44280, Malatya, Turkey.
| | - Ahmet Koç
- Department of Genetics, Faculty of Medicine, İnönü University, Malatya, Turkey
| | - Nevin Gürbüz
- Department of Chemistry, Faculty of Science and Art, İnönü University, 44280, Malatya, Turkey
- Drug Application and Research Center, İnönü University, 44280, Malatya, Turkey
| | - İsmail Özdemir
- Department of Chemistry, Faculty of Science and Art, İnönü University, 44280, Malatya, Turkey
- Drug Application and Research Center, İnönü University, 44280, Malatya, Turkey
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An B, Chen P, Tao Y. The roles of membrane permeability and efflux pumps in the toxicity of bisphenol S analogues (2,4-bisphenol S and bis-(3-allyl-4-hydroxyphenyl) sulfone) to Escherichia coli K12. CHEMOSPHERE 2023; 329:138697. [PMID: 37062394 DOI: 10.1016/j.chemosphere.2023.138697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Bisphenol S (BPS) analogues are a group of recently reported emerging contaminants in the environment. Bacteria are important components of food webs. However, the potential risks of BPS analogues in bacteria have not been fully addressed. The toxicity effects and related mechanisms of two BPS analogues with different molecular weights (2,4-bisphenol S (2,4-BPS) and bis-(3-allyl-4-hydroxyphenyl) sulfone (TGSA)) on Escherichia coli K12 were compared. The minimum inhibitory concentration (MIC) of 2,4-BPS in the wild-type of E. coli K12 was lower than that of TGSA. The membrane permeability of the wild-type increased significantly after exposed to the same concentrations (0.5-50 nmol L-1) of 2,4-BPS and TGSA. In addition, 2,4-BPS induced more significant changes in membrane permeability than TGSA. Hormetic effects of 2,4-BPS and TGSA in the wild-type strain were noted in the levels of outer membrane proteins (ompC and ompF), multidrug efflux pump acriflavine resistance B (acrB) and type II topoisomerases. Transcriptomic results indicated these two BPS analogues inhibited the function of ABC transporters. In contrast to TGSA, 2,4-BPS affected DNA replication, tricarboxylic acid cycle, oxidative phosphorylation, and inhibited energy metabolism. Compared with wild-type strain, the ΔacrB mutant strain showed enhanced susceptibility to 2,4-BPS and TGSA with their MICs reduced by 20% and 11%, respectively. Deletion of the acrB affected the growth characteristics and induced stronger oxidative stress than the wild-type strain when exposed to 2,4-BPS or TGSA. The results suggested that 2,4-BPS were more toxic to E. coli K12 than TGSA in the concentration range of 0.5-50 nmol L-1, which was supported by the evidence from their impacts on membrane permeability and efflux pumps.
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Affiliation(s)
- Baihui An
- College of Oceanography, Hohai University, Nanjing, 210024, China
| | - Pengyu Chen
- College of Oceanography, Hohai University, Nanjing, 210024, China
| | - Yuqiang Tao
- College of Oceanography, Hohai University, Nanjing, 210024, China.
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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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Antibacterial mechanism of lactobionic acid against Shewanella baltica and Shewanella putrefaciens and its application on refrigerated shrimp. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2022.102291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Dobričić V, Savić J, Tomašič T, Durcik M, Zidar N, Mašič LP, Ilaš J, Kikelj D, Čudina O. High-performance liquid chromatography evaluation of lipophilicity and QSRR modeling of a series of dual DNA gyrase and topoisomerase IV inhibitors. ACTA CHROMATOGR 2022. [DOI: 10.1556/1326.2022.01096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
AbstractBacterial DNA gyrase and topoisomerase IV control the topological state of DNA during replication and represent important antibacterial drug targets. To be successful as drug candidates, newly synthesized compounds must possess optimal lipophilicity, which enables efficient delivery to the site of action. In this study, retention behavior of twenty-three previously synthesized dual DNA gyrase and topoisomerase IV inhibitors was tested in RP-HPLC system, consisting of C8 column and acetonitrile/phosphate buffer (pH 5.5 and pH 7.4) mobile phase. logD was calculated at both pH values and the best correlation with logD was obtained for retention parameter φ0, indicating that this RP-HPLC system could be used as an alternative to the shake-flask determination of lipophilicity. Subsequent QSRR analysis revealed that intrinsic lipophilicity (logP) and molecular weight (bcutm13) have a positive, while solubility (bcutp3) has a negative influence on this retention parameter.
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Affiliation(s)
- Vladimir Dobričić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Jelena Savić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Tihomir Tomašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Durcik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Olivera Čudina
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
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Wound Healing, Antimicrobial and Antioxidant Properties of Clinacanthus nutans (Burm.f.) Lindau and Strobilanthes crispus (L.) Blume Extracts. Molecules 2022; 27:molecules27051722. [PMID: 35268823 PMCID: PMC8911986 DOI: 10.3390/molecules27051722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022] Open
Abstract
Clinacanthus nutans is known to be an anticancer and antiviral agent, and Strobilanthes crispus has proven to be an antidiuretic and antidiabetic agent. However, there is a high possibility that these plants possess multiple beneficial properties, such as antimicrobial and wound healing properties. This study aims to assess the wound healing, antioxidant, and antimicrobial properties of Clinacanthus nutans and Strobilanthes crispus. The Clinacanthus nutans and Strobilanthes crispus leaves were dried, ground, and extracted with ethanol, acetone, and chloroform through cold maceration. In a modified scratch assay with co-incubation of skin fibroblast and Methicillin-resistant Staphylococcus aureus, Clinacanthus nutans and Strobilanthes crispus extracts were assessed for their wound healing potential, and the antimicrobial activities of Clinacanthus nutans and Strobilanthes crispus extracts were performed on a panel of Gram-positive and Gram-negative bacteria on Mueller–Hinton agar based on a disc diffusion assay. To assess for antioxidant potential, 2,2-diphenyl-1-picrylhydrazyl (DPPH), total phenolic and total flavonoid assays were conducted. In the modified scratch assay, Clinacanthus nutans extracts aided in the wound healing activity while in the presence of MRSA, and Strobilanthes crispus extracts were superior in antimicrobial and wound healing activities. In addition, Strobilanthes crispus extracts were superior to Clinacanthus nutans extracts against Pseudomonas aeruginosa on Mueller–Hinton agar. Acetone-extracted Clinacanthus nutans contained the highest level of antioxidant in comparison with other Clinacanthus nutans extracts.
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Abd El-Hameed RH, Sayed AI, Mahmoud Ali S, Mosa MA, Khoder ZM, Fatahala SS. Synthesis of novel pyrroles and fused pyrroles as antifungal and antibacterial agents. J Enzyme Inhib Med Chem 2021; 36:2183-2198. [PMID: 34602000 PMCID: PMC8491725 DOI: 10.1080/14756366.2021.1984904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 09/12/2021] [Accepted: 09/20/2021] [Indexed: 11/22/2022] Open
Abstract
Pyrroles and its fused forms possess antimicrobial activities, they can easily interact with biomolecules of living systems. A series of substituted pyrroles, and its fused pyrimidines and triazines forms have been synthesised, all newly synthesised compound structures were confirmed by spectroscopic analysis. Generally, the compounds inhibited growth of some important human pathogens, the best effect was given by: 2a, 3c, 4d on Gram-positive bacteria and was higher on yeast (C. albicans), by 5c on Gram-negative bacteria and by 5a then 3c on filamentous fungi (A. fumigatus and F. oxysporum). Such results present good antibacterial and antifungal potential candidates to help overcome the global problem of antibiotic resistance and opportunistic infections outbreak. Compound 3c gave the best anti-phytopathogenic effect at a 50-fold lower concentration than Kocide 2000, introducing a safe commercial candidate for agricultural use. The effect of the compounds on DNA was monitored to detect the mode of action.
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Affiliation(s)
- Rania Helmy Abd El-Hameed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Helwan, Cairo, Egypt
| | - Amira Ibrahim Sayed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Helwan, Cairo, Egypt
| | - Shima Mahmoud Ali
- Department of Chemistry, The state University of New York at Buffalo, New York, NY, USA
| | - Mohamed A. Mosa
- Microbiology and Immunology Department, Faculty of Pharmacy, Helwan University, Helwan, Cairo, Egypt
| | - Zainab M. Khoder
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Helwan, Cairo, Egypt
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Samar Said Fatahala
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Helwan, Cairo, Egypt
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Kowalczyk A, Paneth A, Trojanowski D, Paneth P, Zakrzewska-Czerwińska J, Stączek P. Thiosemicarbazide Derivatives Decrease the ATPase Activity of Staphylococcus aureus Topoisomerase IV, Inhibit Mycobacterial Growth, and Affect Replication in Mycobacterium smegmatis. Int J Mol Sci 2021; 22:ijms22083881. [PMID: 33918623 PMCID: PMC8069432 DOI: 10.3390/ijms22083881] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 11/16/2022] Open
Abstract
Compounds targeting bacterial topoisomerases are of interest for the development of antibacterial agents. Our previous studies culminated in the synthesis and characterization of small-molecular weight thiosemicarbazides as the initial prototypes of a novel class of gyrase and topoisomerase IV inhibitors. To expand these findings with further details on the mode of action of the most potent compounds, enzymatic studies combined with a molecular docking approach were carried out, the results of which are presented herein. The biochemical assay for 1-(indol-2-oyl)-4-(4-nitrophenyl) thiosemicarbazide (4) and 4-benzoyl-1-(indol-2-oyl) thiosemicarbazide (7), showing strong inhibitory activity against Staphylococcus aureus topoisomerase IV, confirmed that these compounds reduce the ability of the ParE subunit to hydrolyze ATP rather than act by stabilizing the cleavage complex. Compound 7 showed better antibacterial activity than compound 4 against clinical strains of S. aureus and representatives of the Mycobacterium genus. In vivo studies using time-lapse microfluidic microscopy, which allowed for the monitoring of fluorescently labelled replisomes, revealed that compound 7 caused an extension of the replication process duration in Mycobacterium smegmatis, as well as the growth arrest of bacterial cells. Despite some similarities to the mechanism of action of novobiocin, these compounds show additional, unique properties, and can thus be considered a novel group of inhibitors of the ATPase activity of bacterial type IIA topoisomerases.
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Affiliation(s)
- Aleksandra Kowalczyk
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland;
| | - Agata Paneth
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
- Correspondence: (A.P.); (P.S.)
| | - Damian Trojanowski
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland; (D.T.); (J.Z.-C.)
| | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Łódź University of Technology, Żeromskiego 116, 90-924 Łódź, Poland;
- International Centre for Research on Innovative Biobased Materials (ICRI-BioM)—International Research Agenda, Łódź University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Jolanta Zakrzewska-Czerwińska
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland; (D.T.); (J.Z.-C.)
| | - Paweł Stączek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland;
- Correspondence: (A.P.); (P.S.)
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Ibrahim TS, Almalki AJ, Moustafa AH, Allam RM, Abuo-Rahma GEDA, El Subbagh HI, Mohamed MFA. Novel 1,2,4-oxadiazole-chalcone/oxime hybrids as potential antibacterial DNA gyrase inhibitors: Design, synthesis, ADMET prediction and molecular docking study. Bioorg Chem 2021; 111:104885. [PMID: 33838559 DOI: 10.1016/j.bioorg.2021.104885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 01/19/2023]
Abstract
New antibacterial drugs are urgently needed to tackle the rapid rise in multi-drug resistant bacteria. DNA gyrase is a validated target for the development of new antibacterial drugs. Thus, in the present investigation, a novel series of 1,2,4-oxadiazole-chalcone/oxime (6a-f) and (7a-f) were synthesized and characterized by IR, NMR (1H and 13C) and elemental analyses. The title compounds were evaluated for their in-vitro antimicrobial activity by the modified agar diffusion method as well as their E. coli DNA gyrase inhibitory activity. The minimum inhibitory concentration (MIC) and the structure activity relationships (SARs) were evaluated. Among all, compounds 6a, 6c-e, 7b and 7e were the most potent and proved to possess broad spectrum activity against the tested Gram-positive and Gram-negative organisms. Additionally, compounds 6a (against S. aureus), 6c (against B. subtilis and E. hirae), 6e (against E. hirae), 6f, 7a and 7c (against E. coli) and 7d (against B. subtilis), with MIC value of 3.12 μM were two-fold more potent than the standard ciprofloxacin (MIC = 6.25 μM). Mechanistically, compounds 6c, 7c, 7e and 7b had good inhibitory activity against E. coli gyrase with IC50 values of 17.05, 13.4, 16.9, and 19.6 µM, respectively, in comparison with novobiocin (IC50 = 12.3 µM) and ciprofloxacin (IC50 = 10.5 µM). The molecular docking results at DNA gyrase active site revealed that the most potent compounds 6c and 7c have binding mode and docking scores comparable to that of ciprofloxacin and novobiocin suggesting their antibacterial activity via inhibition of DNA gyrase. Finally, the predicted parameters of Lipinski's rule of five and ADMET analysis showed that 6c and 7c had good drug-likeness and acceptable physicochemical properties. Therefore, the hybridization of the chalcone and oxadiazole moieties could be promising lead as antibacterial candidate which merit further future structural optimizations.
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Affiliation(s)
- Tarek S Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt.
| | - Ahmad J Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Amr H Moustafa
- Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Rasha M Allam
- Pharmacology Department, National Research Centre, Cairo 12622 (ID: 60014618), Egypt
| | - Gamal El-Din A Abuo-Rahma
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia 61519, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New Minia, Minia, Egypt
| | - Hussein I El Subbagh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, 35516 Mansoura, Egypt
| | - Mamdouh F A Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sohag University, 82524 Sohag, Egypt.
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Green KD, Punetha A, Chandrika NT, Hou C, Garneau-Tsodikova S, Tsodikov OV. Development of Single-Stranded DNA Bisintercalating Inhibitors of Primase DnaG as Antibiotics. ChemMedChem 2021; 16:1986-1995. [PMID: 33711198 DOI: 10.1002/cmdc.202100001] [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: 01/01/2021] [Revised: 03/02/2021] [Indexed: 11/07/2022]
Abstract
Many essential enzymes in bacteria remain promising potential targets of antibacterial agents. In this study, we discovered that dequalinium, a topical antibacterial agent, is an inhibitor of Staphylococcus aureus primase DnaG (SaDnaG) with low-micromolar minimum inhibitory concentrations against several S. aureus strains, including methicillin-resistant bacteria. Mechanistic studies of dequalinium and a series of nine of its synthesized analogues revealed that these compounds are single-stranded DNA bisintercalators that penetrate a bacterium by compromising its membrane. The best compound of this series likely interacts with DnaG directly, inhibits both staphylococcal cell growth and biofilm formation, and displays no significant hemolytic activity or toxicity to mammalian cells. This compound is an excellent lead for further development of a novel anti-staphylococcal therapeutic.
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Affiliation(s)
- Keith D Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536-0596, USA
| | - Ankita Punetha
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536-0596, USA
| | | | - Caixia Hou
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536-0596, USA
| | | | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536-0596, USA
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Dai J, Li C, Cui H, Lin L. Unraveling the anti-bacterial mechanism of Litsea cubeba essential oil against E. coli O157:H7 and its application in vegetable juices. Int J Food Microbiol 2020; 338:108989. [PMID: 33257098 DOI: 10.1016/j.ijfoodmicro.2020.108989] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022]
Abstract
Recently, natural essential oils have been extensively studied for anti-bacterial application in foods due to their safety and high biological activity. Herein, Litsea cubeba essential oil (LC-EO) was applied as a natural anti-bacterial agent for exploring its anti-bacterial mechanism against Enterohemorrhagic Escherichia coli O157:H7 (EHEC O157:H7). The LC-EO could effectively inhibit the growth of EHEC O157:H7 and the minimal inhibitory concentration (MIC) was 0.5 mg/mL. In the study of anti-bacterial mechanism, the LC-EO was proved with good membrane penetration ability, which could destroy bacterial cell structure and disorder membrane permeability, thereby causing the leakage of intracellular organic matters. Furthermore, the inhibitory effects of LC-EO on physiological metabolism of EHEC O157:H7, including respiratory metabolism, enzyme activity, the replication of nucleic acid and the transcription level of main virulence genes (stx1, stx2, ehxA, eae), were also demonstrated in this study. Specially, the possible action mechanism of different components of LC-EO on bacterial genetic material was revealed deeply on molecular level by the molecular docking technology. Finally, the results of application evaluation indicated that the addition of LC-EO at MIC in different vegetable juices could maintain anti-bacterial rate above 99.9% for 4 days without remarkable influence on foods sensory quality. The information in this study provides the necessary theoretical foundation for extending the application of LC-EO in food preservation.
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Affiliation(s)
- Jinming Dai
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410007, China
| | - Haiying Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Lin Lin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410007, China.
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Novel Antibiotics Targeting Bacterial Replicative DNA Polymerases. Antibiotics (Basel) 2020; 9:antibiotics9110776. [PMID: 33158178 PMCID: PMC7694242 DOI: 10.3390/antibiotics9110776] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
Multidrug resistance is a worldwide problem that is an increasing threat to global health. Therefore, the development of new antibiotics that inhibit novel targets is of great urgency. Some of the most successful antibiotics inhibit RNA transcription, RNA translation, and DNA replication. Transcription and translation are inhibited by directly targeting the RNA polymerase or ribosome, respectively. DNA replication, in contrast, is inhibited indirectly through targeting of DNA gyrases, and there are currently no antibiotics that inhibit DNA replication by directly targeting the replisome. This contrasts with antiviral therapies where the viral replicases are extensively targeted. In the last two decades there has been a steady increase in the number of compounds that target the bacterial replisome. In particular a variety of inhibitors of the bacterial replicative polymerases PolC and DnaE have been described, with one of the DNA polymerase inhibitors entering clinical trials for the first time. In this review we will discuss past and current work on inhibition of DNA replication, and the potential of bacterial DNA polymerase inhibitors in particular as attractive targets for a new generation of antibiotics.
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Maseykina AA, Stepanenko IS, Yamashkin SA, Slastnikov ED. An impact of 1H-indol-4-, -5-, -6-, -7-ylamines-substituted compounds on the microbial cell genetic apparatus. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2020. [DOI: 10.15789/2220-7619-teo-1451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The study of new antimicrobial compounds includes determining the mechanism of their effect on the microbial cell. As a rule, an effect for the majority of current synthetic antimicrobials is associated either with suppressed DNA synthesis, or with inhibiting bacterial protein production at translational or transcriptional level. A number of sensitive and easy-todo methods are available for screening and monitoring potential genotoxic activity of a wide range of natural and synthetic compounds. To date, the Ames test has been widely used, which is based on the sensitivity of Salmonella strains to carcinogenic chemicals, although some compounds resulting in Ames negative reactions could actually be carcinogenic to animals. Likewise, the SOS chromotest represents a SOS transcriptional analysis able to assess DNA damage caused by chemical and physical mutagens by measuring the expression of a reporter gene (β-galactosidase) encoding the β-galactosidase enzyme that metabolizes ortho-nitrophenyl galactopyranoside resulting in emerging a yellow-colored compound detected at wavelength 420 nm. Next, the induction of β-galactosidase is normalized by the activity of alkaline phosphatase, an enzyme expressed constitutively by Escherichia coli. SOS chromotest is also widely used for genotoxicological studies providing a quick answer (several hours) and requiring no survival of the test strain. Dose-response curves for various chemicals consist of a linear region, which slope corresponds to the SOS induction. Therefore, the SOS chromotest was selected for the study allowing to identify DNA-mediated effects of the analyzed compounds. The aim of the study was to evaluate the SOSinducing activity for 1H-indol-4-, -5-, -6-, -7-ylamines-substituted antimicrobial compounds. The Escherichia coli PQ 37 with the genotype F-thr leu his-4 pyrD thi galE lacΔU169 srl300::Th10 rpoB rpsL uvrA rfa trp::Mis+ sfiA:: Mud (Ar, lac) cts was used as a test strain. Due to the link of the sfi A::lac Z genes, lacZ β-galactosidase gene expression in the strain PQ 37 is controlled by the sfiA gene promoter, one of the components in the E. coli SOS regulon. Activity of β-galactosidase assessed relative to constitutive microbial alkaline phosphatase reflects SOS-inducing activity triggered by examined compounds in the SOS chromotest that also allows to control their toxic effects on bacterial cells. The data showed that 4,4,4-trifluoroN-(6-methoxy-1,2,3-trimethyl-1H-indol-5-yl)-3-oxobutanamide (1), 4,4,4-trifluoro-N-(6-methyl-2-phenyl-1H-indol-5-yl)- 3-oxobutanamide (2) and N-(1,5-dimethyl-2-phenyl-1H-indol-6-yl)-4,4,4-trifluoro-3-oxobutanamide (3) exerted no SOSinducing activity at the examined concentrations. In contrast, 4-Hydroxy-8-phenyl-4-(trifluoromethyl)-1,3,4,7-tetrahydro- 2H-pyrrolo [2,3-h]-quinoliN-2-one (4), 9-hydroxy-5-methyl-2-phenyl-9-(trifluoromethyl)-1,6,8,9-tetrahydro-7Н-pyrrolo- [2,3-f]-quinoliN-7-one (5), 6-hydroxy-2,3-dimethyl-6-(trifluoromethyl)-1,6,7,9-tetrahydro-8H-pyrrolo[3,2-h]quinoliN-8- one (6) and 1,2,3,9-tetramethyl-6-(trifluoromethyl)-1,9-dihydro-8H-pyrrolo [3,2-h]-quinoliN-8-one (7) displayed a dosedependent SOS-inducing activity at bactericidal concentrations. The data obtained allowed us to identify compounds 4, 5, 6, 7, which mechanism of action relies on affecting microbial cell DNA.
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14
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Miggiano R, Morrone C, Rossi F, Rizzi M. Targeting Genome Integrity in Mycobacterium Tuberculosis: From Nucleotide Synthesis to DNA Replication and Repair. Molecules 2020; 25:E1205. [PMID: 32156001 PMCID: PMC7179400 DOI: 10.3390/molecules25051205] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), an ancient disease which still today causes 1.4 million deaths worldwide per year. Long-term, multi-agent anti-tubercular regimens can lead to the anticipated non-compliance of the patient and increased drug toxicity, which in turn can contribute to the emergence of drug-resistant MTB strains that are not susceptible to first- and second-line available drugs. Hence, there is an urgent need for innovative antitubercular drugs and vaccines. A number of biochemical processes are required to maintain the correct homeostasis of DNA metabolism in all organisms. Here we focused on reviewing our current knowledge and understanding of biochemical and structural aspects of relevance for drug discovery, for some such processes in MTB, and particularly DNA synthesis, synthesis of its nucleotide precursors, and processes that guarantee DNA integrity and genome stability. Overall, the area of drug discovery in DNA metabolism appears very much alive, rich of investigations and promising with respect to new antitubercular drug candidates. However, the complexity of molecular events that occur in DNA metabolic processes requires an accurate characterization of mechanistic details in order to avoid major flaws, and therefore the failure, of drug discovery approaches targeting genome integrity.
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Affiliation(s)
- Riccardo Miggiano
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy; (C.M.); (F.R.)
| | | | | | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy; (C.M.); (F.R.)
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15
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Second-generation 4,5,6,7-tetrahydrobenzo[ d]thiazoles as novel DNA gyrase inhibitors. Future Med Chem 2020; 12:277-297. [PMID: 32043377 DOI: 10.4155/fmc-2019-0127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: DNA gyrase and topoisomerase IV are essential bacterial enzymes, and in the fight against bacterial resistance, they are important targets for the development of novel antibacterial drugs. Results: Building from our first generation of 4,5,6,7-tetrahydrobenzo[d]thiazole-based DNA gyrase inhibitors, we designed and prepared an optimized series of analogs that show improved inhibition of DNA gyrase and topoisomerase IV from Staphylococcus aureus and Escherichia coli, with IC50 values in the nanomolar range. Importantly, these inhibitors also show improved antibacterial activity against Gram-positive strains. Conclusion: The most promising inhibitor, 29, is active against Enterococcus faecalis, Enterococcus faecium and S. aureus wild-type and resistant strains, with minimum inhibitory concentrations between 4 and 8 μg/ml, which represents good starting point for development of novel antibacterials.
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16
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Watching DNA Replication Inhibitors in Action: Exploiting Time-Lapse Microfluidic Microscopy as a Tool for Target-Drug Interaction Studies in Mycobacterium. Antimicrob Agents Chemother 2019; 63:AAC.00739-19. [PMID: 31383667 PMCID: PMC6761567 DOI: 10.1128/aac.00739-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023] Open
Abstract
Spreading resistance to antibiotics and the emergence of multidrug-resistant strains have become frequent in many bacterial species, including mycobacteria, which are the causative agents of severe diseases and which have profound impacts on global health. Here, we used a system of microfluidics, fluorescence microscopy, and target-tagged fluorescent reporter strains of Mycobacterium smegmatis to perform real-time monitoring of replisome and chromosome dynamics following the addition of replication-altering drugs (novobiocin, nalidixic acid, and griselimycin) at the single-cell level. We found that novobiocin stalled replication forks and caused relaxation of the nucleoid and that nalidixic acid triggered rapid replisome collapse and compaction of the nucleoid, while griselimycin caused replisome instability, with the subsequent overinitiation of chromosome replication and overrelaxation of the nucleoid. In addition to study target-drug interactions, our system also enabled us to observe how the tested antibiotics affected the physiology of mycobacterial cells (i.e., growth, chromosome segregation, etc.).
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17
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Yi L, Lü X. New Strategy on Antimicrobial-resistance: Inhibitors of DNA Replication Enzymes. Curr Med Chem 2019; 26:1761-1787. [PMID: 29110590 DOI: 10.2174/0929867324666171106160326] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/31/2017] [Accepted: 10/30/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Antimicrobial resistance is found in all microorganisms and has become one of the biggest threats to global health. New antimicrobials with different action mechanisms are effective weapons to fight against antibiotic-resistance. OBJECTIVE This review aims to find potential drugs which can be further developed into clinic practice and provide clues for developing more effective antimicrobials. METHODS DNA replication universally exists in all living organisms and is a complicated process in which multiple enzymes are involved in. Enzymes in bacterial DNA replication of initiation and elongation phases bring abundant targets for antimicrobial development as they are conserved and indispensable. In this review, enzyme inhibitors of DNA helicase, DNA primase, topoisomerases, DNA polymerase and DNA ligase were discussed. Special attentions were paid to structures, activities and action modes of these enzyme inhibitors. RESULTS Among these enzymes, type II topoisomerase is the most validated target with abundant inhibitors. For type II topoisomerase inhibitors (excluding quinolones), NBTIs and benzimidazole urea derivatives are the most promising inhibitors because of their good antimicrobial activity and physicochemical properties. Simultaneously, DNA gyrase targeted drugs are particularly attractive in the treatment of tuberculosis as DNA gyrase is the sole type II topoisomerase in Mycobacterium tuberculosis. Relatively, exploitation of antimicrobial inhibitors of the other DNA replication enzymes are primeval, in which inhibitors of topo III are even blank so far. CONCLUSION This review demonstrates that inhibitors of DNA replication enzymes are abundant, diverse and promising, many of which can be developed into antimicrobials to deal with antibioticresistance.
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Affiliation(s)
- Lanhua Yi
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province 712100, China
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18
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Hou C, Biswas T, Tsodikov OV. Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events. Biochemistry 2018; 57:2084-2093. [PMID: 29558114 DOI: 10.1021/acs.biochem.8b00036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial primase DnaG is an essential nucleic acid polymerase that generates primers for replication of chromosomal DNA. The mechanism of DnaG remains unclear due to the paucity of structural information on DnaG in complexes with other replisome components. Here we report the first crystal structures of noncovalent DnaG-DNA complexes, obtained with the RNA polymerase domain of Mycobacterium tuberculosis DnaG and various DNA ligands. One structure, obtained with ds DNA, reveals interactions with DnaG as it slides on ds DNA and suggests how DnaG binds template for primer synthesis. In another structure, DNA in the active site of DnaG mimics the primer, providing insight into mechanisms for the nucleotide transfer and DNA translocation. In conjunction with the recent cryo-EM structure of the bacteriophage T7 replisome, this study yields a model for primer elongation and hand-off to DNA polymerase.
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Affiliation(s)
- Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , Lexington , Kentucky 40536 , United States
| | - Tapan Biswas
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , Lexington , Kentucky 40536 , United States
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19
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van Eijk E, Wittekoek B, Kuijper EJ, Smits WK. DNA replication proteins as potential targets for antimicrobials in drug-resistant bacterial pathogens. J Antimicrob Chemother 2018; 72:1275-1284. [PMID: 28073967 PMCID: PMC5400081 DOI: 10.1093/jac/dkw548] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
With the impending crisis of antimicrobial resistance, there is an urgent need to develop novel antimicrobials to combat difficult infections and MDR pathogenic microorganisms. DNA replication is essential for cell viability and is therefore an attractive target for antimicrobials. Although several antimicrobials targeting DNA replication proteins have been developed to date, gyrase/topoisomerase inhibitors are the only class widely used in the clinic. Given the numerous essential proteins in the bacterial replisome that may serve as a potential target for inhibitors and the relative paucity of suitable compounds, it is evident that antimicrobials targeting the replisome are underdeveloped so far. In this review, we report on the diversity of antimicrobial compounds targeting DNA replication and highlight some of the challenges in developing new drugs that target this process.
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20
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Reiche MA, Warner DF, Mizrahi V. Targeting DNA Replication and Repair for the Development of Novel Therapeutics against Tuberculosis. Front Mol Biosci 2017; 4:75. [PMID: 29184888 PMCID: PMC5694481 DOI: 10.3389/fmolb.2017.00075] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 10/31/2017] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), an infectious disease which results in approximately 10 million incident cases and 1.4 million deaths globally each year, making it the leading cause of mortality from infection. An effective frontline combination chemotherapy exists for TB; however, this regimen requires the administration of four drugs in a 2 month long intensive phase followed by a continuation phase of a further 4 months with two of the original drugs, and is only effective for the treatment of drug-sensitive TB. The emergence and global spread of multidrug-resistant (MDR) as well as extensively drug-resistant (XDR) strains of M. tuberculosis, and the complications posed by co-infection with the human immunodeficiency virus (HIV) and other co-morbidities such as diabetes, have prompted urgent efforts to develop shorter regimens comprising new compounds with novel mechanisms of action. This demands that researchers re-visit cellular pathways and functions that are essential to M. tuberculosis survival and replication in the host but which are inadequately represented amongst the targets of current anti-mycobacterial agents. Here, we consider the DNA replication and repair machinery as a source of new targets for anti-TB drug development. Like most bacteria, M. tuberculosis encodes a complex array of proteins which ensure faithful and accurate replication and repair of the chromosomal DNA. Many of these are essential; so, too, are enzymes in the ancillary pathways of nucleotide biosynthesis, salvage, and re-cycling, suggesting the potential to inhibit replication and repair functions at multiple stages. To this end, we provide an update on the state of chemotherapeutic inhibition of DNA synthesis and related pathways in M. tuberculosis. Given the established links between genotoxicity and mutagenesis, we also consider the potential implications of targeting DNA metabolic pathways implicated in the development of drug resistance in M. tuberculosis, an organism which is unusual in relying exclusively on de novo mutations and chromosomal rearrangements for evolution, including the acquisition of drug resistance. In that context, we conclude by discussing the feasibility of targeting mutagenic pathways in an ancillary, “anti-evolution” strategy aimed at protecting existing and future TB drugs.
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Affiliation(s)
- Michael A Reiche
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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21
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Abstract
Faithful replication and maintenance of the genome are essential to the ability of any organism to survive and propagate. For an obligate pathogen such as Mycobacterium tuberculosis that has to complete successive cycles of transmission, infection, and disease in order to retain a foothold in the human population, this requires that genome replication and maintenance must be accomplished under the metabolic, immune, and antibiotic stresses encountered during passage through variable host environments. Comparative genomic analyses have established that chromosomal mutations enable M. tuberculosis to adapt to these stresses: the emergence of drug-resistant isolates provides direct evidence of this capacity, so too the well-documented genetic diversity among M. tuberculosis lineages across geographic loci, as well as the microvariation within individual patients that is increasingly observed as whole-genome sequencing methodologies are applied to clinical samples and tuberculosis (TB) disease models. However, the precise mutagenic mechanisms responsible for M. tuberculosis evolution and adaptation are poorly understood. Here, we summarize current knowledge of the machinery responsible for DNA replication in M. tuberculosis, and discuss the potential contribution of the expanded complement of mycobacterial DNA polymerases to mutagenesis. We also consider briefly the possible role of DNA replication-in particular, its regulation and coordination with cell division-in the ability of M. tuberculosis to withstand antibacterial stresses, including host immune effectors and antibiotics, through the generation at the population level of a tolerant state, or through the formation of a subpopulation of persister bacilli-both of which might be relevant to the emergence and fixation of genetic drug resistance.
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22
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Lacriola CJ, Falk SP, Weisblum B. Inhibition of DNA replication in Staphylococcus aureus by tegaserod. J Antibiot (Tokyo) 2017; 70:918-920. [PMID: 28559577 DOI: 10.1038/ja.2017.65] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/12/2017] [Accepted: 04/13/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Christopher J Lacriola
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Shaun P Falk
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Bernard Weisblum
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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23
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Hurley KA, Santos TMA, Fensterwald MR, Rajendran M, Moore JT, Balmond EI, Blahnik BJ, Faulkner KC, Foss MH, Heinrich VA, Lammers MG, Moore LC, Reynolds GD, Shearn-Nance GP, Stearns BA, Yao ZW, Shaw JT, Weibel DB. Targeting quinolone- and aminocoumarin-resistant bacteria with new gyramide analogs that inhibit DNA gyrase. MEDCHEMCOMM 2017; 8:942-951. [PMID: 30034678 PMCID: PMC6051542 DOI: 10.1039/c7md00012j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 02/21/2017] [Indexed: 11/21/2022]
Abstract
Bacterial DNA gyrase is an essential type II topoisomerase that enables cells to overcome topological barriers encountered during replication, transcription, recombination, and repair. This enzyme is ubiquitous in bacteria and represents an important clinical target for antibacterial therapy. In this paper we report the characterization of three exciting new gyramide analogs-from a library of 183 derivatives-that are potent inhibitors of DNA gyrase and are active against clinical strains of gram-negative bacteria (Escherichia coli, Shigella flexneri, and Salmonella enterica; 3 of 10 wild-type strains tested) and gram-positive bacteria (Bacillus spp., Enterococcus spp., Staphylococcus spp., and Streptococcus spp.; all 9 of the wild-type strains tested). E. coli strains resistant to the DNA gyrase inhibitors ciprofloxacin and novobiocin display very little cross-resistance to these new gyramides. In vitro studies demonstrate that the new analogs are potent inhibitors of the DNA supercoiling activity of DNA gyrase (IC50s of 47-170 nM) but do not alter the enzyme's ATPase activity. Although mutations that confer bacterial cells resistant to these new gyramides map to the genes encoding the subunits of the DNA gyrase (gyrA and gyrB genes), overexpression of GyrA, GyrB, or GyrA and GyrB together does not suppress the inhibitory effect of the gyramides. These observations support the hypothesis that the gyramides inhibit DNA gyrase using a mechanism that is unique from other known inhibitors.
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Affiliation(s)
- Katherine A. Hurley
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Thiago M. A. Santos
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Molly R. Fensterwald
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Madhusudan Rajendran
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Jared T. Moore
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Edward I. Balmond
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Brice J. Blahnik
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Katherine C. Faulkner
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Marie H. Foss
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Victoria A. Heinrich
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Matthew G. Lammers
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Lucas C. Moore
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Gregory D. Reynolds
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
| | - Galen P. Shearn-Nance
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | | | - Zi W. Yao
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Jared T. Shaw
- Department of Chemistry
, University of California – Davis
,
Davis
, California
, USA
.
| | - Douglas B. Weibel
- Department of Biochemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
.
- Department of Chemistry
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
- Department of Biomedical Engineering
, University of Wisconsin – Madison
,
Madison
, Wisconsin
, USA
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24
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Hernandez AJ, Richardson CC. Kinetics of Lagging-strand DNA Synthesis In Vitro by the Bacteriophage T7 Replication Proteins. J Vis Exp 2017. [PMID: 28287575 DOI: 10.3791/55312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Here we provide protocols for the kinetic examination of lagging-strand DNA synthesis in vitro by the replication proteins of bacteriophage T7. The T7 replisome is one of the simplest replication systems known, composed of only four proteins, which is an attractive feature for biochemical experiments. Special emphasis is placed on the synthesis of ribonucleotide primers by the T7 primase-helicase, which are used by DNA polymerase to initiate DNA synthesis. Because the mechanisms of DNA replication are conserved across evolution, these protocols should be applicable, or useful as a conceptual springboard, to investigators using other model systems. The protocols described here are highly sensitive and an experienced investigator can perform these experiments and obtain data for analysis in about a day. The only specialized piece of equipment required is a rapid-quench flow instrument, but this piece of equipment is relatively common and available from various commercial sources. The major drawbacks of these assays, however, include the use of radioactivity and the relative low throughput.
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Affiliation(s)
- Alfredo J Hernandez
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School;
| | - Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School
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25
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Zawilak-Pawlik A, Zakrzewska-Czerwińska J. Recent Advances in Helicobacter pylori Replication: Possible Implications in Adaptation to a Pathogenic Lifestyle and Perspectives for Drug Design. Curr Top Microbiol Immunol 2017; 400:73-103. [PMID: 28124150 DOI: 10.1007/978-3-319-50520-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA replication is an important step in the life cycle of every cell that ensures the continuous flow of genetic information from one generation to the next. In all organisms, chromosome replication must be coordinated with overall cell growth. Helicobacter pylori growth strongly depends on its interaction with the host, particularly with the gastric epithelium. Moreover, H. pylori actively searches for an optimal microniche within a stomach, and it has been shown that not every microniche equally supports growth of this bacterium. We postulate that besides nutrients, H. pylori senses different, unknown signals, which presumably also affect chromosome replication to maintain H. pylori propagation at optimal ratio allowing H. pylori to establish a chronic, lifelong infection. Thus, H. pylori chromosome replication and particularly the regulation of this process might be considered important for bacterial pathogenesis. Here, we summarize our current knowledge of chromosome and plasmid replication in H. pylori and discuss the mechanisms responsible for regulating this key cellular process. The results of extensive studies conducted thus far allow us to propose common and unique traits in H. pylori chromosome replication. Interestingly, the repertoire of proteins involved in replication in H. pylori is significantly different to that in E. coli, strongly suggesting that novel factors are engaged in H. pylori chromosome replication and could represent attractive drug targets.
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Affiliation(s)
- Anna Zawilak-Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Ul. Weigla 12, 53-114, Wrocław, Poland.
| | - Jolanta Zakrzewska-Czerwińska
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Ul. Weigla 12, 53-114, Wrocław, Poland
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Ul. Joliot-Curie 14A, 50-383, Wrocław, Poland
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26
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Head BM, Rubinstein E, Meyers AFA. Alternative pre-approved and novel therapies for the treatment of anthrax. BMC Infect Dis 2016; 16:621. [PMID: 27809794 PMCID: PMC5094018 DOI: 10.1186/s12879-016-1951-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 10/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacillus anthracis, the causative agent of anthrax, is a spore forming and toxin producing rod-shaped bacterium that is classified as a category A bioterror agent. This pathogenic microbe can be transmitted to both animals and humans. Clinical presentation depends on the route of entry (direct contact, ingestion, injection or aerosolization) with symptoms ranging from isolated skin infections to more severe manifestations such as cardiac or pulmonary shock, meningitis, and death. To date, anthrax is treatable if antibiotics are administered promptly and continued for 60 days. However, if treatment is delayed or administered improperly, the patient's chances of survival are decreased drastically. In addition, antibiotics are ineffective against the harmful anthrax toxins and spores. Therefore, alternative therapeutics are essential. In this review article, we explore and discuss advances that have been made in anthrax therapy with a primary focus on alternative pre-approved and novel antibiotics as well as anti-toxin therapies. METHODS A literature search was conducted using the University of Manitoba search engine. Using this search engine allowed access to a greater variety of journals/articles that would have otherwise been restricted for general use. In order to be considered for discussion for this review, all articles must have been published later than 2009. RESULTS The alternative pre-approved antibiotics demonstrated high efficacy against B. anthracis both in vitro and in vivo. In addition, the safety profile and clinical pharmacology of these drugs were already known. Compounds that targeted underexploited bacterial processes (DNA replication, RNA synthesis, and cell division) were also very effective in combatting B. anthracis. In addition, these novel compounds prevented bacterial resistance. Targeting B. anthracis virulence, more specifically the anthrax toxins, increased the length of which treatment could be administered. CONCLUSIONS Several novel and pre-existing antibiotics, as well as toxin inhibitors, have shown increasing promise. A combination treatment that targets both bacterial growth and toxin production would be ideal and probably necessary for effectively combatting this armed bacterium.
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Affiliation(s)
- Breanne M. Head
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9 Canada
| | - Ethan Rubinstein
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9 Canada
| | - Adrienne F. A. Meyers
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9 Canada
- National Laboratory for HIV Immunology, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
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Guo J, Joubran C, Luzietti RA, Basarab GS, Grimm SW, Vishwanathan K. Absorption, distribution, metabolism and elimination of 14C-ETX0914, a novel inhibitor of bacterial type-II topoisomerases in rodents. Xenobiotica 2016; 47:31-49. [PMID: 27122100 DOI: 10.3109/00498254.2016.1156186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
1. ETX0914 is a novel bacterial topoisomerase inhibitor that has a novel mode-of-inhibition and is in clinical development for the treatment of infections caused by Neisseria gonorrhoeae. 2. The in vitro biotransformation studies of ETX0914 using mouse, rat, dog and human hepatocytes showed moderate intrinsic clearance in mouse and rat and low intrinsic clearance in dog and human. 3. Following intravenous administration of [14C]-ETX0914 in rats, the mean recovery of administered dose in urine, bile and feces was approximately 15%, 55% and 24%, respectively. Unchanged ETX0914 recovered in urine and bile was less than 5% of the dose, indicating that ETX0914 underwent extensive metabolism in rats. Metabolites M1, M2, M4, M6 and M12 detected in both rat and mouse urine samples were not detected in mouse urine when predosed with 1-aminobenzotriazole, indicating that these metabolites were cytochrome P450 mediated products. The major fecal metabolites observed in rats were not formed when ETX0914 was incubated with fresh feces from germ free rats under sterile condition or in incubations with rat intestinal microsome and cytosol, suggesting that most likely ETX0914 was directly excreted into gut lumen where metabolites were formed as intestinal microflora-mediated products. The major sites of metabolism by CYP enzymes were in the morpholine and oxazolidinone rings while it was benzisoxazole reduction with the gut microflora.
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Affiliation(s)
- Jian Guo
- a Department of DMPK AstraZeneca Pharmaceuticals , Waltham , MA , USA.,b Department of DMPK , Celgene Corporation , Bedford , MA , USA
| | - Camil Joubran
- c Department of Chemistry of Infection Innovative Medicine , AstraZeneca Pharmaceuticals , Waltham , MA , USA.,d Analytical Development, Alkermes , Waltham , MA , USA
| | - Ricardo A Luzietti
- a Department of DMPK AstraZeneca Pharmaceuticals , Waltham , MA , USA.,e Full Spectrum Analytics Inc , CA , USA
| | - Gregory S Basarab
- c Department of Chemistry of Infection Innovative Medicine , AstraZeneca Pharmaceuticals , Waltham , MA , USA.,f Department of Chemistry , Drug Discovery and Development Centre, University of Cape Town , Rondebosch , South Africa , and
| | - Scott W Grimm
- c Department of Chemistry of Infection Innovative Medicine , AstraZeneca Pharmaceuticals , Waltham , MA , USA
| | - Karthick Vishwanathan
- a Department of DMPK AstraZeneca Pharmaceuticals , Waltham , MA , USA.,g Early Clinical Development, AstraZeneca Pharmaceuticals , Waltham , MA , USA
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Cross JB, Zhang J, Yang Q, Mesleh MF, Romero JAC, Wang B, Bevan D, Poutsiaka KM, Epie F, Moy T, Daniel A, Shotwell J, Chamberlain B, Carter N, Andersen O, Barker J, Ryan MD, Metcalf CA, Silverman J, Nguyen K, Lippa B, Dolle RE. Discovery of Pyrazolopyridones as a Novel Class of Gyrase B Inhibitors Using Structure Guided Design. ACS Med Chem Lett 2016; 7:374-8. [PMID: 27096044 DOI: 10.1021/acsmedchemlett.5b00368] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 02/06/2016] [Indexed: 12/20/2022] Open
Abstract
The ATPase subunit of DNA gyrase B is an attractive antibacterial target due to high conservation across bacteria and the essential role it plays in DNA replication. A novel class of pyrazolopyridone inhibitors was discovered by optimizing a fragment screening hit scaffold using structure guided design. These inhibitors show potent Gram-positive antibacterial activity and low resistance incidence against clinically important pathogens.
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Affiliation(s)
- Jason B. Cross
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Jing Zhang
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Qingyi Yang
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Michael F. Mesleh
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | | | - Bin Wang
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Doug Bevan
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Katherine M. Poutsiaka
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Felix Epie
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Terence Moy
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Anu Daniel
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Joseph Shotwell
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Brian Chamberlain
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Nicole Carter
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Ole Andersen
- Evotec U.K., Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - John Barker
- Evotec U.K., Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - M. Dominic Ryan
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Chester A. Metcalf
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Jared Silverman
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Kien Nguyen
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Blaise Lippa
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Roland E. Dolle
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
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Choi SR, Larson MA, Hinrichs SH, Narayanasamy P. Development of potential broad spectrum antimicrobials using C2-symmetric 9-fluorenone alkyl amine. Bioorg Med Chem Lett 2016; 26:1997-9. [PMID: 26965856 DOI: 10.1016/j.bmcl.2016.02.087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/16/2016] [Accepted: 02/29/2016] [Indexed: 12/12/2022]
Abstract
DNA-dependent RNA primase is essential for de novo primer synthesis during DNA replication in all living organisms. Bacterial DnaG primase is an attractive target for inhibition because it is essential, low in copy number and structurally distinct from eukaryotic and archaeal primases. DnaG primase is sensitive to known inhibitors including suramin and doxorubicin. Recently, tilorone was discovered by high throughput screening to be an inhibitor of Bacillus anthracis primase DnaG but it failed to reduce the growth of B. anthracis in vitro. In this study we determined that tilorone also inhibited DnaG primase from Staphylococcus aureus. C2-Symmetric fluorenone-based compounds, similar to tilorone chemical structure were synthesized and tested to identify potential lead compounds that inhibit bacterial growth in B. anthracis, MRSA and Burkholderia thailandensis. These compounds were evaluated by determining the minimum inhibitory concentration (MIC) against several different bacterial species which demonstrated 17.5 and 16 μg/ml MIC profiles. Importantly, some of the fluorenone-based compounds with a long carbon chain showed a relatively low MIC against B. anthracis, S. aureus, MRSA, Francisella tularensis, and B. thailandensis, suggesting it may be a promising lead compound.
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Affiliation(s)
- Seoung-ryoung Choi
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5900, United States
| | - Marilynn A Larson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5900, United States
| | - Steven H Hinrichs
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5900, United States
| | - Prabagaran Narayanasamy
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5900, United States.
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Abstract
The development and application of a highly versatile suite of tools for mycobacterial genetics, coupled with widespread use of "omics" approaches to elucidate the structure, function, and regulation of mycobacterial proteins, has led to spectacular advances in our understanding of the metabolism and physiology of mycobacteria. In this article, we provide an update on nucleotide metabolism and DNA replication in mycobacteria, highlighting key findings from the past 10 to 15 years. In the first section, we focus on nucleotide metabolism, ranging from the biosynthesis, salvage, and interconversion of purine and pyrimidine ribonucleotides to the formation of deoxyribonucleotides. The second part of the article is devoted to DNA replication, with a focus on replication initiation and elongation, as well as DNA unwinding. We provide an overview of replication fidelity and mutation rates in mycobacteria and summarize evidence suggesting that DNA replication occurs during states of low metabolic activity, and conclude by suggesting directions for future research to address key outstanding questions. Although this article focuses primarily on observations from Mycobacterium tuberculosis, it is interspersed, where appropriate, with insights from, and comparisons with, other mycobacterial species as well as better characterized bacterial models such as Escherichia coli. Finally, a common theme underlying almost all studies of mycobacterial metabolism is the potential to identify and validate functions or pathways that can be exploited for tuberculosis drug discovery. In this context, we have specifically highlighted those processes in mycobacterial DNA replication that might satisfy this critical requirement.
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Pergolizzi G, Cominetti MMD, Butt JN, Field RA, Bowater RP, Wagner GK. Base-modified NAD and AMP derivatives and their activity against bacterial DNA ligases. Org Biomol Chem 2015; 13:6380-98. [PMID: 25974621 DOI: 10.1039/c5ob00294j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We report the chemical synthesis and conformational analysis of a collection of 2-, 6- and 8-substituted derivatives of β-NAD(+) and AMP, and their biochemical evaluation against NAD(+)-dependent DNA ligases from Escherichia coli and Mycobacterium tuberculosis. Bacterial DNA ligases are validated anti-microbial targets, and new strategies for their inhibition are therefore of considerable scientific and practical interest. Our study includes several pairs of β-NAD(+) and AMP derivatives with the same substitution pattern at the adenine base. This has enabled the first direct comparison of co-substrate and inhibitor behaviour against bacterial DNA ligases. Our results suggest that an additional substituent in position 6 or 8 of the adenine base in β-NAD(+) is detrimental for activity as either co-substrate or inhibitor. In contrast, substituents in position 2 are not only tolerated, but appear to give rise to a new mode of inhibition, which targets the conformational changes these DNA ligases undergo during catalysis. Using a molecular modelling approach, we highlight that these findings have important implications for our understanding of ligase mechanism and inhibition, and may provide a promising starting point for the rational design of a new class of inhibitors against NAD(+)-dependent DNA ligases.
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Affiliation(s)
- Giulia Pergolizzi
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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Hou Z, Zhou Y, Li J, Zhang X, Shi X, Xue X, Li Z, Ma B, Wang Y, Li M, Luo X. Selective in vivo and in vitro activities of 3,3'-4-nitrobenzylidene-bis-4-hydroxycoumarin against methicillin-resistant Staphylococcus aureus by inhibition of DNA polymerase III. Sci Rep 2015; 5:13637. [PMID: 26323712 PMCID: PMC5378903 DOI: 10.1038/srep13637] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 07/31/2015] [Indexed: 01/08/2023] Open
Abstract
As the persistent resistance of Staphylococcus aureus to available antibiotics is associated with high infection incidence, mortality rate and treatment cost, novel antibacterial agents with innovative therapeutic targets must be developed. 3,3′-(4-Nitrobenzylidene)-bis-(4-hydroxycoumarin) (NBH), a dicoumarin derivative, was reported to exert antibacterial activity. This study investigated the underlying mechanisms of in vivo and in vitro activities of NBH against S. aureus. NBH exerted bactericidal effects against the tested S. aureus and Staphylococcus epidermidis strains in vitro, with low cytotoxicity and resistance and high plasma stability. NBH also exhibited therapeutic effects in vivo on septicaemic mice. Results of molecular docking and analysis on morphological change, DNA production and polymerase inhibition suggested that DNA polymerase could be the target of NBH. These findings indicated that dicoumarin derivatives, which interfere with DNA replication, could be developed as a potential agent against S. aureus, particularly methicillin-resistant strains.
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Affiliation(s)
- Zheng Hou
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Ying Zhou
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Jing Li
- School of Chemical Engineering, Xi'an University, Xi'an, Shaanxi, 710065, China
| | - Xinlei Zhang
- School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Xin Shi
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Xiaoyan Xue
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Zhi Li
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Bo Ma
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Yukun Wang
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Mingkai Li
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Xiaoxing Luo
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
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Chiriac AI, Kloss F, Krämer J, Vuong C, Hertweck C, Sahl HG. Mode of action of closthioamide: the first member of the polythioamide class of bacterial DNA gyrase inhibitors. J Antimicrob Chemother 2015; 70:2576-88. [PMID: 26174721 DOI: 10.1093/jac/dkv161] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 05/23/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The spread of MDR bacteria represents a serious threat to human society and novel antibiotic drugs, preferably from new chemical classes, are urgently needed. Closthioamide was isolated from the strictly anaerobic bacterium Clostridium cellulolyticum and belongs to a new class of natural products, the polythioamides. Here, we investigated the antimicrobial activity and mechanism of action of closthioamide. METHODS For assessing the antimicrobial activity of closthioamide, MIC values and killing kinetics were determined. To identify its target pathway, whole-cell-based assays were used including analysis of macromolecular synthesis and recording the susceptibility profile of a library of clones with down-regulated potential target genes. Subsequently, the inhibitory effect of closthioamide on the activity of isolated target enzymes, e.g. DNA gyrase and topoisomerase IV, was evaluated. RESULTS Closthioamide had broad-spectrum activity against Gram-positive bacteria. Notably, closthioamide was very potent against MRSA and VRE strains. Closthioamide impaired DNA replication and inhibited DNA gyrase activity, in particular the ATPase function of gyrase and of topoisomerase IV, whereas there was little effect on the cleavage-rejoining function. Closthioamide also inhibited the relaxation activity of DNA gyrase, which does not require ATP hydrolysis, and thus may allosterically rather than directly interfere with the ATPase activity of gyrase. Cross-resistance to ciprofloxacin and novobiocin could not be detected in experimental mutants and clinical isolates. CONCLUSIONS Closthioamide, a member of an unprecedented class of antibiotics, is a potent inhibitor of bacterial DNA gyrase; however, its molecular mechanism differs from that of the quinolones and aminocoumarins.
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Affiliation(s)
- Alina Iulia Chiriac
- Pharmaceutical Microbiology Section, Institute for Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Florian Kloss
- Biomolecular Chemistry Department, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany
| | - Jonas Krämer
- Pharmaceutical Microbiology Section, Institute for Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Cuong Vuong
- Department of Bacteriology, AiCuris GmbH & Co. KG, Wuppertal, Germany
| | - Christian Hertweck
- Biomolecular Chemistry Department, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany
| | - Hans-Georg Sahl
- Pharmaceutical Microbiology Section, Institute for Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
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Tomašič T, Katsamakas S, Hodnik Ž, Ilaš J, Brvar M, Solmajer T, Montalvão S, Tammela P, Banjanac M, Ergović G, Anderluh M, Peterlin Mašič L, Kikelj D. Discovery of 4,5,6,7-Tetrahydrobenzo[1,2-d]thiazoles as Novel DNA Gyrase Inhibitors Targeting the ATP-Binding Site. J Med Chem 2015; 58:5501-21. [PMID: 26098163 DOI: 10.1021/acs.jmedchem.5b00489] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial DNA gyrase and topoisomerase IV are essential enzymes that control the topological state of DNA during replication and validated antibacterial drug targets. Starting from a library of marine alkaloid oroidin analogues, we identified low micromolar inhibitors of Escherichia coli DNA gyrase based on the 5,6,7,8-tetrahydroquinazoline and 4,5,6,7-tetrahydrobenzo[1,2-d]thiazole scaffolds. Structure-based optimization of the initial hits resulted in low nanomolar E. coli DNA gyrase inhibitors, some of which exhibited micromolar inhibition of E. coli topoisomerase IV and of Staphylococcus aureus homologues. Some of the compounds possessed modest antibacterial activity against Gram positive bacterial strains, while their evaluation against wild-type, impA and ΔtolC E. coli strains suggests that they are efflux pump substrates and/or do not possess the physicochemical properties necessary for cell wall penetration. Our study provides a rationale for optimization of this class of compounds toward balanced dual DNA gyrase and topoisomerase IV inhibitors with antibacterial activity.
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Affiliation(s)
- Tihomir Tomašič
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Sotirios Katsamakas
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.,‡Faculty of Health Sciences, School of Pharmacy, Department of Pharmaceutical Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Žiga Hodnik
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Matjaž Brvar
- §Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Tom Solmajer
- §Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Sofia Montalvão
- ∥Faculty of Pharmacy, Centre for Drug Research, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Päivi Tammela
- ∥Faculty of Pharmacy, Centre for Drug Research, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Mihailo Banjanac
- ⊥Galapagos Istraživački Ctr D.o.o, Prilaz Baruna Filipovića 29, HR-10000 Zagreb, Croatia
| | - Gabrijela Ergović
- ⊥Galapagos Istraživački Ctr D.o.o, Prilaz Baruna Filipovića 29, HR-10000 Zagreb, Croatia
| | - Marko Anderluh
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Danijel Kikelj
- †Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
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Chen GY, Ng FM, Tan YW, Poulsen A, Seetoh W, Lin G, Kang C, Then SW, Ahmad NH, Wong YL, Ng HQ, Chia CSB, Lau QY, Hill J, Hung AW, Keller TH. Application of Fragment-Based Drug Discovery against DNA Gyrase B. Chempluschem 2015; 80:1250-1254. [PMID: 31973307 DOI: 10.1002/cplu.201500197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 11/11/2022]
Abstract
Bacterial resistance to antibiotics remains a serious threat to global health. The gyrase B enzyme is a well-validated target for developing antibacterial drugs. Despite being an attractive target for antibiotic development, there are currently no gyrase B inhibitory drugs on the market. A fragment screen using 1,800 compounds identified 14 fragments that bind to Escherichia coli (E. coli) gyrase B. The detailed characterization of binding is described for all 14 fragments. With the aid of X-ray crystallography, modifications on a low-affinity fragment (KD =253 μM, IC50 =634 μM) has led to the development of a new class of potent phenyl aminopyrazole inhibitors against E. coli gyrase B (IC50 =160 nM). The study presented here combines the use of a set of biophysical techniques including differential scanning fluorimetry, nuclear magnetic resonance, isothermal titration calorimetry, and X-ray crystallography to methodically identify, quantify, and optimize fragments into new chemical leads.
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Affiliation(s)
- Guo-Ying Chen
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Fui Mee Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Yih Wan Tan
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Anders Poulsen
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Weiguang Seetoh
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Grace Lin
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Siew Wen Then
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Nur Huda Ahmad
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Ying Lei Wong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - C S Brian Chia
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Qiu Ying Lau
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 11 Biopolis Way, Helios #03-10/11, Singapore 138667 (Singapore)
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Boudet J, Devillier JC, Allain FHT, Lipps G. Structures to complement the archaeo-eukaryotic primases catalytic cycle description: What's next? Comput Struct Biotechnol J 2015; 13:339-51. [PMID: 25987967 PMCID: PMC4434180 DOI: 10.1016/j.csbj.2015.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/20/2015] [Accepted: 04/24/2015] [Indexed: 12/25/2022] Open
Abstract
DNA replication is a crucial stage in the transfer of genetic information from parent to daughter cells. This mechanism involves multiple proteins with one key player being the primase. Primases are single-stranded DNA dependent RNA polymerases. On the leading strand, they synthesize the primer once allowing DNA elongation while on the lagging strand primers are generated repeatedly (Okazaki fragments). Primases have the unique ability to create the first phosphodiester bond yielding a dinucleotide which is initially elongated by primases and then by DNA polymerases. Primase activity has been studied in the last decades but the detailed molecular steps explaining some unique features remain unclear. High-resolution structures of free and bound primases domains have brought significant insights in the understanding of the primase reaction cycle. Here, we give a short review of the structural work conducted in the field of archaeo-eukaryotic primases and we underline the missing “pictures” of the active forms of the enzyme which are of major interest. We organized our analysis with respect to the progression through the catalytic pathway.
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Affiliation(s)
- Julien Boudet
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
- Corresponding author. Tel.: + 41 446330723; fax: + 41 446331294.
| | - Jean-Christophe Devillier
- University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland
| | - Frédéric H.-T. Allain
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Georg Lipps
- University of Applied Sciences and Arts Northwestern Switzerland, Gründenstrasse 40, 4132 Muttenz, Switzerland
- Corresponding author. Tel.: + 41 614674301; fax: + 41 614674701.
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Identification of in vivo-induced bacterial protein antigens during calf infection with Chlamydia psittaci. Int J Med Microbiol 2015; 305:310-21. [DOI: 10.1016/j.ijmm.2014.12.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/19/2014] [Accepted: 12/20/2014] [Indexed: 01/21/2023] Open
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Surivet JP, Zumbrunn C, Rueedi G, Bur D, Bruyère T, Locher H, Ritz D, Seiler P, Kohl C, Ertel EA, Hess P, Gauvin JC, Mirre A, Kaegi V, Dos Santos M, Kraemer S, Gaertner M, Delers J, Enderlin-Paput M, Weiss M, Sube R, Hadana H, Keck W, Hubschwerlen C. Novel tetrahydropyran-based bacterial topoisomerase inhibitors with potent anti-gram positive activity and improved safety profile. J Med Chem 2014; 58:927-42. [PMID: 25494934 DOI: 10.1021/jm501590q] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Novel antibacterial drugs that are effective against infections caused by multidrug resistant pathogens are urgently needed. In a previous report, we have shown that tetrahydropyran-based inhibitors of bacterial type II topoisomerases (DNA gyrase and topoisomerase IV) display potent antibacterial activity and exhibit no target-mediated cross-resistance with fluoroquinolones. During the course of our optimization program, lead compound 5 was deprioritized due to adverse findings in cardiovascular safety studies. In the effort of mitigating these findings and optimizing further the pharmacological profile of this class of compounds, we have identified a subseries of tetrahydropyran-based molecules that are potent DNA gyrase and topoisomerase IV inhibitors and display excellent antibacterial activity against Gram positive pathogens, including clinically relevant resistant isolates. One representative of this class, compound 32d, elicited only weak inhibition of hERG K(+) channels and hNaV1.5 Na(+) channels, and no effects were observed on cardiovascular parameters in anesthetized guinea pigs. In vivo efficacy in animal infection models has been demonstrated against Staphylococcus aureus and Streptococcus pneumoniae strains.
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Affiliation(s)
- Jean-Philippe Surivet
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
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Basarab GS, Brassil P, Doig P, Galullo V, Haimes HB, Kern G, Kutschke A, McNulty J, Schuck VJA, Stone G, Gowravaram M. Novel DNA Gyrase Inhibiting Spiropyrimidinetriones with a Benzisoxazole Scaffold: SAR and in Vivo Characterization. J Med Chem 2014; 57:9078-95. [DOI: 10.1021/jm501174m] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Gregory S. Basarab
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Patrick Brassil
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Peter Doig
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Vincent Galullo
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Howard B. Haimes
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Gunther Kern
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Amy Kutschke
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - John McNulty
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Virna J. A. Schuck
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Gregory Stone
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Madhusudhan Gowravaram
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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A novel high-throughput cell-based assay aimed at identifying inhibitors of DNA metabolism in bacteria. Antimicrob Agents Chemother 2014; 58:7264-72. [PMID: 25246396 DOI: 10.1128/aac.03475-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacterial biosensor strains can be useful tools for the discovery and characterization of antibacterial compounds. A plasmid-based reporter vector containing a transcriptional fusion between the recA promoter and green fluorescence protein gene was introduced into an Escherichia coli ΔtolC strain to create a biosensor strain that selectively senses inhibitors of DNA metabolism via the SOS response. The strain was used to develop a high-throughput assay to identify new inhibitors of DNA metabolism. Screening of the AstraZeneca compound library with this strain identified known inhibitors of DNA metabolism, as well as novel chemotypes. The cellular target of one novel series was elucidated as DNA gyrase through genetic characterization of laboratory-generated resistant mutants followed by 50% inhibitory concentration measurements in a DNA gyrase activity assay. These studies validated the use of this antibiotic biosensor strain to identify novel selective inhibitors of DNA metabolism by high-throughput screening.
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Guo J, Joubran C, Luzietti RA, Zhou F, Basarab GS, Vishwanathan K. In vitro and in vivo metabolism of 14C-AZ11, a novel inhibitor of bacterial DNA gyrase/type II topoisomerase. Xenobiotica 2014; 45:158-70. [PMID: 25142218 DOI: 10.3109/00498254.2014.952799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
1. (2R,4S,4aS)-11-Fluoro-2,4-dimethyl-8-((S)-4-methyl-2-oxooxazolidin-3-yl)-2,4,4a,6-tetrahydro-1H,1'H-spiro [isoxazolo[4,5-g][1,4]oxazino[4,3-a]quinoline-5,5'-pyrimidine]-2',4',6'(3'H)-trione (AZ11) is a novel mode-of-inhibition bacterial topoisomerase inhibitor that entered preclinical development for the treatment of Gram-positive bacteria infection. 2. The in vitro biotransformation studies of AZ11 using mouse, rat, dog and human hepatocytes showed low-intrinsic clearance in all species attributed to microsomal metabolism. 3. After a single intravenous administration of [14C]AZ11 in bile duct cannulated rats, the mean percentage of dose recovered in rat urine, bile and feces was approximately 18, 36 and 42%, respectively. Unchanged AZ11 recovered in rat urine and bile was less than 9% of the dose, indicating that AZ11 underwent extensive metabolism in rats. 4. The most abundant in vivo metabolite detected in urine and bile was M1 formed via ring opening on the piperidine and morpholine rings accounting for 20% of the administered dose. The major fecal metabolite was M5, which accounted for approximately 32% of administered dose. M5 was not formed when AZ11 incubated with rat intestinal microsomes and cytosol but was formed when incubated with fresh rat feces, suggesting that unchanged AZ11 was directly excreted into gut lumen where M5 formed as an intestinal microflora-mediated product. This process could have significant impact on bioavailability or exposure of AZ11 in rat.
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Affiliation(s)
- Jian Guo
- Department of DMPK AstraZeneca Pharmaceuticals, Waltham, MA, USA
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Moriyama T, Tajima N, Sekine K, Sato N. Localization and phylogenetic analysis of enzymes related to organellar genome replication in the unicellular rhodophyte Cyanidioschyzon merolae. Genome Biol Evol 2014; 6:228-37. [PMID: 24407855 PMCID: PMC3914683 DOI: 10.1093/gbe/evu009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Plants and algae possess plastids and mitochondria harboring their own genomes, which are replicated by the apparatus consisting of DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, and primer removal enzyme. In the higher plant Arabidopsis thaliana, organellar replication-related enzymes (OREs) are similar in plastids and mitochondria because many of them are dually targeted to plastids and mitochondria. In the red algae, there is a report about a DNA replicase, plant/protist organellar DNA polymerase, which is localized to both plastids and mitochondria. However, other OREs remain unclear in algae. Here, we identified OREs possibly localized to organelles in the unicellular rhodophyte Cyanidioschyzon merolae. We then examined intracellular localization of green fluorescent protein-fusion proteins of these enzymes in C. merolae, whose cell has a single plastid and a single mitochondrion and is suitable for localization analysis, demonstrating that the plastid and the mitochondrion contain markedly different components of replication machinery. Phylogenetic analyses revealed that the organelle replication apparatus was composed of enzymes of various different origins, such as proteobacterial, cyanobacterial, and eukaryotic, in both red algae and green plants. Especially in the red alga, many enzymes of cyanobacterial origin remained. Finally, on the basis of the results of localization and phylogenetic analyses, we propose a model on the succession of OREs in eukaryotes.
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Affiliation(s)
- Takashi Moriyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan
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Shapiro AB. Complete steady-state rate equation for DNA ligase and its use for measuring product kinetic parameters of NAD⁺-dependent DNA ligase from Haemophilus influenzae. BMC Res Notes 2014; 7:287. [PMID: 24885075 PMCID: PMC4022432 DOI: 10.1186/1756-0500-7-287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 05/01/2014] [Indexed: 11/25/2022] Open
Abstract
Background DNA ligase seals the nicks in the phosphodiester backbone between Okazaki fragments during DNA replication. DNA ligase has an unusual Bi Ter Ping Pong kinetic mechanism. Its substrates in eubacteria are NAD+ and nicked DNA (nDNA). Its products are nicotinamide mononucleotide (NMN), adenosine 5′-monophosphate (AMP), and sealed DNA. Investigation of the kinetic mechanism and measurement of the kinetic constants of DNA ligase using steady-state kinetics would benefit from the availability of the complete steady-state rate equation, including terms for product concentrations and product-related kinetic constants, which has not previously been published. Results The rate equations for two possible Bi Ter kinetic mechanisms for DNA ligase, including products, are reported. The mechanisms differ according to whether the last two products, AMP and sealed DNA, are released in an ordered or rapid-equilibrium random (RER) manner. Steady-state kinetic studies of product inhibition by NMN and AMP were performed with Haemophilus influenzae NAD+-dependent DNA ligase. The complete rate equation enabled measurement of dissociation constants for NAD+, NMN, and AMP and eliminated one of 3 possible product release mechanisms. Conclusions Steady-state kinetic product inhibition experiments and complete steady-state kinetic rate equations were used to measure dissociation constants of NAD+, NMN, and AMP and eliminate the possibility that AMP is the second product released in an ordered mechanism. Determining by steady-state kinetics whether the release of sealed DNA and AMP products goes by an ordered (AMP last off) or RER mechanism was shown to require a product inhibition study using sealed DNA.
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Affiliation(s)
- Adam B Shapiro
- Biology Department, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.
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Zettler J, Xia H, Burkard N, Kulik A, Grond S, Heide L, Apel AK. New aminocoumarins from the rare actinomycete Catenulispora acidiphila DSM 44928: identification, structure elucidation, and heterologous production. Chembiochem 2014; 15:612-21. [PMID: 24554531 DOI: 10.1002/cbic.201300712] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Indexed: 11/08/2022]
Abstract
Genome mining led to the discovery of a novel aminocoumarin gene cluster in the rare actinomycete Catenulispora acidiphila DSM 44928. Sequence analysis revealed the presence of genes putatively involved in export/resistance, regulation, and biosynthesis of the aminocoumarin moiety and its halogenation, as well as several genes with so far unknown function. Two new aminocoumarins, cacibiocin A and B, were identified in the culture broth of C. acidiphila. Heterologous expression of the putative gene cluster in Streptomyces coelicolor M1152 confirmed that this cluster is responsible for cacibiocin biosynthesis. Furthermore, total production levels of cacibiocins could be increased by heterologous expression and screening of different culture media from an initial yield of 4.9 mg L(-1) in C. acidiphila to 60 mg L(-1) in S. coelicolor M1152. By HR-MS and NMR analysis, cacibiocin A was found to contain a 3-amino-4,7-dihydroxycoumarin moiety linked by an amide bond to a pyrrole-2,5-dicarboxylic acid. The latter structural motif has not been identified previously in any natural compound. Additionally, cacibiocin B contains two chlorine atoms at positions 6' and 8' of the aminocoumarin moiety.
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Affiliation(s)
- Judith Zettler
- Eberhard-Karls-Universität Tübingen, Pharmazeutische Biologie, Auf der Morgenstelle 8, 72076 Tübingen (Germany); German Centre for Infection Research (DZIF), Partner site Tübingen (Germany)
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Moriyama T, Sato N. Enzymes involved in organellar DNA replication in photosynthetic eukaryotes. FRONTIERS IN PLANT SCIENCE 2014; 5:480. [PMID: 25278952 PMCID: PMC4166229 DOI: 10.3389/fpls.2014.00480] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 08/30/2014] [Indexed: 05/18/2023]
Abstract
Plastids and mitochondria possess their own genomes. Although the replication mechanisms of these organellar genomes remain unclear in photosynthetic eukaryotes, several organelle-localized enzymes related to genome replication, including DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, primer removal enzyme, and several DNA recombination-related enzymes, have been identified. In the reference Eudicot plant Arabidopsis thaliana, the replication-related enzymes of plastids and mitochondria are similar because many of them are dual targeted to both organelles, whereas in the red alga Cyanidioschyzon merolae, plastids and mitochondria contain different replication machinery components. The enzymes involved in organellar genome replication in green plants and red algae were derived from different origins, including proteobacterial, cyanobacterial, and eukaryotic lineages. In the present review, we summarize the available data for enzymes related to organellar genome replication in green plants and red algae. In addition, based on the type and distribution of replication enzymes in photosynthetic eukaryotes, we discuss the transitional history of replication enzymes in the organelles of plants.
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Affiliation(s)
- Takashi Moriyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of TokyoTokyo, Japan
- Japan Science and Technology Agency – Core Research for Evolutional Science and TechnologyTokyo, Japan
| | - Naoki Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of TokyoTokyo, Japan
- Japan Science and Technology Agency – Core Research for Evolutional Science and TechnologyTokyo, Japan
- *Correspondence: Naoki Sato, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan e-mail:
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47
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Mayer C, Janin YL. Non-quinolone inhibitors of bacterial type IIA topoisomerases: a feat of bioisosterism. Chem Rev 2013; 114:2313-42. [PMID: 24313284 DOI: 10.1021/cr4003984] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Claudine Mayer
- Unité de Microbiologie Structurale, Département de Biologie Structurale et Chimie, Institut Pasteur , 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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Biswas T, Green KD, Garneau-Tsodikova S, Tsodikov OV. Discovery of inhibitors of Bacillus anthracis primase DnaG. Biochemistry 2013; 52:6905-10. [PMID: 24004110 DOI: 10.1021/bi4011286] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Primase DnaG is an essential bacterial enzyme that synthesizes short ribonucleotide primers required for chromosomal DNA replication. Inhibitors of DnaG can serve as leads for development of new antibacterials and biochemical probes. We recently developed a nonradioactive in vitro primase-pyrophosphatase assay to identify and analyze DnaG inhibitors. Application of this assay to DnaG from Bacillus anthracis (Ba DnaG), a dangerous pathogen, yielded several inhibitors, which include agents with DNA intercalating properties (doxorubicin and tilorone) as well as those that do not intercalate into DNA (suramin). A polyanionic agent and inhibitor of eukaryotic primases, suramin, identified by this assay as a low-micromolar Ba DnaG inhibitor, was recently shown to be also a low-micromolar inhibitor of Mycobacterium tuberculosis DnaG (Mtb DnaG). In contrast, another low-micromolar Ba DnaG inhibitor, tilorone, is much more potent against Ba DnaG than against Mtb DnaG, despite homology between these enzymes, suggesting that DnaG can be targeted selectively.
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Affiliation(s)
- Tapan Biswas
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
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Mitton-Fry MJ, Brickner SJ, Hamel JC, Brennan L, Casavant JM, Chen M, Chen T, Ding X, Driscoll J, Hardink J, Hoang T, Hua E, Huband MD, Maloney M, Marfat A, McCurdy SP, McLeod D, Plotkin M, Reilly U, Robinson S, Schafer J, Shepard RM, Smith JF, Stone GG, Subramanyam C, Yoon K, Yuan W, Zaniewski RP, Zook C. Novel quinoline derivatives as inhibitors of bacterial DNA gyrase and topoisomerase IV. Bioorg Med Chem Lett 2013; 23:2955-61. [DOI: 10.1016/j.bmcl.2013.03.047] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 01/12/2023]
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