scholarly journals Towards Conformation-Sensitive Inhibition of Gyrase: Implications of Mechanistic Insight for the Identification and Improvement of Inhibitors

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1234
Author(s):  
Dagmar Klostermeier
Keyword(s):  
Conformational Changes ◽  
Bacterial Infections ◽  
Dna Supercoiling ◽  
Full Potential ◽  
Resistance Mutations ◽  
Allosteric Inhibitors ◽  
Strand Breaks ◽  
Medical Need ◽  
Negative Supercoiling ◽  
Gyrase Inhibitors

Gyrase is a bacterial type IIA topoisomerase that catalyzes negative supercoiling of DNA. The enzyme is essential in bacteria and is a validated drug target in the treatment of bacterial infections. Inhibition of gyrase activity is achieved by competitive inhibitors that interfere with ATP- or DNA-binding, or by gyrase poisons that stabilize cleavage complexes of gyrase covalently bound to the DNA, leading to double-strand breaks and cell death. Many of the current inhibitors suffer from severe side effects, while others rapidly lose their antibiotic activity due to resistance mutations, generating an unmet medical need for novel, improved gyrase inhibitors. DNA supercoiling by gyrase is associated with a series of nucleotide- and DNA-induced conformational changes, yet the full potential of interfering with these conformational changes as a strategy to identify novel, improved gyrase inhibitors has not been explored so far. This review highlights recent insights into the mechanism of DNA supercoiling by gyrase and illustrates the implications for the identification and development of conformation-sensitive and allosteric inhibitors.

scholarly journals nifH Promoter Activity Is Regulated by DNA Supercoiling in Sinorhizobium meliloti

2005 ◽  
Vol 37 (4) ◽  
pp. 221-226 ◽  
Author(s):  
Yan-Jie Liu ◽  
Biao Hu ◽  
Jia-Bi Zhu ◽  
Shan-Jiong Shen ◽  
Guan-Qiao Yu
Keyword(s):  
Gene Expression ◽  
Promoter Activity ◽  
Sinorhizobium Meliloti ◽  
Dna Gyrase ◽  
Dna Supercoiling ◽  
Wild Type ◽  
Promoter Activation ◽  
The Status ◽  
Negative Supercoiling ◽  
Gyrase Inhibitors

AbstractIn prokaryotes, DNA supercoiling regulates the expression of many genes; for example, the expression of Klebsiella pneumoniae nifLA operon depends on DNA negative supercoiling in anaerobically grown cells, which indicates that DNA supercoiling might play a role in gene regulation of the anaerobic response. Since the expression of the nifH promoter in Sinorhizobium meliloti is not repressed by oxygen, it is proposed that the status of DNA supercoiling may not affect the expression of the nifH promoter. We tested this hypothesis by analyzing nifH promoter activity in wild-type and gyr Escherichia coli in the presence and absence of DNA gyrase inhibitors. Our results show that gene expression driven by the S. meliloti nifH promoter requires the presence of active DNA gyrase. Because DNA gyrase increases the number of negative superhelical turns in DNA in the presence of ATP, our data indicate that negative supercoiling is also important for nifH promoter activity. Our study also shows that the DNA supercoiling-dependent S. meliloti nifH promoter activity is related to the trans-acting factors NtrC and NifA that activate it. DNA supercoiling appeared to have a stronger effect on NtrC-activated nifH promoter activity than on NifA-activated promoter activity. Collectively, these results from the S. meliloti nifH promoter model system seem to indicate that, in addition to regulating gene expression during anaerobic signaling, DNA supercoiling may also provide a favorable topology for trans-acting factor binding and promoter activation regardless of oxygen status.

scholarly journals The Radio-mitigative Effect of CpG-Oligodeoxynucleotides on Mice After Exposure to Carbon Ions Radiation.

2021 ◽  
Author(s):  
Chao Zhang ◽  
Hua Fu ◽  
Xiang-hui Zhu ◽  
Sha Li ◽  
Zhong-ze Tian ◽  
...  
Keyword(s):  
Bacterial Infections ◽  
Heavy Ion ◽  
Double Strand Breaks ◽  
Tunel Staining ◽  
Cpg Odn ◽  
Carbon Ions ◽  
Strand Breaks ◽  
Cpg Oligodeoxynucleotides ◽  
Tnf Α ◽  
Immune Tissues

Abstract Background: Heavy ion radiation constitutes a major health risk for astronaut in space flight, potential damage to healthy tissues surrounding the tumor target along its penetrating path should still be considered in hydrotherapy. Therefore, there is a demand for reliable countermeasure against heavy ions radiation. In this study, we will estimate the radiomitigative effect of CpG-ODN on immune tissues after carbon ions radiation (CIR). Methods: Firstly, the 30 days’ survival of mice was observed, peripheral blood cell was counted, the injury of three principal immune tissues (including bone marrow, thymus and spleen) was evaluated by histological examination, apoptosis and double strand breaks (DSB) were detected by TUNEL staining and γ-H2AX immunohistochemistry respectively, and cytokine (G-CSF, IL-6 and TNF-α) was measured by ELISA assay. Results: the 30 days’ survival improved, the injury of three principal immune tissues were obviously ameliorated, the number of γ-H2AX foci and TUNEL-positive nuclei decreased, and G-CSF, IL-6 and TNF-α expression increased by CpG-ODN treatment after CIR. Conclusion: CpG-ODN could enhanced mice survival, and ameliorate immune tissues injury, the mechanism may be that CpG-ODN induced cytokines production and inhibited the double strand breaks (DSB) and apoptosis in order to stimulate the generation and mobilization of the immune cells and reestablish immune system to combat bacterial infections.

scholarly journals Crystal Structures of Zidovudine- or Lamivudine-Resistant Human Immunodeficiency Virus Type 1 Reverse Transcriptases Containing Mutations at Codons 41, 184, and 215

2002 ◽  
Vol 76 (19) ◽  
pp. 10015-10019 ◽  
Author(s):  
P. P. Chamberlain ◽  
J. Ren ◽  
C. E. Nichols ◽  
L. Douglas ◽  
J. Lennerstrand ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Conformational Changes ◽  
Model Building ◽  
Resistance Mutations ◽  
Reverse Transcriptases ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT Six structures of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) containing combinations of resistance mutations for zidovudine (AZT) (M41L and T215Y) or lamivudine (M184V) have been determined as inhibitor complexes. Minimal conformational changes in the polymerase or nonnucleoside RT inhibitor sites compared to the mutant RTMC (D67N, K70R, T215F, and K219N) are observed, indicating that such changes may occur only with certain combinations of mutations. Model building M41L and T215Y into HIV-1 RT-DNA and docking in ATP that is utilized in the pyrophosphorolysis reaction for AZT resistance indicates that some conformational rearrangement appears necessary in RT for ATP to interact simultaneously with the M41L and T215Y mutations.

scholarly journals Increased Survival of Antibiotic-Resistant Escherichia coli inside Macrophages

2012 ◽  
Vol 57 (1) ◽  
pp. 189-195 ◽  
Author(s):  
Migla Miskinyte ◽  
Isabel Gordo
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Bacterial Infections ◽  
Resistance Mutation ◽  
Fitness Cost ◽  
Resistance Mutations ◽  
Content Type ◽  
E Coli ◽  
Fitness Effects ◽  
K 12

ABSTRACTMutations causing antibiotic resistance usually incur a fitness cost in the absence of antibiotics. The magnitude of such costs is known to vary with the environment. Little is known about the fitness effects of antibiotic resistance mutations when bacteria confront the host's immune system. Here, we study the fitness effects of mutations in therpoB,rpsL, andgyrAgenes, which confer resistance to rifampin, streptomycin, and nalidixic acid, respectively. These antibiotics are frequently used in the treatment of bacterial infections. We measured two important fitness traits—growth rate and survival ability—of 12Escherichia coliK-12 strains, each carrying a single resistance mutation, in the presence of macrophages. Strikingly, we found that 67% of the mutants survived better than the susceptible bacteria in the intracellular niche of the phagocytic cells. In particular, allE. colistreptomycin-resistant mutants exhibited an intracellular advantage. On the other hand, 42% of the mutants incurred a high fitness cost when the bacteria were allowed to divide outside of macrophages. This study shows that single nonsynonymous changes affecting fundamental processes in the cell can contribute to prolonged survival ofE. coliin the context of an infection.

Identification of Rifampicin Resistance Mutations in Escherichia coli, Including an Unusual Deletion Mutation

2017 ◽  
Vol 27 (6) ◽  
pp. 356-362 ◽  
Author(s):  
Eugene Y. Wu ◽  
Angela K. Hilliker
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Bacterial Infections ◽  
Deletion Mutant ◽  
Deletion Mutation ◽  
Rifampicin Resistance ◽  
Clinical Settings ◽  
Resistance Mutations ◽  
Gene Encoding ◽  
Β Chain

Rifampicin is an effective antibiotic against mycobacterial and other bacterial infections, but resistance readily emerges in laboratory and clinical settings. We screened <i>Escherichia coli</i> for rifampicin resistance and identified numerous mutations to the gene encoding the β-chain of RNA polymerase (<i>rpoB</i>), including an unusual 9-nucleotide deletion mutation. Structural modeling of the deletion mutant indicates locations of potential steric clashes with rifampicin. Sequence conservation in the region near the deletion mutation suggests a similar mutation may also confer resistance during the treatment of tuberculosis.

An insight to the toxic effect of Sulfamerazine on Porcine Pancreatic Amylase and Lactate Dehydrogenase Activity: An in vitro study

2021 ◽  
Vol 15 ◽  
Author(s):  
Avirup Malla ◽  
Koel Mukherjee ◽  
Mukulika Mandal ◽  
Aishwarya Mukherjee ◽  
Runa Sur ◽  
...  
Keyword(s):  
Lactate Dehydrogenase ◽  
Lactic Acidosis ◽  
Conformational Changes ◽  
Bacterial Infections ◽  
Titration Calorimetry ◽  
Dependent Manner ◽  
Pancreatic Amylase ◽  
Lactate Dehydrogenase Activity ◽  
Tract Infections

Background: Sulfamerazine, a sulfonamide has been routinely used to treat various bacterial infections namely Pneumonia, Urinary tract infections, Shigellosis, Bronchitis, Prostatitis, and many more. It interferes with the bacterial folic acid biosynthesis albeit higher eukaryotes are not susceptible to its action due to the inherent absence of this specific pathway. Objective: In spite of its constant use, Sulfamerazine administration evokes serious issues like development of antibacterial resistance through environmental contamination although how it affects eukaryotic system, specifically its target identification has not been addressed in detail. Methods: Hela Cells are cultured as per standard method, amylase and lactate dehydrogenase assay are conducted using standard procedure with spectrophotometer. Binding thermodynamics and conformational study has been estimated with isothermal titration calorimetry as well as with docking. Results: Experimental observations reveal that Sulfamerazine inhibits porcine pancreatic amylase in a noncompetitive mode (IC50 of 0.96 mM). Binding of the drug to porcine pancreatic amylase is entropy driven with conformational changes of the protein as indicated by concomitant red shift. It enhances the inhibitory effects of acarbose and cetapin on their in vitro pancreatic amylase activity. It augments lipid peroxidation and promotes lactic acidosis in a dose dependent manner. Docking studies ensure effective interactions between Sulfamerazine and proteins like lactic dehydrogenase and porcine pancreatic amylase. Conclusion: Detailed study is to be conducted to confirm whether molecular scaffold of Sulfamerazine might serve as an effective repurposed drug acting as a lead molecule for the design of antidiabetic drug of future use. Alternatively, it should be prescribed with caution under specific medical situations like diabetes, cancer, hepatic disorders manifesting lactic acidosis to avoid crisis.

The Flu and Richard Pfeiffer

2019 ◽  
pp. 23-56
Author(s):  
Janet R. Gilsdorf
Keyword(s):  
Influenza Virus ◽  
Bacterial Meningitis ◽  
Respiratory Tract ◽  
Haemophilus Influenzae ◽  
Bacterial Infections ◽  
Scientific Understanding ◽  
Nutritional Requirements ◽  
Full Potential ◽  
Human Pathogen ◽  
Evolutionary Patterns

For decades, scientists puzzled over which influenza virus was actually responsible for the Russian pandemic. Finally, in 2014, phylogenetic techniques (examining evolutionary patterns of the virus genes) and seroarcheologic techniques (measuring antibodies likely present in people at various points in time) were applied to the question of which virus caused the Russian flu of 1889–1892. Thus, Pfeiffer’s proclamation that his bacillus caused influenza was finally proven wrong. His identification of Bacillus influenzae in the respiratory tract, however, was a major contribution to the scientific understanding of bacterial infections and moved the field of bacteriology forward in allowing other investigators to unearth its full potential as an important human pathogen. Further, in the course of his studies of B. influenzae, Pfeiffer pioneered the field of nutritional requirements of bacteria. Finally, Pfeiffer’s identification of Haemophilus influenzae launched subsequent studies of the causes of bacterial meningitis and initiated in-depth explorations of bacterial meningitis-causing pathogens that ground our concepts of pathogenesis, and guide our management, of the infection.

Gyrase inhibitors and intracellular DNA supercoiling

1986 ◽  
Vol 14 (2) ◽  
pp. 499-501 ◽  
Author(s):  
ROBERT J. FRANCO ◽  
KARL DRLICA
Keyword(s):  
Dna Supercoiling ◽  
Gyrase Inhibitors

scholarly journals Correlated protein conformational states and membrane dynamics during attack by pore-forming toxins

2019 ◽  
Vol 116 (26) ◽  
pp. 12839-12844 ◽  
Author(s):  
Ilanila I. Ponmalar ◽  
Ramesh Cheerla ◽  
K. Ganapathy Ayappa ◽  
Jaydeep K. Basu
Keyword(s):  
Conformational Changes ◽  
Pore Formation ◽  
Bacterial Infections ◽  
Cell Lysis ◽  
Membrane Dynamics ◽  
Correlation Spectroscopy ◽  
Listeriolysin O ◽  
Conformational States ◽  
Wide Range ◽  
Membrane Bound

Pore-forming toxins (PFTs) are a class of proteins implicated in a wide range of virulent bacterial infections and diseases. These toxins bind to target membranes and subsequently oligomerize to form functional pores that eventually lead to cell lysis. While the protein undergoes large conformational changes on the bilayer, the connection between intermediate oligomeric states and lipid reorganization during pore formation is largely unexplored. Cholesterol-dependent cytolysins (CDCs) are a subclass of PFTs widely implicated in food poisoning and other related infections. Using a prototypical CDC, listeriolysin O (LLO), we provide a microscopic connection between pore formation, lipid dynamics, and leakage kinetics by using a combination of Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) measurements on single giant unilamellar vesicles (GUVs). Upon exposure to LLO, two distinct populations of GUVs with widely different leakage kinetics emerge. We attribute these differences to the existence of oligomeric intermediates, sampling various membrane-bound conformational states of the protein, and their intimate coupling to lipid rearrangement and dynamics. Molecular dynamics simulations capture the influence of various membrane-bound conformational states on the lipid and cholesterol dynamics, providing molecular interpretations to the FRET and FCS experiments. Our study establishes a microscopic connection between membrane binding and conformational changes and their influence on lipid reorganization during PFT-mediated cell lysis. Additionally, our study provides insights into membrane-mediated protein interactions widely implicated in cell signaling, fusion, folding, and other biomolecular processes.

scholarly journals Mechanistic insight into the role of Poly(ADP-ribosyl)ation in DNA topology modulation and response to DNA damage

Mutagenesis ◽  
2019 ◽  
Vol 35 (1) ◽  
pp. 107-118
Author(s):  
Bakhyt T Matkarimov ◽  
Dmitry O Zharkov ◽  
Murat K Saparbaev
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Genotoxic Stress ◽  
Strand Break ◽  
Dna Supercoiling ◽  
Dna Strand Breaks ◽  
Chromosomal Dna ◽  
Dna Breaks ◽  
Strand Breaks ◽  
Dna Strand

Abstract Genotoxic stress generates single- and double-strand DNA breaks either through direct damage by reactive oxygen species or as intermediates of DNA repair. Failure to detect and repair DNA strand breaks leads to deleterious consequences such as chromosomal aberrations, genomic instability and cell death. DNA strand breaks disrupt the superhelical state of cellular DNA, which further disturbs the chromatin architecture and gene activity regulation. Proteins from the poly(ADP-ribose) polymerase (PARP) family, such as PARP1 and PARP2, use NAD+ as a substrate to catalyse the synthesis of polymeric chains consisting of ADP-ribose units covalently attached to an acceptor molecule. PARP1 and PARP2 are regarded as DNA damage sensors that, upon activation by strand breaks, poly(ADP-ribosyl)ate themselves and nuclear acceptor proteins. Noteworthy, the regularly branched structure of poly(ADP-ribose) polymer suggests that the mechanism of its synthesis may involve circular movement of PARP1 around the DNA helix, with a branching point in PAR corresponding to one complete 360° turn. We propose that PARP1 stays bound to a DNA strand break end, but rotates around the helix displaced by the growing poly(ADP-ribose) chain, and that this rotation could introduce positive supercoils into damaged chromosomal DNA. This topology modulation would enable nucleosome displacement and chromatin decondensation around the lesion site, facilitating the access of DNA repair proteins or transcription factors. PARP1-mediated DNA supercoiling can be transmitted over long distances, resulting in changes in the high-order chromatin structures. The available structures of PARP1 are consistent with the strand break-induced PAR synthesis as a driving force for PARP1 rotation around the DNA axis.

Sign in / Sign up

Export Citation Format

Share Document