Review
Biochemistry & Molecular Biology
Sian Thistlethwaite, Laura N. Jeffreys, Hazel M. Girvan, Kirsty J. McLean, Andrew W. Munro
Summary: BM3 is a catalytically self-sufficient flavocytochrome fusion protein that can be engineered to produce a variety of drug-like compounds. Through modification of key residues within the BM3 active site, its catalytic repertoire can be expanded to generate diverse metabolites.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Environmental Sciences
Dayse Carvalho da Silva Martins, Iasmin Tavares Resende, Bruno Jose Rocha da Silva
Summary: Pesticides are potentially toxic to target organisms and harmful to human health and the environment. Various degradation processes have been studied, but there are still gaps. This review focuses on the catalytic degradation of pesticides using porphyrins, which have been shown to be effective catalysts for degradation and a useful tool for studying degradation products. However, achieving complete mineralization of pesticides without intermediate products remains challenging.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jiang Zhu, Ruinan Qu, Yawei Wang, Ruoyao Ni, Kai Tian, Chan Yang, Mei Li, Michael Kristensen, Xinghui Qiu
Summary: Many insect species have developed various resistance mechanisms in response to insecticide selection. This study focuses on understanding the molecular mechanisms of P450-mediated insecticide resistance using the house fly. The results highlight the common involvement of the CncC pathway in adaptive evolution and provide evidence for parallel evolution in P450-mediated insecticide resistance.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Pharmacology & Pharmacy
Sara N. Salerno, Andrea Edginton, Jacqueline G. Gerhart, Matthew M. Laughon, Namasivayam Ambalavanan, Gregory M. Sokol, Chi D. Hornik, Dan Stewart, Mary Mills, Karen Martz, Daniel Gonzalez
Summary: This study utilized PBPK modeling to investigate the impact of sildenafil and fluconazole on pediatric pharmacokinetics, finding that reducing sildenafil dosage can mitigate DDIs in infants.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2021)
Article
Pharmacology & Pharmacy
Alexander V. Dmitriev, Anastassia V. Rudik, Dmitry A. Karasev, Pavel V. Pogodin, Alexey A. Lagunin, Dmitry A. Filimonov, Vladimir V. Poroikov
Summary: This study aimed to create a computer model for predicting drug-drug interactions mediated by seven important P450 cytochromes. Using 2500 records as a training set, structure-activity relationship models were developed using PASS software and PoSMNA descriptors to predict metabolism-mediated DDIs between molecules. The average accuracy of the predictions was around 0.92, and the SAR models are publicly available for predicting DDIs mediated by the most important cytochrome P450 enzymes.
Article
Chemistry, Medicinal
Yanjun Feng, Changda Gong, Jieyu Zhu, Guixia Liu, Yun Tang, Weihua Li
Summary: CYP3A4 is a major drug-metabolizing enzyme in the human body, responsible for metabolizing approximately 50% of clinically used drugs. This study used docking-based approaches with geometric features to predict the sites of metabolism for CYP3A4 substrates. Analysis of a large dataset of 474 substrates revealed a widely observed geometric pattern called the close proximity of sites of metabolism. Several structure-based models were constructed based on this pattern, demonstrating better performance than models based on Fe-SOM distance. To further improve prediction performance, the structure-based models were combined with the ligand-based model SMARTCyp, resulting in one combined model that showed good performance on an external substrate set.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Toxicology
Yisheng He, Wei Lian, Liang Ding, Xiaoyu Fan, Jiang Ma, Qing-Yu Zhang, Xinxin Ding, Ge Lin
Summary: This study revealed the essential role of hepatic P450 enzymes in the bioactivation of PAs and the subsequent lung injury caused by circulating metabolites. The results provide scientific evidence for the application of MCT in animal lung injury models and emphasize the importance of investigating lung diseases associated with exposure to various PAs.
ARCHIVES OF TOXICOLOGY
(2021)
Article
Pharmacology & Pharmacy
Lenka Jourova, Stefan Satka, Veronika Frybortova, Iveta Zapletalova, Pavel Anzenbacher, Eva Anzenbacherova, Petra Petr Hermanova, Barbora Drabonova, Dagmar Srutkova, Hana Kozakova, Tomas Hudcovic
Summary: The development of inflammatory bowel disease (IBD) is closely related to changes in the gut microbiota. Butyrate, a gut microbiome-derived metabolite with anti-inflammatory effects, shows promise as a potential treatment option for IBD. This study aimed to investigate the protective effects of sodium butyrate (SB) administration on colonic inflammation and its effects on hepatic drug metabolism. The results revealed that butyrate pre-treatment can alleviate gut inflammation and improve the integrity of the colonic epithelium in mice with induced colitis. Additionally, butyrate was found to affect the expression and enzyme activity of certain cytochromes P450 (CYPs) in the liver. These findings highlight the importance of understanding the impact of gut inflammation and therapeutic interventions on drug metabolism in the context of IBD therapy.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Pharmacology & Pharmacy
Lenka Jourova, Stefan Satka, Veronika Frybortova, Iveta Zapletalova, Pavel Anzenbacher, Eva Anzenbacherova, Petra Petr Hermanova, Barbora Drabonova, Dagmar Srutkova, Hana Kozakova, Tomas Hudcovic
Summary: This study demonstrates that pretreatment with butyrate can alleviate colonic inflammation and affect hepatic drug metabolism enzyme activity in mice, highlighting the importance of investigating the gut-liver axis in inflammatory bowel disease and microbiome-targeted interventions.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Ramesh Muthusamy, Prasad Bharatam
Summary: Drug metabolism studies are crucial for enhancing therapeutic efficacy of new drugs by optimizing metabolic profiles. Molecular modeling approaches play a key role in predicting metabolic profiles and assisting in the design of novel drug candidates with efficient metabolic profiles.
CURRENT DRUG METABOLISM
(2021)
Article
Multidisciplinary Sciences
Tamara Heintze, Kathrin Klein, Ute Hofmann, Ulrich M. Zanger
Summary: The use of lentiviral transduction to deliver Cas9 and sgRNAs in HepaRG cells resulted in efficient knockdown of POR and revealed differential effects on drug-metabolizing CYP enzymes. Knockdown of POR also affected the expression of CYPs at mRNA and protein levels. The study highlights the importance of POR/NADPH- and CYB5/NADH-electron transport systems in influencing human drug metabolism, with implications for future research on hepatic functions.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Sarah M. Glass, Yasuhiro Tateishi, F. Peter Guengerich, Hong-Jaan Wang
Summary: Cytochrome P450 (P450, CYP) 27C1 is expressed in human skin and catalyzes the 3,4-desaturation of retinoids. The function of the desaturated retinoids in human skin is currently unknown. The study suggests that the desaturation process may serve as a protective mechanism to maintain active retinoid levels in the body.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Wojciech Plonka, Conrad Stork, Martin Sicho, Johannes Kirchmair
Summary: The majority of approved drugs are metabolized by five major CYP isozymes, inhibition of these isozymes can lead to drug-drug interactions. There are numerous machine learning models available for predicting the inhibition of CYP isozymes. This study combines data from various sources to train classification models, achieving competitive performance and providing freely accessible models for academic research.
BIOORGANIC & MEDICINAL CHEMISTRY
(2021)
Article
Engineering, Environmental
Xiang Wang, Zhong-Hong Zhang, Kuan-Kuan Yuan, Hui-Ying Xu, Guo-Hui He, Libin Yang, Joseph Buhagiar, Wei-Dong Yang, Yalei Zhang, Carol Sze Ki Lin, Hong -Ye Li
Summary: Microalgae-based antibiotic removal treatment has gained attention due to its low carbon and sustainable advantages. By using a suitable carbon source, microalgae can enhance the removal of pollutants through co-metabolism. However, there is limited knowledge about the removal of fluoroquinolone using a microalgae-mediated co-metabolism system. This study investigated the biotic processes of Haematococcus lacustris in a co-metabolism system with glycerol, which achieved significant removal efficiencies of 79.73% for ofloxacin (OFL) and 54.10% for enrofloxacin (ENR), respectively. The study also identified the metabolites and pathways involved in the biodegradation of fluoroquinolone by H. lacustris, and demonstrated the involvement of cytochrome P450 (CYP450) enzymes in this process. Molecular dynamic simulation further confirmed the binding conformation of fluoroquinolones with CYP450. These findings provide a microalgae-based approach for sustainable biodegradation of antibiotics using a co-metabolism strategy with glycerol, leading to the accumulation of valuable products.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Engineering, Environmental
Huanni Zhang, Xiaoqing Wang, Runqian Song, Wen Ding, Fei Li, Li Ji
Summary: Metabolism, especially by CYP450 enzymes, plays a crucial role in mediating the toxification and detoxification of xenobiotics in humans. The metabolic pathways of emerging pollutants, which could potentially cause idiosyncratic toxicity, are often overlooked. This study focused on the sulfonamide antibiotics pollution in aqueous systems and investigated the metabolic processes of sulfamethoxazole (SMX), specifically the coupling and fragmenting initiated by amino H-abstraction catalyzed by human CYP450 enzymes. The findings emphasized the importance of using computations prior to experiments in environmental chemistry and toxicology.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Jing-yi Zhou, Rui-rui Yang, Jie Chang, Jia Song, Zi-sheng Fan, Ying-hui Zhang, Cheng-hao Lu, Hua-liang Jiang, Ming-yue Zheng, Su-lin Zhang
Summary: This study describes the discovery and identification of a novel BCL-2 inhibitor, DC-B01, which targets the BH4 domain of BCL-2. The results indicate that DC-B01 induces cell apoptosis, inhibits tumor growth, and suppresses the transcriptional activity of c-Myc by disrupting the interaction between BCL-2 and c-Myc.
ACTA PHARMACOLOGICA SINICA
(2023)
Article
Chemistry, Multidisciplinary
Jia Song, Rui-rui Yang, Jie Chang, Ya-dan Liu, Cheng-hao Lu, Li-fan Chen, Hao Guo, Ying-hui Zhang, Zi-sheng Fan, Jing-yi Zhou, Gui-zhen Zhou, Ke-ke Zhang, Xiao-min Luo, Kai-xian Chen, Hua-liang Jiang, Su-lin Zhang, Ming-yue Zheng
Summary: Several novel types of cGAS inhibitors have been discovered, among which compound 3 displayed the highest potency and selectivity at the cellular level. It exhibited better anti-inflammatory effects than existing inhibitors and has the potential to be used for the treatment of inflammatory diseases.
ACTA PHARMACOLOGICA SINICA
(2023)
Article
Chemistry, Multidisciplinary
Lan-song Xu, Su-xin Zheng, Liang-he Mei, Ke-xin Yang, Ya-fang Wang, Qiang Zhou, Xiang-tai Kong, Ming-yue Zheng, Hua-liang Jiang, Cheng-ying Xie
Summary: A novel and highly potent KRAS(G12C) inhibitor, 143D, was identified through a structure-based and focused chemical library analysis. It showed comparable antitumor efficacy to AMG510 and MRTX849 and selectively inhibited cell proliferation by downregulating KRAS(G12C)-dependent signal transduction, inducing cell cycle arrest and apoptosis.
ACTA PHARMACOLOGICA SINICA
(2023)
Article
Engineering, Electrical & Electronic
Wangyong Chen, Mingyue Zheng, Yaoyang Lyu, Linlin Cai
Summary: The temperature issue is a critical concern in integrated circuit design, especially for advanced technology. This study presents a new insight into the zero-temperature-coefficient (ZTC) based design strategy to minimize temperature-induced delay variation in digital circuits. An effective current-based method is developed to determine the ZTC point (V-ZTC) for standard cells, which is demonstrated on advanced gate-all-around (GAA) nanosheet (NS) FETs using calibrated TCAD simulation. The results show that operating near V-ZTC can significantly reduce frequency variation and achieve power-performance trade-offs.
IEEE TRANSACTIONS ON ELECTRON DEVICES
(2023)
Review
Nursing
Yunting Luo, Xianqiong Feng, Dandan Wang, Xu Qiao, Xujia Xiao, Shiqi Jia, Mingyue Zheng, Jan D. Reinhardt
Summary: This qualitative review summarizes the subjective experiences of clinical nurses caring for patients with COVID-19, highlighting the difficulties and challenges they face. The findings emphasize the need for support from organizations, families, and society, as well as the importance of exploring positive coping strategies and paying attention to nurses' experiences and voices.
JOURNAL OF CLINICAL NURSING
(2023)
Article
Engineering, Manufacturing
Junfeng Xiao, Qiuquan Guo, Yang Bai, Mingyue Zheng, Yong Sun, Liwen Zhang, Dongxing Zhang, Jun Yang
Summary: In this study, a simple method of 3D printing functional devices using plant-inspired polyphenols is reported. The compatibility of different polyphenols with 3D printing resin is assessed and two polyphenols are selected. The polyphenols can be distributed anywhere on the 3D printed objects, allowing for versatile secondary reactions and fabrication of functional objects with novel surface properties.
ADDITIVE MANUFACTURING
(2023)
Article
Biochemistry & Molecular Biology
Yangyang Cao, Xiaohui Liu, Jingjing Zhang, Zhongmin Liu, Yan Fu, Dong Zhang, Mingyue Zheng, Haiyan Zhang, Ming-Hua Xu
Summary: This study describes the design, synthesis, and evaluation of coumarin-derived small molecule fluorophores for A beta imaging. A novel fluorescence probe XCYC-3, which includes an aromatic coumarin framework embedded into the pi bridge of a push-pull chromophore, was found to efficiently recognize aggregated A beta and have good blood-brain barrier permeability. In vitro staining and in vivo imaging studies demonstrated its efficiency in recognizing A beta plaques in the brain of AD transgenic mice. These findings suggest that XCYC-3 is a promising fluorescence imaging agent for A beta and may contribute to the development of potent NIR fluorescent probes for A beta diagnosis in the future.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Yingle Mao, Weijie Zhang, Zunyun Fu, Yanqiong Liu, Lin Chen, Xin Lian, Dan Zhuo, Jiewei Wu, Mingyue Zheng, Cangsong Liao
Summary: C(sp(3))-H oxyfunctionalization, the insertion of an O-atom into C(sp(3))-H bonds, is a challenging task in organic chemistry for site and stereoselectivity. Biocatalytic C(sp(3))-H oxyfunctionalization overcomes the limitations of small-molecule-mediated approaches by delivering catalyst-controlled selectivity. We have developed a subfamily of α-ketoglutarate-dependent iron dioxygenases that catalyze the site- and stereodivergent oxyfunctionalization of secondary and tertiary C(sp(3))-H bonds, providing concise synthetic routes towards four types of 92 α- and β-hydroxy acids with high efficiency and selectivity. This method offers a biocatalytic approach for the production of valuable chiral hydroxy acid building blocks.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Yunxia Wang, Zhen Chen, Ziqi Pan, Shijie Huang, Jin Liu, Weiqi Xia, Hongning Zhang, Mingyue Zheng, Honglin Li, Tingjun Hou, Feng Zhu
Summary: RNAincoder is a deep learning-based encoder that provides comprehensive RNA encoding features and enables representation of any RNA-associated interactions. It identifies the optimal performance in RNA-associated interaction prediction by scanning all possible feature combinations.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Xiaohong Liu, Wei Zhang, Xiaochu Tong, Feisheng Zhong, Zhaojun Li, Zhaoping Xiong, Jiacheng Xiong, Xiaolong Wu, Zunyun Fu, Xiaoqin Tan, Zhiguo Liu, Sulin Zhang, Hualiang Jiang, Xutong Li, Mingyue Zheng
Summary: Artificial intelligence (AI)-based molecular design methods, particularly deep generative models, have allowed us to explore unknown chemical space without brute-force exploration. However, the challenge lies in synthesizing and evaluating the designed molecules efficiently. This study proposes MolFilterGAN, a novel molecular filtering method, which surpasses conventional screening approaches. The evaluation of MolFilterGAN on DDR1 inhibitors and external ligand sets proves its effectiveness in triaging bioactive compounds and accelerating molecular discovery.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Chemistry, Multidisciplinary
Zimei Zhang, Gang Wang, Rui Li, Lin Ni, RunZe Zhang, Kaiyang Cheng, Qun Ren, Xiangtai Kong, Shengkun Ni, Xiaochu Tong, Li Luo, Dingyan Wang, Xiaojie Lu, Mingyue Zheng, Xutong Li
Summary: An autoregressive torsion angle prediction model Tora3D is proposed for the quick generation of diverse molecular conformations and 3D-based molecular representation, contributing to a wide range of downstream drug design tasks.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Medicine, Research & Experimental
Yu-Pei Zhuang, Hong-Li Zhou, Hai-Bin Chen, Ming-Yue Zheng, Yu-Wei Liang, Yu-Tian Gu, Wen-Ting Li, Wen -Li Qiu, Hong-Guang Zhou
Summary: Colorectal cancer (CRC) has suboptimal response to immunotherapy, possibly due to the influence of gut microbiota on immune responses. Understanding how gut microbiota modulates immune responses is crucial to improve outcomes for CRC patients and overcome resistance.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Nursing
Yunting Luo, Xianqiong Feng, Dandan Wang, Mingyue Zheng, Jan D. Reinhardt
Summary: This study aimed to explore the early experiences of frontline nurses in China during the COVID-19 pandemic through social media posts. It used an explanatory sequential mixed-method design, employing text mining for sentiment analysis, the chi-square test to compare sentiment classification ratios across different months, statistical analysis of word frequency, and thematic analysis. The primary sentiments expressed in the posts were positive and neutral. The number of posts with positive emotions was lowest in January, peaked in March, and gradually declined in April 2020. Nurse-oriented narrative themes emerged, such as seeing and being seen, moving forward amid adversity and support, and returning to everyday life and constructing meaning. The study found that the sentiments of Chinese nurses towards the pandemic fluctuated, starting with positive emotions but not sustained. The study recommends encouraging nurses to engage in expressive writing while adhering to ethical guidelines.
NURSING & HEALTH SCIENCES
(2023)
Article
Engineering, Electrical & Electronic
Yaoyang Lyu, Wangyong Chen, Mingyue Zheng, Binyu Yin, Jinning Li, Linlin Cai
Summary: This study proposes a machine learning-based approach for device modeling with process variations, which is verified on advanced Nanosheet FETs. The artificial neural network algorithm accurately captures the impacts of global and local variations on circuit performance, improving modeling efficiency.
IEEE JOURNAL OF THE ELECTRON DEVICES SOCIETY
(2023)
Article
Chemistry, Medicinal
Meiying Liu, Guizhen Zhou, Wenhong Su, Yuejiao Gu, Mingshan Gao, Kun Wang, Ruifeng Huo, Yupeng Li, Zehui Zhou, Kaixian Chen, Mingyue Zheng, Sulin Zhang, Tianfeng Xu
Summary: The study designed and synthesized a series of new SOS1 inhibitors, and one representative compound 8u showed comparable activities to the reported SOS1 inhibitor BI-3406 in both the biochemical assay and the 3-D cell growth inhibition assay. Compound 8u exhibited good cellular activities against a panel of KRAS G12-mutated cancer cell lines, inhibited downstream ERK and AKT activation in MIA PaCa-2 and AsPC-1 cells, and demonstrated synergistic antiproliferative effects when used in combination with KRAS G12C or G12D inhibitors. Further modifications of these new compounds may lead to a promising SOS1 inhibitor with favorable druglike properties for the treatment of KRAS-mutated patients.
ACS MEDICINAL CHEMISTRY LETTERS
(2023)