Article
Cell Biology
Baoyu Chen, Wenhui Dong, Tinghui Shao, Xiulian Miao, Yan Guo, Xingyu Liu, Yifei Feng
Summary: The KDM4-DBC1-SIRT1 pathway was found to regulate EMT and contribute to the development of intestinal fibrosis. Depletion or inhibition of KDM4A attenuated TGF-beta induced EMT and normalized SIRT1 activity. Therefore, targeting this pathway may be a potential strategy for treating intestinal fibrosis in IBDs.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Oncology
Chandtip Chandhasin, Van Dang, Frank Perabo, Joselyn Del Rosario, Young K. Chen, Ellen Filvaroff, Jeffrey A. Stafford, Michael Clarke
Summary: The dysregulation of KDM4 has been linked to various cancer processes, and a new pan-inhibitor called TACH101 has shown potent antiproliferative activity and inhibits tumor growth. Additionally, TACH101 reduces the population of tumor-initiating cells.
Article
Cell Biology
Shivendra Singh, Ahmed Abu-Zaid, Hongjian Jin, Jie Fang, Qiong Wu, Tingting Wang, Helin Feng, Waise Quarni, Ying Shao, Lily Maxham, Alireza Abdolvahabi, Mi-Kyung Yun, Sivaraja Vaithiyalingam, Haiyan Tan, John Bowling, Victoria Honnell, Brandon Young, Yian Guo, Richa Bajpai, Shondra M. Pruett-Miller, Gerard C. Grosveld, Mark Hatley, Beisi Xu, Yiping Fan, Gang Wu, Eleanor Y. Chen, Taosheng Chen, Peter W. Lewis, Zoran Rankovic, Yimei Li, Andrew J. Murphy, John Easton, Junmin Peng, Xiang Chen, Ruoning Wang, Stephen W. White, Andrew M. Davidoff, Jun Yang
Summary: This study identifies KDM4B as a therapeutic vulnerability for PAX3-FOXO1(+) RMS. Inhibition of KDM4B delays tumor growth and suppresses the expression of core oncogenic transcription factors, causing epigenetic alterations of PAX3-FOXO1-governed superenhancers.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Review
Immunology
Liyan Dong, Jiaxing Zhu, Anyi Deng, Junping Wei, Jiawei Li, Xinru Mao, Zhenghu Jia
Summary: The study aims to elucidate the correlation between histone demethylase and gastric cancer. The results show that histone modification plays an important role in gastric cancer, including downstream gene expression regulation and epigenetic effects. Histone methyltransferase and histone demethylases are involved in the regulation of histone methylation status, which in turn affects various biological processes involved in the recognition of histone methylation modification. This is especially important in the regulation of chromatin function and the occurrence of gastric cancer and embryonic development.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Cell Biology
Jai-Shin Liu, Wei-Kai Fang, Shan-Min Yang, Meng-Chen Wu, Tsan-Jan Chen, Chih-Ming Chen, Tung-Yueh Lin, Kai-Lun Liu, Chien-Ming Wu, Yun-Ching Chen, Chih-Pin Chuu, Ling-Yu Wang, Hsing-Pang Hsieh, Hsing-Jien Kung, Wen-Ching Wang
Summary: Myricetin, identified as a potent alpha-ketoglutarate-type inhibitor, blocks the demethylation activity by KDM4s and reduces the proliferation of both androgen-dependent and androgen-independent CRPC cells. A synergistic cytotoxic effect is observed for the combination of myricetin and enzalutamide on CRPC cells. PLGA-encapsulated myricetin in combination with enzalutamide shows significant antitumor activity in a CRPC xenograft model, suggesting its potential effectiveness for CRPC.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Anand Chopra, William G. Willmore, Kyle K. Biggar
Summary: JmjC KDMs are a type of demethylase that not only are associated with histone demethylation, but also with non-histone demethylation. Recent findings have highlighted the importance of KDM3A in promoting cancerous phenotypes, which can provide insights into the mechanisms through which it exerts its oncogenic functions.
Article
Chemistry, Physical
Hongjun Dong, Michelle C. Y. Chang
Summary: Ketoreductases are a key member of the oxidoreductase family with significant applications in biotechnology and metabolic engineering. The study provides insights into the substrate selectivity of a mitochondrial ketoreductase AsHadh2 from Ascaris suum and identifies mutations that alter the selectivity for specific substrates, shedding light on the factors impacting substrate selectivity in enzymatic systems.
Article
Biochemistry & Molecular Biology
Matthew Hoekstra, Nashira H. Ridgeway, Kyle K. Biggar
Summary: The KDM5/JARID1 sub-family consists of lysine-specific histone demethylases that are dependent on 2-oxoglutarate and Fe(II) and characterized by their Jumonji catalytic domains. The KDM5 family is known for its ability to remove tri-/di-methyl modifications from lysine-4 of histone H3, which is associated with active gene expression. Recent evidence suggests that KDM5 may play a role in disease beyond H3-K4 demethylation, highlighting the importance of investigating its demethylation of non-histone proteins.
JOURNAL OF BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Cathy J. Spangler, Aleksandra Skrajna, Caroline A. Foley, Anh Nguyen, Gabrielle R. Budziszewski, Dalal N. Azzam, Eyla C. Arteaga, Holly C. Simmons, Charlotte B. Smith, Nathaniel A. Wesley, Emily M. Wilkerson, Jeanne-Marie E. McPherson, Dmitri Kireev, Lindsey I. James, Stephen V. Frye, Dennis Goldfarb, Robert K. McGinty
Summary: The nucleosome acidic patch serves as a hub for chromatin interaction and allows enzymes, such as the H3K36 demethylase KDM2A, to bind to nucleosomes. However, the molecular mechanisms governing the substrate specificity of KDM2A and its related paralog, KDM2B, remain unclear. By using cryogenic electron microscopy, researchers discovered that the binding of KDM2A and KDM2B to nucleosomes is paralog-specific and facilitated by DNA unwrapping and histone charge shielding.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Carlos F. Rodriguez, Paloma Escudero-Bravo, Lucia Diaz, Paola Bartoccioni, Carmen Garcia-Martin, Joan G. Gilabert, Jasminka Boskovic, Victor Guallar, Ekaitz Errasti-Murugarren, Oscar Llorca, Manuel Palacin
Summary: Members of the HAT family show exquisite preference for exchanging certain amino acids, with substrate specificity determining their physiological function and role in human diseases. Molecular determinants governing substrate specificity within the HAT family are elucidated through structural studies, providing insights into potential pathogenic mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Matthew Hoekstra, Kyle K. Biggar
Summary: The study focuses on the role of KDM5A in regulating gene expression through histone methylation and suggests its potential involvement with non-histone proteins. By examining a library of 180 peptide substrates, a recognition motif was identified and successfully used to predict and validate high-ranking substrates. The approach demonstrated the utility in identifying candidate substrates applicable to Fe(II)-and 2-oxoglutarate dependent demethylases.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Yanjing Li, Lijie Zhao, Yuebin Zhang, Ping Wu, Ying Xu, Jun Mencius, Yongxin Zheng, Xiaoman Wang, Wancheng Xu, Naizhe Huang, Xianwen Ye, Ming Lei, Pan Shi, Changlin Tian, Chao Peng, Guohui Li, Zhijun Liu, Shu Quan, Yong Chen
Summary: This study develops methodologies to measure the methylation rate difference between different states of methylation and demonstrates that MLL proteins possess distinct product specificities. Structural analyses reveal that the dynamics of conserved tyrosine residues fine-tune the product specificity, and the variation in intramolecular interaction affects the dynamics, determining the product specificities of MLL proteins.
Article
Chemistry, Multidisciplinary
Yang-Oujie Bao, Meng Zhang, Xue Qiao, Min Ye
Summary: We report a C-glycosyltransferase PlCGT from Pueraria lobata that exhibits efficient C-glycosylation activities toward isoflavones and phloroglucinol derivatives. Homology modelling reveals a narrow hydrophobic pocket responsible for substrate selectivity and an unusual Asn16-Asp124 dyad that may mediate the S(N)2-like mechanism in C-glycosylation.
CHEMICAL COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Saeko Yokotsuka-Ishida, Masayuki Nakamura, Yoko Tomiyasu, Mio Nagai, Yuko Kato, Akiyuki Tomiyasu, Hiromi Umehara, Takehiro Hayashi, Natsuki Sasaki, Shu-ichi Ueno, Akira Sano
Summary: The importance of epigenetic control in the development of the central nervous system, particularly abnormal histone methylation modifiers, has attracted attention. This study focused on a Japanese family with symptoms including Marfan syndrome-like minor physical anomalies, intellectual disability, and schizophrenia. A missense mutation in the KDM2B gene was identified as a possible cause, leading to decreased KDM2B expression and potentially causing the observed conditions.
JOURNAL OF HUMAN GENETICS
(2021)
Article
Biology
Dominik Layer, Juergen Kopp, Miriam Fontanillo, Maja Koehn, Karine Lapouge, Irmgard Sinning
Summary: Layer et al. present a crystal structure of Naa20, the catalytic subunit of an N-terminal acetyltransferase NatB, in complex with its competitive inhibitor CoA-Ac-MDEL. They find that Naa20 alone can acetylate NatB in vitro while Naa25, the auxiliary subunit of Naa20, increases the substrate affinity of Naa20. This study provides insights into the development of NAT inhibitors.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Benjamin G. G. Saward, Thomas M. M. Leissing, Ian J. J. Clifton, Anthony Tumber, Christopher M. M. Timperley, Richard J. J. Hopkinson, Christopher J. J. Schofield
Summary: Transient receptor potential (TRP) channels play important roles in environmental sensing in animals. TRPA1 is responsible for sensing AITC and other electrophilic irritants, while TRPV3 is involved in skin maintenance. This study reports on the catalysis of asparaginyl hydroxylation of the ankyrin repeat domains (ARDs) of TRPA1 and TRPV3 by FIH. The results confirm previous findings on TRPV3 hydroxylation and identify a specific sequence in TRPA1 that undergoes hydroxylation. Structural studies reveal similarities and differences in the binding modes of TRPA1 and TRPV3 to FIH.
Article
Multidisciplinary Sciences
Ryan A. Herold, Raphael Reinbold, Christopher J. Schofield, Fraser A. Armstrong
Summary: Electrochemical studies reveal that nanoconfinement significantly increases the efficiency of enzyme-catalyzed cascade reactions. By using a nanoporous conducting indium tin oxide film and entrapping Isocitrate dehydrogenase 1 (IDH1), the complete electrochemical oxidation of isocitrate to 2-oxoglutarate is achieved using only the NADP(H) cofactor carried into the electrode pores. The results demonstrate the power of nanoconfinement in facilitating multistep enzyme catalysis and provide insights into the role of nicotinamide cofactors as redox carriers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Vildan A. Turkmen, Jordi C. J. Hintzen, Anthony Tumber, Laust Moesgaard, Eidarus Salah, Jacob Kongsted, Christopher J. Schofield, Jasmin Mecinovic
Summary: Non-haem Fe(ii) and 2-oxoglutarate (2OG) dependent oxygenases catalyze oxidation of proteins, and this study focuses on the substrate selectivity and inhibition of human ribosomal oxygenases (ROX) MINA53 and NO66. The results show that MINA53 and NO66 have narrow substrate selectivity compared to other human JmjC hydroxylases. Inhibition assays also suggest that the activities of MINA53/NO66 might be regulated in vivo by competition with non-oxidized proteins/peptides.
RSC CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lukas Gericke, Dipali Mhaindarkar, Lukas C. Karst, Soren Jahn, Marco Kuge, Michael K. F. Mohr, Jana Gagsteiger, Nicolas V. Cornelissen, Xiaojin Wen, Silja Mordhorst, Henning J. Jessen, Andrea Rentmeister, Florian P. Seebeck, Gunhild Layer, Christoph Loenarz, Jennifer N. Andexer
Summary: S-Adenosylmethionine (SAM) is a versatile enzyme cofactor involved in various reactions. However, the high cost and instability of SAM hinder its investigation and usage. Here, we present a set of efficient one-pot systems to supply or regenerate SAM and its analogues for different classes of enzymes, demonstrating their potential in diverse chemistry and mechanistic studies.
Article
Biochemistry & Molecular Biology
Patricia Bencic, Michael Keppler, Marco Kuge, Danye Qiu, Lena M. Schuette, Markus Haener, Katharina Strack, Henning J. Jessen, Jennifer N. Andexer, Christoph Loenarz
Summary: Recent advances in mRNA therapeutics have led to the development of efficient toolkits for incorporating nucleoside analogues into mRNA. In this study, we utilized a versatile enzyme cascade to triphosphorylate a wide range of nucleoside analogues. The preparation of nucleoside triphosphates containing various core structures was successfully achieved using capillary electrophoresis coupled to mass spectrometry. This methodology enabled the transcription and purification of functional mRNA containing these nucleoside analogues, followed by mass spectrometric verification of analogue incorporation. The impact of commercially unavailable nucleoside analogues on mRNA properties was explored using translational recoding analysis.
Article
Chemistry, Medicinal
Shuang Liu, Martine Abboud, Victor Mikhailov, Xiao Liu, Raphael Reinbold, Christopher J. Schofield
Summary: This study reported the binding and inhibition studies of 13 IDH1/2 variant inhibitors on wild-type IDH1 and its cancer-associated variant, IDH1 R132H. Interestingly, all the variant inhibitors were able to bind wild-type IDH1 despite not inhibiting it or only weakly inhibiting it. The selectivity of the IDH1 R132H variant over wild-type IDH1 is not primarily related to the affinities of the inhibitors for the resting forms of the enzymes. The independent binding of Mg2+ and 2-oxoglutarate to the IDH1 variant makes it more susceptible to allosteric inhibition compared to the tighter binding of the isocitrate-Mg2+ complex substrate to wild-type IDH1. The results highlight that binding affinity does not necessarily correlate with inhibition selectivity and have implications for interpreting inhibitor screening results with IDH and related enzymes.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Plant Sciences
Daniela J. Sueldo, Alice Godson, Farnusch Kaschani, Daniel Krahn, Till Kessenbrock, Pierre Buscaill, Christopher J. Schofield, Markus Kaiser, Renier A. L. van Der Hoorn
Summary: This study reports the dynamics of extracellular hydrolases in Nicotiana benthamiana upon infection with Pseudomonas syringae. The activity of 82 hydrolases, mostly serine hydrolases, increases during infection, while the activity of 60 hydrolases, mostly glycosidases and cysteine proteases, is suppressed. The study also reveals the antibacterial activity of NbPR3 and its essential active site substitution.
Article
Chemistry, Multidisciplinary
H. T. Henry Chan, A. Sofia F. Oliveira, Christopher J. Schofield, Adrian J. Mulholland, Fernanda Duarte
Summary: The SARS-CoV-2 main protease (M-pro) is crucial in the coronavirus lifecycle by breaking down viral polyproteins. This study used dynamical nonequilibrium molecular dynamics (D-NEMD) simulations to examine the behavior of M-pro with and without substrates. The results reveal communication between M-pro subunits and identify networks associated with allosteric inhibition and nirmatrelvir resistance. These findings suggest that certain mutations can lead to drug resistance by altering the allosteric behavior of M-pro. Overall, the study demonstrates the usefulness of D-NEMD in identifying functionally relevant allosteric sites and networks, including those relevant to drug resistance.
Article
Chemistry, Multidisciplinary
Ryan A. Herold, Christopher J. Schofield, Fraser A. Armstrong
Summary: The study utilizes a nanoporous electrode material, the e-Leaf, to control enzyme cascades and gain detailed kinetic insight into an anti-cancer drug mechanism. The e-Leaf allows for the quantification of IDH1 R132H inhibition kinetics and reveals factors underlying inhibitor residence time. The study highlights the importance of this method in obtaining detailed kinetic and mechanistic information that is difficult to obtain using conventional techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
David J. Fallon, Alex Phillipou, Christopher J. Schofield, David House, Nicholas C. O. Tomkinson, Jacob T. Bush
Summary: This article presents the development and optimization of a photoaffinity labelling (PAL) displacement assay. It uses a highly efficient PAL probe to assess the relative binding affinities of compounds to specific binding sites in multiple recombinant protein domains in tandem. The assay was validated using a test set of 264 compounds annotated with activity against the bromodomain and extra-terminal domain (BET) family in ChEMBL. The obtained pIC50 values correlated well with orthogonal TR-FRET data, highlighting the potential of this accessible PAL biochemical screening platform.
BIOCHEMICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Lennart Brewitz, H. T. Henry Chan, Petra Lukacik, Claire Strain-Damerell, Martin A. Walsh, Fernanda Duarte, Christopher J. Schofield
Summary: This study investigates the DUB activity of PLpro and confirms its activity using mass spectrometry. The results suggest that the sequence and binding of substrates affect the catalysis of PLpro, and human proteins conjugated to ISG15 are better substrates. The study also implies the potential of using N epsilon-lysine-branched oligopeptides for substrate identification and monitoring catalysis by human DUBs.
BIOORGANIC & MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
William D. Figg Jr, Giorgia Fiorini, Rasheduzzaman Chowdhury, Yu Nakashima, Anthony Tumber, Michael A. McDonough, Christopher J. Schofield
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Chemistry, Multidisciplinary
Mariska de Munnik, Pauline A. A. Lang, Francisco De Dios Anton, Monica Cacho, Robert H. Bates, Jurgen Brem, Beatriz Rodriguez Miquel, Christopher J. Schofield
Summary: Disrupting bacterial cell wall biosynthesis in Mycobacterium tuberculosis is a promising approach for treating tuberculosis. In this study, a high-throughput assay was used to identify potent inhibitors of L,D-transpeptidase Ldt(Mt2), which plays an essential role in the formation of cell wall peptidoglycan. These inhibitors were found to react covalently with the catalytic cysteine of Ldt(Mt2) and showed bactericidal effects on M. tuberculosis.
Article
Biochemistry & Molecular Biology
Anthony Tumber, Eidarus Salah, Lennart Brewitz, Thomas P. Corner, Christopher J. Schofield
Summary: Jumonji-C (JmjC) domain-containing protein 5 (JMJD5) is an oxygenase linked to circadian rhythm and cancer biology. Synthetic 2OG derivatives with cyclic carbon backbones are alternative cosubstrates of JMJD5, demonstrating structural similarity to factor inhibiting hypoxia-inducible transcription factor HIF-a (FIH). Broad-spectrum 2OG oxygenase inhibitors are also efficient JMJD5 inhibitors, while clinical inhibitors like roxadustat do not inhibit JMJD5. Solid phase extraction coupled to mass spectrometry assays will facilitate the development of selective JMJD5 inhibitors for cellular studies.
RSC CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
H. T. Henry Chan, Lennart Brewitz, Petra Lukacik, Claire Strain-Damerell, Martin A. Walsh, Christopher J. Schofield, Fernanda Duarte
Summary: This study investigates how SARS-CoV-2 PLpro binds viral polyprotein-derived oligopeptide substrates through molecular dynamics, docking, and quantum mechanics/molecular mechanics calculations. The results show that a proline located at the P2' position promotes catalysis.
RSC CHEMICAL BIOLOGY
(2023)