Article
Biochemistry & Molecular Biology
Hebatalla Mohamed, Amna Ghith, Stephen G. Bell
Summary: The cytochrome P450 superfamily of enzymes can catalyse oxidation reactions and their heme and active site environment can be studied using UV-visible absorbance spectroscopy. The binding of imidazole and pyridine-based ligands to different forms of bacterial cytochrome P450 enzymes was evaluated using this technique. The majority of ligands interacted with the heme as expected, but differences in heme environment were observed across enzyme/ligand combinations.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Review
Pharmacology & Pharmacy
Xiaokang Wang, Jiaoyu Rao, Zhiyi Tan, Tianrong Xun, Jingqian Zhao, Xixiao Yang
Summary: This article summarizes the impact of new inflammatory-response signaling pathways on the activity and expression of CYP drug-metabolizing enzymes, and provides an overview of drugs that have the potential to regulate drug-metabolizing enzyme activity. The aim of the research is to inspire the development of clinical drug treatment processes that consider the impact of the inflammatory environment on drug treatment, as well as provide research targets for those studying drug metabolism.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Cell Biology
Lukas S. Wijaya, Carina Rau, Theresa S. Braun, Serif Marangoz, Vincent Spegg, Matthijs Vlasveld, Wiebke Albrecht, Tim Brecklinghaus, Hennicke Kamp, Joost B. Beltman, Jan G. Hengstler, Bob van de Water, Marcel Leist, Stefan Schildknecht
Summary: This study found that the antibiotic NFT can transiently elevate intracellular glutathione levels by regulating the Nrf2-GCL axis, enhancing cells' resistance to various stressors.
CELL BIOLOGY AND TOXICOLOGY
(2022)
Article
Toxicology
Luise Hochmuth, Christiane Korner, Fritzi Ott, Daniela Volke, Kaja Blagotinsek Cokan, Peter Juvan, Mario Brosch, Ute Hofmann, Ralf Hoffmann, Damjana Rozman, Thomas Berg, Madlen Matz-Soja
Summary: The liver is one of the most sexually dimorphic organs, with significant differences in metabolic pathways and disease prevalence between males and females. Research shows that sex affects gene expression, proteome, and metabolome parameters of liver cells, which may have important implications for drug metabolism, treatment, and efficacy.
ARCHIVES OF TOXICOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Maria Norlin, Kjell Wikvall
Summary: Vitamin D signaling plays a crucial role in maintaining calcium balance for bone health and has various functions in different tissues. Disturbances in vitamin D signaling are associated with numerous diseases. This review focuses on the identification of bioactivating enzymes and their genes involved in the production of active vitamin D metabolites. It evaluates species- and tissue-specific expression, enzyme kinetics, substrate specificity, and the consequences of gene mutations. The roles of different vitamin D receptors and alternative bioactivation pathways are also discussed. Although significant progress has been made in understanding vitamin D bioactivation enzymes, further research is needed to fully comprehend the pleiotropic effects and the mechanisms of enzymatic activation in vitamin D-induced responses.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Pharmacology & Pharmacy
Sangsoo Daniel Kim, Larry Morgan, Elyse Hargreaves, Xiaoying Zhang, Zhihui Jiang, Monica Antenos, Ben Li, Gordon M. Kirby
Summary: The study found that DE can regulate the gene expression of Cyp2a5 by activating CAR, thus increasing bilirubin clearance, providing new insights for the treatment of neonatal jaundice.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Pharmacology & Pharmacy
Yan Li, Ying-Yuan Lu, Jun Jia, Meng Fang, Lin Zhao, Yong Jiang, Yan Shi, Peng-Fei Tu, Xiao-Yu Guo
Summary: This study established an in vitro evaluation system based on human-induced hepatocytes (hiHeps) for studying the impact of drugs on CYP3A4, 1A2, 2B6, 2C9, and 2C19 enzymes. The system proved to be effective and stable, providing a powerful tool for drug research on the activity of CYP enzymes.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Cell Biology
Anne Vonada, Amita Tiyaboonchai, Sean Nygaard, Jeffrey Posey, Alexander Mack Peters, Shelley R. Winn, Alessio Cantore, Luigi Naldini, Cary O. Harding, Markus Grompe
Summary: The study demonstrates that therapeutic modified hepatocytes can be efficiently selected in preclinical models by using mildly hepatotoxic acetaminophen, leading to significant expansion of transgene-bearing hepatocytes and reaching therapeutic thresholds in genetic liver diseases.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Cell & Tissue Engineering
Saeko Akiyama, Noriaki Saku, Shoko Miyata, Kenta Ite, Masashi Toyoda, Tohru Kimura, Masahiko Kuroda, Atsuko Nakazawa, Mureo Kasahara, Hidenori Nonaka, Akihide Kamiya, Tohru Kiyono, Tohru Kobayshi, Yasufumi Murakami, Akihiro Umezawa
Summary: The study established a simple in vitro culture system which enables efficient proliferation of hepatocytes through the use of cytocidal antibiotics. This provides a stable supply of hepatocytes for drug discovery research at a significant cost reduction.
STEM CELL RESEARCH & THERAPY
(2022)
Article
Pharmacology & Pharmacy
Tamara Heintze, Denise Wilhelm, Thierry Schmidlin, Ute Hofmann, Ulrich M. Zanger, Matthias Schwab, Kathrin Klein
Summary: The study systematically investigated the impact of POR knockdown on a human hepatic cell model, revealing its widespread role in various metabolic pathways including drug metabolism and endogenous substance synthesis. POR disruption resulted in deregulated bile acid and cholesterol biosynthesis, as well as downregulation of key transcriptional regulators. Additionally, global protein expression was affected, with metabolic pathways and lipid metabolism being downregulated. The study provides valuable insights into the effects of diminished POR expression on drug and endogenous metabolism.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Dawit M. Weldemichael, Kun Zhou, Shi-jia Su, Lin Zhao, Mario Andrea Marchisio, Matthias Bureik
Summary: Among 50 human microsomal CYPs, 38 were found to significantly increase production of superoxide anions (O-2(-center dot)) in the absence of substrate. Some CYPs were intermediate strength O-2(-center dot) producers, while others were even stronger, with CYP2B6, CYP5A1, CYP2A13, CYP51A1, and CYP1A2 being the strongest producers.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Chemistry, Analytical
Jiawei Chang, Hao Chen, Jia Chen, Xuehu Sun, Xuesheng Wu, Lei Liu, Zhouwei Xu, Weidong Chen, Jianlin Zhang, Xingyu Wang, Qingwang Liu
Summary: This study investigated the in vitro metabolism of cabozantinib in animal species and humans, revealing various metabolites and major metabolic pathways. The research showed that cabozantinib is primarily metabolized by the enzyme CYP3A4, providing valuable metabolic data for safety and efficacy assessment of the drug.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2021)
Article
Pharmacology & Pharmacy
Larry Morgan, Monica Antenos, Gordon M. Kirby
Summary: The study found that DTTox and 2-mercaptoethanol can induce the expression of Cyp2a5 protein in mouse liver cells. In addition, DTTox transactivates Cyp2a5 by activating the transcription factor nuclear factor-(erythroid-derived 2)-like 2 (Nrf2). Overexpression of Cyp2a5 partially protects cells during reductive ER stress by reducing XBP-1 mRNA splicing and caspase-3 cleavage.
Article
Chemistry, Multidisciplinary
Jing Liu, Lauritz Harken, Yiling Yang, Xiulan Xie, Shu-Ming Li
Summary: This study reports two important gene clusters involved in the biosynthesis of mycocyclosin and guatyromycine. By reconstructing the biosynthetic pathways and conducting biochemical investigations, it was found that the enzymes encoded by these genes can catalyze both intramolecular oxidation and intermolecular nucleobase transfer reactions, leading to the synthesis of specific natural products.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biotechnology & Applied Microbiology
Thomas Hilberath, Alessandra Raffaele, Leonie M. Windeln, Vlada B. Urlacher
Summary: Cytochromes P450 have great potential for biocatalysis by catalyzing oxidation of diverse compounds. Using recombinant lyophilized E. coli cells as P450-biocatalysts showed promise for broader application, with co-expression of alcohol dehydrogenase crucial for optimizing P450 activity. Wet resting cells and lyophilized cells were compared, revealing the latter as more suitable for effective P450-mediated biocatalysis.
Article
Chemistry, Multidisciplinary
Zhong Guo, Oleh Smutok, Wayne A. Johnston, Cagla Ergun Ayva, Patricia Walden, Brett McWhinney, Jacobus P. J. Ungerer, Artem Melman, Evgeny Katz, Kirill Alexandrov
Summary: This study presents a technique for constructing modular electrochemical biosensors based on PQQ-GDH, which have high affinity and sensitivity for measuring concentrations of small molecules and proteins. This biosensor technology shows excellent performance in detecting Cyclosporine A.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Zhong Guo, Rinky D. Parakra, Ying Xiong, Wayne A. Johnston, Patricia Walden, Selvakumar Edwardraja, Shayli Varasteh Moradi, Jacobus P. J. Ungerer, Hui-wang Ai, Jonathan J. Phillips, Kirill Alexandrov
Summary: This study constructs a synthetic allosteric version of circular permutated NanoLuc luciferase, enabling protein allosteric regulation and creating biosensors for proteins and small molecules, capable of quantifying their cognate ligands in human fluids.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Zhong Guo, Oleh Smutok, Wayne A. Johnston, Patricia Walden, Jacobus P. J. Ungerer, Thomas S. Peat, Janet Newman, Jake Parker, Tom Nebl, Caryn Hepburn, Artem Melman, Richard J. Suderman, Evgeny Katz, Kirill Alexandrov
Summary: The study aims to investigate the optimal strategy for developing artificial small molecule:protein complexes that function as chemically induced dimerization (CID) systems. By using methotrexate-controlled CID systems, the critical role of drug-induced conformational change in ligand-controlled protein complex assembly is revealed. The utility of the developed CID is demonstrated by constructing an electrochemical biosensor of methotrexate for quantification in human serum, as well as developing a multiplexed bioelectronic system for repeated measurements of multiple analytes using methotrexate and functionally related biosensor of rapamycin.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Marcos H. Vinde, Da Cao, Rebecca J. Chesterfield, Kaori Yoneyama, Yosephine Gumulya, Raine E. S. Thomson, Tebogo Matila, Birgitta E. Ebert, Christine A. Beveridge, Claudia E. Vickers, Elizabeth M. J. Gillam
Summary: This study explores the functional evolution of the highly conserved CYP711A P450 family and reveals their role in the diversification of the phytohormone strigolactone.
Article
Biochemistry & Molecular Biology
Cagla Ergun Ayva, Maria M. Fiorito, Zhong Guo, Selvakumar Edwardraja, Joe A. Kaczmarski, Dejan Gagoski, Patricia Walden, Wayne A. Johnston, Colin J. Jackson, Tom Nebl, Kirill Alexandrov
Summary: This study presents an in vitro expression-based platform for analyzing chimeric protein libraries. The researchers focused on chimeras between PQQ-glucose dehydrogenase and calmodulin. Through screening, they identified 50 chimeras that were activated by calmodulin-binding peptides. Analysis of the active chimeras revealed an anticorrelation between their dynamic range and response times. Structural changes induced by the receptor domains were investigated using CD spectroscopy and hydrogen-deuterium exchange mass spectrometry.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kurt L. Harris, Raine E. S. Thomson, Yosephine Gumulya, Gabriel Foley, Saskya E. Carrera-Pacheco, Parnayan Syed, Tomasz Janosik, Ann-Sofie Sandinge, Shalini Andersson, Ulrik Jurva, Mikael Boden, Elizabeth M. J. Gillam
Summary: The cytochrome P450 family 1 enzymes (CYP1s) are a diverse family of hemoprotein monooxygenases that metabolize many xenobiotics, including numerous environmental carcinogens. The study found that CYP1 enzymes have diversified their functions through evolution, such as caffeine metabolism and increased activity toward specific substrates. Additionally, the thermostability of CYP1 enzymes has increased over time.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Biochemistry & Molecular Biology
Raine E. S. Thomson, Saskya E. Carrera-Pacheco, Elizabeth M. J. Gillam
Summary: The engineering of proteins to improve stability is important for various applications. Structural information is needed for rational design approaches, while bioinspired methods based on phylogenetic analyses show promise when structures are unavailable. This review provides an overview of factors important for successful inference of thermostable proteins using ancestral sequence reconstruction.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Stephanie M. Ryan, Roland Ruscher, Wayne A. Johnston, Darren A. Pickering, Malcolm W. Kennedy, Brian O. Smith, Linda Jones, Geraldine Buitrago, Matt A. Field, Adrian J. Esterman, Connor P. McHugh, Daniel J. Browne, Martha M. Cooper, Rachael Y. M. Ryan, Denise L. Doolan, Christian R. Engwerda, Kim Miles, Makedonka Mitreva, John Croese, Tony Rahman, Kirill Alexandrov, Paul R. Giacomin, Alex Loukas
Summary: A biologics discovery and validation pipeline was used to generate and screen a recombinant cell-free secretome library of helminth-derived immunomodulatory proteins. The identified proteins offer promise as novel and safe biologics for the treatment of inflammatory diseases.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Gabriel Foley, Ariane Mora, Connie M. Ross, Scott Bottoms, Leander Sutzl, Marnie L. Lamprecht, Julian Zaugg, Alexandra Essebier, Brad Balderson, Rhys Newell, Raine E. S. Thomson, Bostjan Kobe, Ross T. Barnard, Luke Guddat, Gerhard Schenk, Jorg Carsten, Yosephine Gumulya, Burkhard Rost, Dietmar Haltrich, Volker Sieber, Elizabeth M. J. Gillam, Mikael Boden
Summary: Ancestral sequence reconstruction is a powerful technique for recovering ancestral diversity and identifying building blocks using large data sets. The GRASP method efficiently implements maximum likelihood methods and uses partial order graphs to represent insertion and deletion events. By exploring variation over evolutionary time, GRASP enables the engineering of biologically active ancestral variants.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Review
Pharmacology & Pharmacy
Elizabeth M. J. Gillam, Valerie M. Kramlinger
Summary: The study of drug metabolism is crucial for drug discovery and development as it affects the clearance and duration of action of drugs. Biotransformation can produce active or toxic products, complicating drug evaluation but also allowing exploration of new compounds. Preclinical drug biotransformation studies help predict drug pharmacokinetics and optimize dosing, while engineered recombinant enzymes improve efficiency and offer synthetic approaches for drug optimization.
DRUG METABOLISM AND DISPOSITION
(2023)
Article
Plant Sciences
Silas B. Mellor, James B. Y. H. Behrendorff, Johan O. Ipsen, Christoph Crocoll, Tomas Laursen, Elizabeth M. J. Gillam, Mathias Pribil
Summary: Photosynthetic organelles, such as chloroplasts in plants, can convert solar energy into chemical energy, making them ideal for engineering small molecule bioproduction. This study explores the potential of using plant chloroplasts to produce indoxyl-beta-D-glucoside (indican), a precursor of indigo dye, by introducing an engineered biosynthetic pathway. The researchers demonstrate that P450 enzymes can function in chloroplasts and optimize the design to improve productivity. Furthermore, they find that increasing tryptophan supply does not enhance indican production, suggesting that P450 activity is the limiting factor. These findings have implications for metabolic engineering in photosynthetic hosts for the production of valuable chemicals or drug metabolites.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Shayli Varasteh Moradi, Yue Wu, Patricia Walden, Zhenling Cui, Wayne A. Johnston, Dmitri Petrov, Kirill Alexandrov
Summary: Researchers used CFPS technology combined with AlphaLISA protein interaction technology to identify intraviral and viral-human protein interactions of SARS-CoV-2, providing potential targets for the development of antiviral therapeutics.
Article
Chemistry, Organic
Luke R. Churchman, Peter D. Giang, Julia B. Buczynski, Jeanette E. Stok, Stephen G. Bell, James J. De Voss
Summary: Ten substituted norcaranes were synthesized as mechanistic probes of monooxygenase enzymes, and their potential was evaluated through enzyme binding experiments and the generation of product standards.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Materials Science, Multidisciplinary
Laura Navone, Kaylee Moffitt, Wayne A. Johnston, Tim Mercer, Crystal Cooper, Kirsten Spann, Robert E. Speight
Summary: The use of personal protective equipment, face masks, and ventilation is crucial in controlling the spread of respiratory viruses. This study introduces bioengineered textiles that can capture viral particles, offering additional protection in PPE, facemasks, ventilation, and furnishings. The peptides on the surface of the textile are capable of capturing SARS-CoV-2 viral particles, greatly reducing onward infection.
COMMUNICATIONS MATERIALS
(2022)
Meeting Abstract
Chemistry, Multidisciplinary
Elizabeth M. J. Gillam, Raine E. S. Thomson, Stephlina A. D'Cunha, Kurt L. Harris, Gabriel Foley, Mikael Boden, Aaron G. Bart, Emily E. Scott
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES
(2021)