Article
Biochemistry & Molecular Biology
Soziema E. E. Dauda, Jessica A. A. Collins, Jo Ann W. Byl, Yanran Lu, Jack C. C. Yalowich, Mark J. J. Mitton-Fry, Neil Osheroff
Summary: Novel bacterial topoisomerase inhibitors (NBTIs) are a new class of antibiotics that target gyrase and topoisomerase IV. NBTIs can induce gyrase/topoisomerase IV-mediated single-stranded DNA breaks and suppress the generation of double-stranded breaks. However, some dioxane-linked amide NBTIs have been found to induce double-stranded DNA breaks mediated by Staphylococcus aureus gyrase. The compound OSUAB-185 induces single-stranded and suppressed double-stranded DNA breaks mediated by Neisseria gonorrhoeae gyrase, while stabilizing both single- and double-stranded DNA breaks mediated by topoisomerase IV.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Corbin J. England, Tanner C. Gray, Shubha R. L. Malla, Samantha A. Oliveira, Benjamin R. Martin, Gary W. Beall, L. Kevin Lewis
Summary: The precipitation of double-stranded DNA by group 2 metals at high pH levels was effective, particularly with calcium, leading to the retention of DNA structural integrity in the precipitates formed. Neutralization of negative surface charges and cation bridging were proposed as mechanisms for this process.
ANALYTICAL BIOCHEMISTRY
(2021)
Review
Polymer Science
Jiafu Shen, Yu Dai, Fan Xia, Xiaojin Zhang
Summary: This article reviews the synthesis and theoretical simulation of M2 +-hydrogels, the effect of M2 + on hydrogels, and their applications in energy storage, sensing, biomedicine, resource utilization, and environmental remediation. The challenges of M2 +-hydrogels are also discussed.
PROGRESS IN POLYMER SCIENCE
(2022)
Review
Geriatrics & Gerontology
Morgan Crewe, Ram Madabhushi
Summary: The nervous system is susceptible to genomic instability and mutations in DNA damage response factors can lead to neurological disorders. The main sources and mechanisms of DNA damage relevant to neuronal dysfunction are not well understood. Topoisomerase-mediated DNA damage may be a significant underlying source of neuronal dysfunction.
FRONTIERS IN AGING NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Zhi-Yuan Feng, Yang-Fang Yun, Xiang Li, Jingjing Zhang
Summary: CRISPR-LbuCas13a is a revolutionary tool for in vitro diagnosis, requiring Mg2+ for its nuclease activity. Experimental results showed that both Mn2+ and Ca2+ can replace Mg2+ as cofactors of LbuCas13a, while Ni2+, Zn2+, Cu2+, or Fe2+ inhibit its cleavage activity and Pb2+ has no significant effect.
Article
Multidisciplinary Sciences
Arnaud Vanden Broeck, Christophe Lotz, Robert Drillien, Lea Haas, Claire Bedez, Valerie Lamour
Summary: Human type IIA topoisomerases play a crucial role in regulating DNA topology and chromosome organization. The isoform Topo II alpha is a key target for anti-cancer compounds, forming ternary cleavage complexes with DNA. This study provides cryo-EM structures of the entire Topo II alpha nucleoprotein complex, shedding light on the allosteric connections between different domains and the role of the non-conserved C-terminal domain in regulating enzyme activities.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Medicinal
Martina Durcik, Akos Nyerges, Ziga Skok, Darja Gramec Skledar, Jurij Trontelj, Nace Zidar, Janez Ilas, Anamarija Zega, Cristina D. Cruz, Paivi Tammela, Martin Welin, Yengo R. Kimbung, Dorota Focht, Ondrej Benek, Tamas Revesz, Gabor Draskovits, Petra Eva Szili, Lejla Daruka, Csaba Pal, Danijel Kikelj, Lucija Peterlin Masic, Tihomir Tomasic
Summary: The rise in multidrug-resistant bacteria highlights the need for new antibacterial agents less prone to resistance. Compounds simultaneously inhibiting multiple bacterial targets, like 31h, show promising antibacterial activities without cytotoxicity and potency against various pathogens, including those resistant to other drugs. The structural derivatives of 31h could represent a step towards clinically efficacious multitargeting antimicrobials resilient to existing antimicrobial resistance.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Abdul Malik P. Peedikakkal, Isam H. Aljundi
Summary: This study prepared mixed metal metal-organic frameworks M-MOF-5 using the post-synthetic exchange technique and found that Ni-MOF-5 and Co-MOF-5 demonstrated higher hydrogen uptake capacities compared to the parent MOF-5. The Fe-MOF-5 exhibited decreased uptake due to the formation of discrete complexes with less crystalline nature. The Sips model was effective in describing the hydrogen adsorption isotherms in this study, with Ni- and Co-MOF-5 showing unique hydrogen uptakes, paving the way for further improvement in hydrogen uptake.
APPLIED SCIENCES-BASEL
(2021)
Article
Chemistry, Physical
Arepati Azhati, Lu Han, Zhibei Qu, Zhouhong Ren, Xi Liu, Liwei Chen, Shunai Che
Summary: The self-assembly of DNA plays a significant role in understanding structural formation in living organisms and materials chemistry. This study investigates the impact of metal ions on the chiral self-assembly of DNA and discovers that certain metal ions induce the formation of chiral DNA complexes. The study also explores the interaction between metal ions and DNA, providing insights into the mechanism of chiral stacking.
Article
Engineering, Environmental
J. Tapiador, E. Garcia-Rojas, P. Lopez-Paton, Guillermo Calleja, Gisela Orcajo, Carmen Martos, Pedro Leo
Summary: The concentration of carbon dioxide has reached unprecedented levels. The valorization of CO2 into high value-added chemicals can stabilize the concentration of this atmospheric pollutant. The influence of metal in the catalytic reaction is key, with Zn-MOF-74 showing the highest catalytic activity and selectivity values above 93% regardless of the epoxides studied.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2023)
Article
Chemistry, Analytical
Evangelos Skotadis, Evangelos Aslanidis, Georgios Tsekenis, Chryssi Panagopoulou, Annita Rapesi, Georgia Tzourmana, Stella Kennou, Spyridon Ladas, Angelos Zeniou, Dimitris Tsoukalas
Summary: A hybrid noble nanoparticle/DNAzyme electrochemical biosensor is developed for the detection of Pb2+, Cd2+, and Cr3+. This sensor combines the selective interaction of DNAzymes with heavy metal ions and metallic nanoparticles. The sensor shows promising results for the detection of all three target ions in concentrations below their maximum permitted levels in tap water. It has great potential for integration in autonomous and remote sensing systems due to its low power, simple fabrication, and easy automation.
Article
Chemistry, Multidisciplinary
Yajie Wang, Feihong Meng, Tong Lu, Chunyun Wang, Fei Li
Summary: This study reveals the significant role of divalent metal ions in the aggregation and cytotoxicity of hIAPP, with metal-associated hIAPP oligomers showing reduced ability to damage lipid membranes. The interaction between metal ions and hIAPP oligomers can affect the extent of membrane damage, depending on the peptide-to-metal ratio. Additionally, the abundance of oligomer species with altered disruptive ability can influence the membrane damage caused by hIAPP oligomers.
Review
Chemistry, Medicinal
Scott Grossman, Colin W. G. Fishwick, Martin J. McPhillie
Summary: Increases in antibiotic usage have led to antimicrobial resistance and reduced effectiveness of antimicrobial treatments. Researchers have been looking for new bioactive molecules to inhibit bacterial topoisomerases through non-intercalating agents and alternative mechanisms, such as allosteric site inhibitors and ATPase domain inhibitors, to overcome bacterial resistance to fluoroquinolones.
Review
Biochemistry & Molecular Biology
Vita Vidmar, Marlene Vayssieres, Valerie Lamour
Summary: DNA topoisomerases play a crucial role in resolving topological problems in DNA. They can recognize DNA topology and catalyze various reactions by cutting and rejoining DNA. While the mechanisms of DNA cleavage and re-ligation have been extensively studied, the structural rearrangements required for DNA-gate opening and strand transfer, especially in type IA topoisomerases, remain unclear.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Shantanu Aggarwal, Sayan Mondal, Soumik Siddhanta, Engleng Bharat, Easa Nagamalleswari, Valakunja Nagaraja, Chandrabhas Narayana
Summary: The study demonstrates the remarkable ability of SERS in tracking the conformational changes in enzyme induced by metal ions. The combination of SERS and MD simulations revealed the role of Ca2+ ions in activating an enzymatic switch in endonuclease activity.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Review
Biochemistry & Molecular Biology
Shannon J. McKie, Keir C. Neuman, Anthony Maxwell
Summary: DNA topoisomerases are essential for cellular survival, playing numerous roles in DNA metabolism. Structural approaches and single-molecule techniques have provided new insights into their interaction and mechanism, while the importance of interactions with other proteins has been highlighted. Novel topoisomerases like topo VIII and Mini-A are expanding our understanding of DNA processes and the vital functions they perform.
Article
Multidisciplinary Sciences
Anja Kolaric, Thomas Germe, Martina Hrast, Clare E. M. Stevenson, David M. Lawson, Nicolas P. Burton, Judit Voros, Anthony Maxwell, Nikola Minovski, Marko Anderluh
Summary: The researchers designed a series of novel NBTIs with improved DNA gyrase-binding moieties, demonstrating their ability to stabilize single-strand cleavage complexes through asymmetric intercalation. Experimental evidence was provided to confirm the previously postulated mechanism of action.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Lipeng Feng, Julia E. A. Mundy, Clare E. M. Stevenson, Lesley A. Mitchenall, David M. Lawson, Kaixia Mi, Anthony Maxwell
Summary: The research demonstrates that MfpA in Mycobacterium smegmatis modulates the activity of gyrase by interacting with the enzyme, protecting it from the effects of drugs. This provides a reference for understanding the mechanism of action of other pentapeptide-repeat proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Analytical
Hak-Sung Jung, Junsang Cho, Keir C. Neuman
Summary: Latent fingerprints are crucial evidence in crime scenes, and an efficient method for detecting them is important in forensic science. This study introduces a new method using stable CsPbBr3 perovskite nanocrystals to develop latent fingerprints on diverse surfaces, providing high resolution images with unique friction ridge arrangements.
ANALYTICA CHIMICA ACTA
(2021)
Editorial Material
Chemistry, Medicinal
Kyle M Orritt, Anthony Maxwell, Colin WG Fishwick, Martin J McPhillie
FUTURE MEDICINAL CHEMISTRY
(2021)
Article
Microbiology
Harriet C. C. Gooch, Raymond Kiu, Steven Rudder, David J. Baker, Lindsay J. Hall, Anthony Maxwell
Summary: Four bacterial strains isolated from the wax moth Galleria mellonella were characterized as a potential new species Enterococcus innesii, through a polyphasic approach including 16S rRNA gene sequence analysis, core-genome analysis, and various phenotypic analyses. The strains showed close relation to Enterococcus casseliflavus and Enterococcus gallinarum, but further analysis revealed distinct genomic characteristics and low similarity with the closest phylogenetic relative, leading to the proposal of a new species designation.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ganesh Shenoy, Jessica Ettedgui, Chandrasekhar Mushti, Jennifer Hong, Kelly Lane, Burchelle Blackman, Hak-Sung Jung, Yasuharu Takagi, Yeonee Seol, Martin Brechbiel, Rolf E. Swenson, Keir C. Neuman
Summary: This article presents a method to enrich the carboxylic acid content on the surface of fluorescent nanodiamonds (FNDs). The method involves reducing oxygen-containing surface groups to alcohols and then converting them to carboxylic acids through a catalyzed reaction. This enrichment process improves the uniformity and functionalization efficiency of the nanodiamonds.
Article
Multidisciplinary Sciences
Gabor M. Harami, Janos Palinkas, Yeonee SeoI, Zoltan J. Kovacs, Mate Gyimesi, Hajnalka Harami-Papp, Keir C. Neuman, Mihaly Kovacs
Summary: In this study, the researchers found that human Bloom's syndrome helicase plays a role in the processing of displacement loops during DNA repair, depending on cellular regulatory mechanisms. In the presence of interaction partners Topoisomerase III alpha-RMI1-RMI2, the helicase's activity shifts towards efficient disruption of displacement loops, aiding genome stability and faithful inheritance.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Shannon J. McKie, Parth Rakesh Desai, Yeonee Seol, Adam M. B. Allen, Anthony Maxwell, Keir C. Neuman
Summary: DNA topoisomerase VI (topo VI) is a type IIB DNA topoisomerase predominantly found in archaea and some bacteria, as well as plants and algae. It has been discovered that topo VI preferentially decatenates DNA crossings by having a preference for certain DNA crossing geometries. Additionally, topo VI exhibits increased ATPase activity, DNA binding, and rate of strand passage with increasing DNA writhe, providing further evidence that it acts as a DNA crossing sensor. The study suggests that topo VI has evolved an intrinsic preference for the unknotting and decatenation of interlinked chromosomes by sensing and preferentially unlinking DNA crossings with geometries close to 90 degrees.
Editorial Material
Biochemistry & Molecular Biology
Gabor M. Harami, Keir C. Neuman
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Masa Sterle, Martina Durcik, Clare E. M. Stevenson, Sara R. Henderson, Petra Eva Szili, Marton Czikkely, David M. Lawson, Anthony Maxwell, Dominique Cahard, Danijel Kikelj, Nace Zidar, Csaba Pal, Lucija Peterlin Masic, Janez Ilas, Tihomir Tomasic, Andrej Emanuel Cotman, Anamarija Zega
Summary: We have developed a new series of DNA gyraseB inhibitors based on 2-aminobenzothiazole, showing promising activity against ESKAPE bacterial pathogens. The chemical space of the benzothiazole-based series was expanded to the C5 position of the benzothiazole ring, resulting in compound E with low nanomolar inhibition of DNA gyrase and broad-spectrum antibacterial activity. Computational analysis revealed that substitution at position C5 can enhance the inhibitory potency of the compounds and modify their physicochemical properties.
Article
Biochemistry & Molecular Biology
Kyle M. Orritt, Lipeng Feng, Juliette F. Newell, Jack N. Sutton, Scott Grossman, Thomas Germe, Lauren R. Abbott, Holly L. Jackson, Benjamin K. L. Bury, Anthony Maxwell, Martin J. McPhillie, Colin W. G. Fishwick
Summary: By 2050, antimicrobial resistance is likely to cause 10 million global deaths annually, resulting in a massive economic burden. However, the discovery of a new medicinal chemistry strategy targeting a different binding site on DNA gyrase may provide a way to overcome this problem. Through computer-based molecular design methods, a series of novel compounds were synthesized and evaluated for their activity. The reported structure-activity relationships offer important insights for further exploration of this new binding site.
RSC MEDICINAL CHEMISTRY
(2022)
Meeting Abstract
Biophysics
Joseph H. Chapman, Keir C. Neuman, J. R. Hogg
BIOPHYSICAL JOURNAL
(2022)