Article
Infectious Diseases
Daniel Golparian, Susanne Jacobsson, Leonor Sanchez-Buso, Maria Luiza Bazzo, Pham Thi Lan, Patricia Galarza, Makoto Ohnishi, Magnus Unemo
Summary: This study investigated the susceptibility to a novel antimicrobial zoliflodacin for the treatment of Neisseria gonorrhoeae and found a very low occurrence of drug-resistant mutations.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Multidisciplinary Sciences
Su Jin Lee, Jueng Soo You, Amal Gharbi, Yong Joo Kim, Mi Suk Lee, Dong Hwan Kim, Keun Woo Lee, In Duk Jung, Yeong Min Park
Summary: The study shows that lysine demethylase (Kdm) plays a key role in sepsis regulation, while 8-hydroxyquinoline-5-carboxylic acid (IOX1) has a significant impact on controlling endotoxemia and bacterial sepsis, as well as suppressing multidrug-resistant bacterial growth through the inhibition of DNA Gyrase.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Angela K. Talley, Archie Thurston, Grayson Moore, Vipul K. Gupta, Myriah Satterfield, Erika Manyak, Suzanne Stokes, Aaron Dane, David Melnick
Summary: SPR720, a novel bacterial DNA gyrase inhibitor, has shown promise in treating nontuberculous mycobacterial pulmonary disease and pulmonary tuberculosis. Clinical trial results demonstrate good tolerability of SPR720 at daily doses up to 1,000 mg for 14 days, with common adverse events being gastrointestinal discomfort and headache, and stable pharmacokinetic profile.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Pharmacology & Pharmacy
Martina Durcik, Ziga Skok, Janez Ilas, Nace Zidar, Anamarija Zega, Petra Eva Szili, Gabor Draskovits, Tamas Revesz, Danijel Kikelj, Akos Nyerges, Csaba Pal, Lucija Peterlin Masic, Tihomir Tomasic
Summary: The discovery of multi-targeting ligands for bacterial enzymes is crucial in combating antimicrobial resistance. The designed hybrids effectively inhibit DNA gyrase and show antibacterial activity against Gram-negative pathogens, providing a promising therapeutic strategy.
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
Microbiology
Uday S. Ganapathy, Ruben Gonzalez Del Rio, Monica Cacho-Izquierdo, Fatima Ortega, Joel Lelievre, David Barros-Aguirre, Wassihun Wedajo Aragaw, Matthew D. Zimmerman, Marissa Lindman, Veronique Dartois, Martin Gengenbacher, Thomas Dick
Summary: Fluoroquinolones are effective against tuberculosis but have limited clinical use for nontuberculous mycobacteria infections due to drug resistance. Researchers tested alternative DNA gyrase inhibitors and found that the MGI EC/11716 not only works against mycobacterium tuberculosis, but also M. abscessus and M. avium. The study showed that EC/11716 is bactericidal against M. abscessus, effective against drug-tolerant biofilms, and successful in a mouse model of M. abscessus lung infection.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Chemistry, Physical
Meredith M. Rickard, Haolin Luo, Ashley De Lio, Martin Gruebele, Taras V. Pogorelov
Summary: The cytoplasm affects the conformation of ATP, with ATP molecules bound to proteins in cells forming specific pitched conformations. These interactions may play functional roles when ATP interacts with protein surfaces.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Padmaja D. Wakchaure, Bishwajit Ganguly
Summary: The FMN riboswitch is a potential drug target for new antibiotics, and the neutral ligand 5FDQD has shown activity against Clostridium difficile infection. Computational simulations revealed that the fluorine atom on the phenyl ring in 5FDQD plays a crucial role in enhancing its binding affinity with the FMN riboswitch.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Microbiology
Aiko Masuko, Iichiro Takata, Kiyoko Fujita, Hirotoshi Okumura, Fumihito Ushiyama, Hideaki Amada, Hiroyuki Sugiyama
Summary: The novel DNA gyrase/topoisomerase IV inhibitor TP0480066 showed potent in vitro and in vivo activities against multidrug-resistant Neisseria gonorrhoeae strains, with no cross-resistance observed with ciprofloxacin. It also demonstrated low frequencies of spontaneous resistance and strong bactericidal activity, suggesting it may be a candidate antimicrobial agent for gonococcal infections.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Chemistry, Multidisciplinary
Jiahui Wu, Nina Svensen, Wenjiao Song, Hyaeyeong Kim, Sulei Zhang, Xing Li, Samie R. Jaffrey
Summary: DNA and RNA can self-assemble into various structures, and there are methods available to achieve RNA self-assembly in cells. The use of dimeric aptamers allows the creation of RNA and RNA-protein assemblies in cells. These studies provide an approach for inducing RNA self-assembly, demonstrate that proteins can be recruited to RNA assemblies to genetically encode intracellular RNA-protein assemblies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Zhan-Yun Zhang, Ding Peng, Lihong Liu, Lin Shen, Wei -Hai Fang
Summary: We propose machine learning models that can predict experimental hydration free energies of molecules without requiring any specific atom, bond, or geometry features as input. Four different types of physically inspired descriptors are used for the predictions. The models, based on the FreeSolv database with around 600 samples, outperform most traditional approaches and other prediction methods using molecular fingerprints. These models are also capable of predicting hydration free energies for new compounds with elements or fragments not seen in the training set. The importance of the descriptors, the impact of dissociation energies of specific covalent bonds, and the presence of outliers with large prediction errors are discussed.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Pier Paolo Poier, Theo Jaffrelot Inizan, Olivier Adjoua, Louis Lagardere, Jean-Philip Piquemal
Summary: Using a deep neuronal network (DNN) model trained on a large data set, researchers propose a transferable density-free many-body dispersion (DNN-MBD) model. The DNN-MBD model bypasses explicit density partitioning and achieves comparable accuracy to other approaches. It reduces computational cost and can be coupled with other models for large-scale calculations.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
E. Duboue-Dijon, J. Henin
Summary: The theory behind computation of absolute binding free energies using explicit-solvent molecular simulations is complex, with counter-intuitive aspects. The role of symmetry and symmetry number corrections are discussed, highlighting potential misconceptions. It is established that partial or missing sampling of symmetric bound states does not affect the calculated decoupling free energies.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Infectious Diseases
Magnus Unemo, Josefine Ahlstrand, Leonor Sanchez-Buso, Michaela Day, David Aanensen, Daniel Golparian, Susanne Jacobsson, Michelle J. Cole
Summary: The study demonstrates the high in vitro susceptibility of zoliflodacin to Neisseria gonorrhoeae isolates in the EU/EEA in 2018, with the target GyrB being highly conserved. Zoliflodacin shows good antimicrobial activity without cross-resistance to other tested antimicrobials.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Article
Chemistry, Multidisciplinary
Zheng Yuan, Dapeng Zhang, Fangzhi Yu, Yangde Ma, Yan Liu, Xiangjun Li, Hailin Wang
Summary: This study demonstrates a new supernuclease's capability for highly efficient cutting of DNA segments, leading to the development of a method that allows precise sequencing of single protected-DNA fragment molecules, and the direct measurement of RecA filament length. This innovative assay shows promise as an analytical tool for studying various protein-DNA interactions involved in DNA replication, transcription, recombination, repair, and gene editing.
Article
Environmental Sciences
Xiaoping Li, Yu Gao, Meng Zhang, Yu Zhang, Ming Zhou, Liyuan Peng, Ana He, Xu Zhang, Xiangyang Yan, Yanhua Wang, Hongtao Yu
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2020)
Article
Environmental Sciences
Xiaoping Li, Yu Zhang, Ting Wu, Xuemeng Sun, Tao Yang, Lijun Wang, Xiaoyu Li, Jingzhi Wang, Yanhua Wang, Hongtao Yu
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Hui Li, Xiaobao Ying, Lina Shang, Bryce Redfern, Nicholas Kypraios, Xuejun Xie, FeiFei Xu, Shaopeng Wang, Jinghua Zhang, Hongju Jian, Hongtao Yu, Dianqiu Lv
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Environmental Sciences
Ana He, Xiaoping Li, Yuwei Ai, Xiaolong Li, Xiaoyun Li, Yuchao Zhang, Yu Gao, Bin Liu, Xu Zhang, Meng Zhang, Liyuan Peng, Ming Zhou, Hongtao Yu
ENVIRONMENT INTERNATIONAL
(2020)
Correction
Multidisciplinary Sciences
Jinseo Park, Ziao Fu, Aurel Frangaj, Jonathan Liu, Lidia Mosyak, Tong Shen, Vesna N. Slavkovich, Kimberly M. Ray, Jaume Taura, Baohua Cao, Yong Geng, Hao Zuo, Yongjun Kou, Robert Grassucci, Shaoxia Chen, Zheng Liu, Xin Lin, Justin P. Williams, William J. Rice, Edward T. Eng, Rick K. Huang, Rajesh K. Soni, Brian Kloss, Zhiheng Yu, Jonathan A. Javitch, Wayne A. Hendrickson, Paul A. Slesinger, Matthias Quick, Joseph Graziano, Hongtao Yu, Oliver Fiehn, Oliver B. Clarke, Joachim Frank, Qing R. Fan
Article
Chemistry, Multidisciplinary
Tongtong Wang, Weibo Gong, Xin He, Zuhao Kou, Gang Tan, Shaojun Zhou, Hongtao Yu, Maohong Fan, Harold H. Kung
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2020)
Review
Biochemistry & Molecular Biology
Yoori Kim, Hongtao Yu
EXPERIMENTAL AND MOLECULAR MEDICINE
(2020)
Review
Oncology
Xiaoyan Chen, Angela Winstead, Hongtao Yu, Jiangnan Peng
Summary: Taccalonolides are a new class of microtubule stabilizers derived from plants of the Tacca genus, showing effectiveness against drug-resistant tumors. Through structural modification via semi-synthesis, their anti-proliferation potency can be significantly increased. The unique mechanism of covalently binding to microtubules and resistance circumvention mechanisms make taccalonolides a promising area of research in cancer therapy.
Article
Environmental Sciences
Yuhan Cao, Xiaoping Li, Feng He, Xuemeng Sun, Xu Zhang, Tao Yang, Jie Dong, Yu Gao, Qishang Zhou, Danqian Shi, Jiwen Wang, Hongtao Yu
Summary: A study on the status of toxic metals in the soil-dust-plant total environment of a Coal-Gas industrial city in NW China found that different toxic metals exhibited varied occurrences in different media, with coal combustion and industrial activities identified as the most significant sources of risk.
Article
Environmental Sciences
Xiaoping Li, Xiangyang Yan, Ting Wu, Xu Zhang, Hongtao Yu
Summary: The study revealed that fine fractions of <1 micron in contaminated soil accumulated more PTMs, with higher mobility and bioaccessibility. It is suggested that further environmental management is necessary to prevent the risk of PTMs from Pb-bearing micro-nano size fractions in industrial contaminated soil.
Article
Water Resources
Xiaoping Li, Hameed Ullah, Xuemeng Sun, Xiangyang Yan, Jie Dong, Yu Gao, Yuhan Cao, Tao Li, Hongtao Yu
Summary: This study investigates the spatial distribution, pollution status, and health risks of potentially toxic metals (PTMs) in urban soil, street dust, and plants in Lanzhou, China. The findings reveal that priority metals from traffic sources show similar transfer trends among soil-dust-plant environments, and coal combustion and industrial emissions are important sources of metals. The study highlights the high carcinogenic risk of toxic metals for children, emphasizing the need for attention to lead contamination and monitoring of children aged 0-6 years old.
EXPOSURE AND HEALTH
(2022)
Article
Cell Biology
Haishan Gao, Faxiang Li, Zhejian Ji, Zhubing Shi, Yang Li, Hongtao Yu
Summary: The conserved ATPase p97/Cdc48 mediates cellular processes by unfolding polyubiquitinated proteins. Recent studies have found that p97/Cdc48 can form double hexamers with ordered pore loops, facilitating substrate unfolding and engagement.
Article
Chemistry, Multidisciplinary
Xiaoyan Chen, Hua Deng, Janai A. Heise, David P. Puthoff, Nabeel Bou-Abboud, Hongtao Yu, Jiangnan Peng
Summary: With the increasing interest in medicinal use and the legalization of cannabis, the cannabis marketplace and farming industry have experienced tremendous growth. A high-performance liquid chromatography (HPLC) method was developed and validated to analyze 104 hemp bud materials from 20 varieties in Maryland, comparing and discussing the THC content in different varieties to identify those with high yield and consistency for cannabinoid production.
Article
Cell Biology
Kai Ma, Man Luo, Guanglei Xie, Xi Wang, Qilin Li, Lei Gao, Hongtao Yu, Xiaochun Yu
Summary: This study reveals that noncoding RNAs, specifically rRNA species, associate with and play an important role in mitotic chromosomes. The proteins Ki-67 and its FHA domain and repeat region are responsible for recognizing and anchoring rRNAs to the chromosomes. Inhibition of chromosome-bound rRNAs impairs mitotic chromosome dispersion.
Article
Geochemistry & Geophysics
Ming Zhou, Xiaoping Li, Meng Zhang, Bin Liu, Yuchao Zhang, Yu Gao, Hameed Ullah, Liyuan Peng, Ana He, Hongtao Yu
JOURNAL OF GEOCHEMICAL EXPLORATION
(2020)