1
|
Li Y, Gao C, Zhao J, Zhao Z, Xie B, Zuo H, Zhang S, Dong J, Chen X, Li H, Bian Y. Screening of peptidyl arginine deiminase 4 inhibitors in traditional herbal medicines. Fitoterapia 2024; 177:106095. [PMID: 38942299 DOI: 10.1016/j.fitote.2024.106095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 05/22/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
Peptidyl arginine deiminase 4 (PAD4) is a promising target for the treatment of metabolic diseases associated with autoimmune and central nervous system disease. By now there are limited numbers of PAD4 inhibitors, and no one is ready for clinical use. This study aims to find efficient and specific PAD4 inhibitors from traditional herbal medicines and to investigate their inhibitory mechanisms. The inhibitory effects of forty-eight extracts from sixteen traditional herbal medicines which are widely used in traditional herbal medicines were investigated. Salvia miltiorrhiza was found to have the most potent PAD4 inhibitory activity. After that, a practical bioactivity-guided fractionation coupling with a chemical profiling strategy was used to identify the fractions from Salvia miltiorrhiza with strong PAD4 inhibition activity, and the major constituents in these bioactive fractions were characterized by LC-MS/MS. Seven compounds were found to have inhibition on PAD4 with IC50 values ranging from 33.52 μM to 667 μM, in which salvianolic acid A showed the most potent inhibitory activity, with an IC50 value of 33.52 μM. Inhibition kinetic analyses indicated that salvianolic acid A effectively inhibited PAD4 in a mixed inhibitory manner, and computer simulation analyses demonstrated that salvianolic acid A binds to PAD4 mainly using hydrogen bonding. Overall, our results suggest that salvianolic acid A from Salvia miltiorrhiza is a potent inhibitor of PAD4, and that salvianolic acid A can be used as a promising lead compound for the development of more potent PAD4 inhibitors.
Collapse
Affiliation(s)
- Yanfeng Li
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Chunli Gao
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Juanjuan Zhao
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Zeyuan Zhao
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Binxi Xie
- Chongqing Cigarette Factory, China Tobacco Chongqing Industrial Co, Ltd, Chongqing 400060, PR China
| | - Haiyue Zuo
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Shengxiang Zhang
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Jianhui Dong
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Xufei Chen
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Hui Li
- Zhengzhou Tobacco Research Institute of CNTC, Fengyang Street 2, Zhengzhou, Henan 450001, PR China.
| | - Yangyang Bian
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China.
| |
Collapse
|
2
|
Araujo-Abad S, Rizzuti B, Soto-Conde L, Vidal M, Abian O, Velazquez-Campoy A, Neira JL, de Juan Romero C. Citrullinating enzyme PADI4 and transcriptional repressor RING1B bind in cancer cells. Int J Biol Macromol 2024; 274:133163. [PMID: 38878927 DOI: 10.1016/j.ijbiomac.2024.133163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/26/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
Polycomb groups (PcGs) are transcriptional repressors, formed by a complex of several proteins, involved in multicellular development and cancer epigenetics. One of these proteins is the E3 ubiquitin-protein ligase RING1 (or RING1B), associated with the regulation of transcriptional repression and responsible for monoubiquitylation of the histone H2A. On the other hand, PADI4 is one of the human isoforms of a family of enzymes implicated in the conversion of arginine to citrulline, and it is also involved in the development of glioblastoma, among other types of cancers. In this work, we showed the association of PADI4 and RING1B in the nucleus and cytosol in several cancer cell lines by using immunofluorescence and proximity ligation assays. Furthermore, we demonstrated that binding was hampered in the presence of GSK484, an enzymatic PADI4 inhibitor, suggesting that RING1B could bind to the active site of PADI4, as confirmed by protein-protein docking simulations. In vitro and in silico findings showed that binding to PADI4 occurred for the isolated fragments corresponding to both the N-terminal (residues 1-221) and C-terminal (residues 228-336) regions of RING1B. Binding to PADI4 was also hampered by GSK484, as shown by isothermal titration calorimetry (ITC) experiments for the sole N-terminal region, and by both NMR and ITC for the C-terminal one. The dissociation constants between PADI4 and any of the two isolated RING1B fragments were in the low micromolar range (~2-10 μM), as measured by fluorescence and ITC. The interaction between RING1B and PADI4 might imply citrullination of the former, leading to several biological consequences, as well as being of potential therapeutic relevance for improving cancer treatment with the generation of new antigens.
Collapse
Affiliation(s)
- Salome Araujo-Abad
- Cancer Research Group, Faculty of Engineering and Applied Sciences, Universidad de Las Américas, 170124 Quito, Ecuador; IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain.
| | - Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | | | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Calle Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche (Alicante), Spain.
| |
Collapse
|
3
|
Zhu D, Lu Y, Yan Z, Deng Q, Hu B, Wang Y, Wang W, Wang Y, Wang Y. A β-Carboline Derivate PAD4 Inhibitor Reshapes Neutrophil Phenotype and Improves the Tumor Immune Microenvironment against Triple-Negative Breast Cancer. J Med Chem 2024; 67:7973-7994. [PMID: 38728549 DOI: 10.1021/acs.jmedchem.4c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Triple-negative breast cancer is a highly aggressive and heterogeneous breast cancer subtype characterized by early metastasis, poor prognosis, and high recurrence. Targeting histone citrullination-mediated chromatin dysregulation to induce epigenetic alterations shows great promise in TNBC therapy. We report the synthesis, optimization, and evaluation of a novel series of β-carboline-derived peptidyl arginine deiminase 4 inhibitors that exhibited potent inhibition of TNBC cell proliferation. The most outstanding PAD4 inhibitor, compound 28, hindered the PAD4-H3cit-NET signaling pathway and inhibited the growth of solid tumors and pulmonary metastatic nodules in the 4T1 in situ mouse model. Furthermore, 28 improved the tumor immune microenvironment by reshaping neutrophil phenotype, upregulating the proportions of dendritic cells and M1 macrophages, and reducing the amount of myeloid-derived suppressor cells. In conclusion, our work offered 28 as an efficacious PAD4 inhibitor that exerts a combination of conventional chemotherapy and immune-boosting effects, which represents a potential therapy strategy for TNBC.
Collapse
Affiliation(s)
- Di Zhu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, P. R. China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, P. R. China
| | - Yu Lu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, P. R. China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, P. R. China
| | - Zhanchao Yan
- The First Affiliated Hospital of Henan University, Center for Clinical Research and Translational Medicine, Laboratory of Epigenetics, Henan University, Kaifeng 475004, P. R. China
| | - Qian Deng
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, P. R. China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, P. R. China
| | - Bo Hu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, P. R. China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, P. R. China
| | - Yinsong Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Wenjing Wang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, P. R. China
| | - Yanming Wang
- The First Affiliated Hospital of Henan University, Center for Clinical Research and Translational Medicine, Laboratory of Epigenetics, Henan University, Kaifeng 475004, P. R. China
| | - Yuji Wang
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, P. R. China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, P. R. China
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing 100069, P. R. China
| |
Collapse
|
4
|
Li X, Hu L, Naeem A, Xiao S, Yang M, Shang H, Zhang J. Neutrophil Extracellular Traps in Tumors and Potential Use of Traditional Herbal Medicine Formulations for Its Regulation. Int J Nanomedicine 2024; 19:2851-2877. [PMID: 38529365 PMCID: PMC10961241 DOI: 10.2147/ijn.s449181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/28/2024] [Indexed: 03/27/2024] Open
Abstract
Neutrophil extracellular traps (NETs) are extracellular fibers composed of deoxyribonucleic acid (DNA) and decorated proteins produced by neutrophils. Recently, NETs have been associated with the development of many diseases, including tumors. Herein, we reviewed the correlation between NETs and tumors. In addition, we detailed active compounds from traditional herbal medicine formulations that inhibit NETs, related nanodrug delivery systems, and antibodies that serve as "guiding moieties" to ensure targeted delivery to NETs. Furthermore, we discussed the strategies used by pathogenic microorganisms to evade NETs.
Collapse
Affiliation(s)
- Xiang Li
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Lei Hu
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Abid Naeem
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, 330004, People’s Republic of China
- School of Life Science, Advanced Research Institute of Multidisciplinary Science, School of Medical Technology, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing, 100081, People’s Republic of China
| | - Shanghua Xiao
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, 330004, People’s Republic of China
| | - Ming Yang
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, 330004, People’s Republic of China
| | - Hongming Shang
- Department of Biochemistry & Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | - Jing Zhang
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, 330006, People’s Republic of China
- Key Laboratory of Modern Preparation of TCM, Ministry of Education, Jiangxi University of Chinese Medicine, Nanchang, Jiangxi, 330004, People’s Republic of China
| |
Collapse
|
5
|
Zhao J, Li Y, Gao C, Zhao Z, Zhang S, Dong J, Zuo H, Chen X, Xie B, Guo Z, Wang Y, Li H, Bian Y. Screening of natural inhibitors against peptidyl arginine deiminase 4 from herbal extracts by a high-performance liquid chromatography ultraviolet-visible based method. J Chromatogr A 2024; 1716:464643. [PMID: 38232639 DOI: 10.1016/j.chroma.2024.464643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/01/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Peptidyl arginine deiminase 4 (PAD4) is an important biocatalytic enzymes involved in the conversion of protein arginine to citrulline, its dysregulation has a great impact on many physiological processes. Recently, PAD4 has emerged as a potential therapeutic target for the treatment of various diseases including rheumatoid arthritis (RA). Traditional Chinese Medicines (TCMs), also known as herbal plants, have gained great attention by the scientific community due to their good therapeutic performance and far fewer side effects observed in the clinical treatment. However, limited researches have been reported to screen natural PAD4 inhibitors from herbal plants. The color developing reagent (COLDER) or fluorescence based methods have been widely used in PAD4 activity assay and inhibitor screening. However, both methods measure the overall absorbance or fluorescence in the reaction solution, which are easy to be affected by the background interference due to colorful extracts from herbal plants. In this study, a simple, and robust high-performance liquid chromatography ultraviolet-visible (HPLC-UV) based method was developed to determine PAD4 activity. The proposed strategy was established based on COLDER principle, while used hydrophilic l-arginine instead of hydrophobic N-benzoyl-l-arginine ethyl ester (BAEE) as a new substrate to determine PAD4 inhibition activity of herbal extracts. The herbal extracts and PAD4 generated hydrophobic l-citrulline were successfully separated by the HPLC, and the developed method was optimized and validated with a known PAD4 inhibitor (GSK484) in comparison with COLDER assay. The IC50 value of GSK484 measured by HPLC-UV method was 153 nM, and the detection limit of the citrulline was 0.5 nmol, respectively, with a linear range of 0.5 nmol to 20 nmol. The IC50 value of the HPLC-UV method was improved by nearly three times compared with COLDER assay (527 nM), and the results indicated the reliability of PAD4 inhibition via HPLC-UV method. The inhibitory effect against PAD4 were fast and accurately screened for the twenty-four extracts from eight herbs. Among them, Ephedra Herba extracts showed significant inhibitory activity against the PAD4 with the IC50 values of three extracts (ethanol, ethyl acetate and water) ranging from 29.11 μg/mL to 41.36 μg/mL, which may help researchers to discover novel natural compounds holding high PAD4 inhibition activity.
Collapse
Affiliation(s)
- Juanjuan Zhao
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Yanfeng Li
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Chunli Gao
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Zeyuan Zhao
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Shengxiang Zhang
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Jianhui Dong
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Haiyue Zuo
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Xufei Chen
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China
| | - Binxi Xie
- Chongqing Cigarette Factory, China Tobacco Chongqing Industrial Co, Ltd, Chongqing 400060, PR China
| | - Zhengwei Guo
- Key Laboratory of Clinical Research and Translational Medicine, The First Affiliated Hospital of Henan University, Kaifeng, Henan Province 475000, PR China
| | - Yanming Wang
- Key Laboratory of Clinical Research and Translational Medicine, The First Affiliated Hospital of Henan University, Kaifeng, Henan Province 475000, PR China
| | - Hui Li
- Zhengzhou Tobacco Research Institute of CNTC, Fengyang Street 2, Zhengzhou, Henan 450001, PR China.
| | - Yangyang Bian
- Key Laboratory of Resource Biology and Modern Biotechnology in Western China, College of Life Science, Northwest University, 229 TaiBai North Road, Xi'an, Shaanxi Province 710069, PR China.
| |
Collapse
|
6
|
Collie GW, Clark MA, Keefe AD, Madin A, Read JA, Rivers EL, Zhang Y. Screening Ultra-Large Encoded Compound Libraries Leads to Novel Protein-Ligand Interactions and High Selectivity. J Med Chem 2024; 67:864-884. [PMID: 38197367 PMCID: PMC10823476 DOI: 10.1021/acs.jmedchem.3c01861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024]
Abstract
The DNA-encoded library (DEL) discovery platform has emerged as a powerful technology for hit identification in recent years. It has become one of the major parallel workstreams for small molecule drug discovery along with other strategies such as HTS and data mining. For many researchers working in the DEL field, it has become increasingly evident that many hits and leads discovered via DEL screening bind to target proteins with unique and unprecedented binding modes. This Perspective is our attempt to analyze reports of DEL screening with the purpose of providing a rigorous and useful account of the binding modes observed for DEL-derived ligands with a focus on binding mode novelty.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Ying Zhang
- X-Chem,
Inc., Waltham, Massachusetts 02453, United States
| |
Collapse
|
7
|
Zainal Fithri HH, Ibrahim Z, Ali EZ. Impact of GSK199 and GSK106 binding on protein arginine deiminase IV stability and flexibility: A computational approach. Comput Biol Chem 2023; 107:107962. [PMID: 37847978 DOI: 10.1016/j.compbiolchem.2023.107962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
Abstract
Protein arginine deiminase IV (PAD4) is a potential target for diseases including rheumatoid arthritis and cancers. Currently, GSK199 is a potent, selective yet reversible PAD4 inhibitor. Its derivative, GSK106, on the other hand, was reported as an inactive compound when tested against PAD4 assay. Although they had similar skeleton, their impact towards PAD4 structural and flexibility is unknown. In order to fill the research gap, the impact of GSK199 and GSK106 binding towards PAD4 stability and flexibility is investigated via a combination of computational methods. Molecular docking indicates that GSK199 and GSK106 are capable to bind at PAD4 pocket by using its back door with -10.6 kcal/mol and -9.6 kcal/mol, respectively. The simulations of both complexes were stable throughout 100 ns. The structure of PAD4 exhibited a tighter packing in the presence of GSK106 compared to GSK199. The RMSF analysis demonstrates significant changes between the PAD4-GSK199 and PAD4-GSK106 simulations in the regions containing residues 136, 160, 220, 438, and 606. The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis shows a marked difference in binding free energies, with -11.339 kcal/mol for the PAD4-GSK199 complex and 1.063 kcal/mol for the PAD4-GSK106 complex. The hydrogen bond analysis revealed that the GSK199 and GSK106 binding to PAD4 are assisted by six hydrogen bonds and three hydrogen bonds, respectively. The visualisation of the MD simulations revealed that GSK199 remained in the PAD4 pocket, whereas GSK106 shifted away from the catalytic site. Meanwhile, molecular dockings of benzoyl arginine amide (BAEE) substrate have shown that BAEE is able to bind to PAD4 catalytic site when GSK106 was present but not when GSK199 occupied the site. Overall, combination of computational approaches successfully described the behaviour of binding pocket of PAD4 structure in the presence of the active and inactive compounds.
Collapse
Affiliation(s)
- Helmi Husaini Zainal Fithri
- Department of Pharmaceutical Chemistry, Kulliyyah of Pharmacy, International Islamic University Malaysia, Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Zalikha Ibrahim
- Department of Pharmaceutical Chemistry, Kulliyyah of Pharmacy, International Islamic University Malaysia, Indera Mahkota, 25200 Kuantan, Pahang, Malaysia; Drug Discovery and Synthetic Chemistry Research Group, Kulliyyah of Pharmacy, International Islamic University Malaysia, Indera Mahkota, 25200 Kuantan, Pahang, Malaysia.
| | - Ernie Zuraida Ali
- Inborn Error of Metabolism and Genetic Unit, Nutrition, Metabolism and Cardiovascular Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Section U13 Setia Alam, 40170 Shah Alam, Selangor, Malaysia
| |
Collapse
|
8
|
Rungratanawanich W, Ballway JW, Wang X, Won KJ, Hardwick JP, Song BJ. Post-translational modifications of histone and non-histone proteins in epigenetic regulation and translational applications in alcohol-associated liver disease: Challenges and research opportunities. Pharmacol Ther 2023; 251:108547. [PMID: 37838219 DOI: 10.1016/j.pharmthera.2023.108547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/30/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Epigenetic regulation is a process that takes place through adaptive cellular pathways influenced by environmental factors and metabolic changes to modulate gene activity with heritable phenotypic variations without altering the DNA sequences of many target genes. Epigenetic regulation can be facilitated by diverse mechanisms: many different types of post-translational modifications (PTMs) of histone and non-histone nuclear proteins, DNA methylation, altered levels of noncoding RNAs, incorporation of histone variants, nucleosomal positioning, chromatin remodeling, etc. These factors modulate chromatin structure and stability with or without the involvement of metabolic products, depending on the cellular context of target cells or environmental stimuli, such as intake of alcohol (ethanol) or Western-style high-fat diets. Alterations of epigenetics have been actively studied, since they are frequently associated with multiple disease states. Consequently, explorations of epigenetic regulation have recently shed light on the pathogenesis and progression of alcohol-associated disorders. In this review, we highlight the roles of various types of PTMs, including less-characterized modifications of nuclear histone and non-histone proteins, in the epigenetic regulation of alcohol-associated liver disease (ALD) and other disorders. We also describe challenges in characterizing specific PTMs and suggest future opportunities for basic and translational research to prevent or treat ALD and many other disease states.
Collapse
Affiliation(s)
- Wiramon Rungratanawanich
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Jacob W Ballway
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Xin Wang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kyoung-Jae Won
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, 90069, USA
| | - James P Hardwick
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA.
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| |
Collapse
|
9
|
Araujo-Abad S, Fuentes-Baile M, Rizzuti B, Bazán JF, Villamarin-Ortiz A, Saceda M, Fernández E, Vidal M, Abian O, Velazquez-Campoy A, de Juan Romero C, Neira JL. The intrinsically disordered, epigenetic factor RYBP binds to the citrullinating enzyme PADI4 in cancer cells. Int J Biol Macromol 2023; 246:125632. [PMID: 37399862 DOI: 10.1016/j.ijbiomac.2023.125632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
RYBP (Ring1 and YY 1 binding protein) is a multifunctional, intrinsically disordered protein (IDP), best described as a transcriptional regulator. It exhibits a ubiquitin-binding functionality, binds to other transcription factors, and has a key role during embryonic development. RYBP, which folds upon binding to DNA, has a Zn-finger domain at its N-terminal region. By contrast, PADI4 is a well-folded protein and it is one the human isoforms of a family of enzymes implicated in the conversion of arginine to citrulline. As both proteins intervene in signaling pathways related to cancer development and are found in the same localizations within the cell, we hypothesized they may interact. We observed their association in the nucleus and cytosol in several cancer cell lines, by using immunofluorescence (IF) and proximity ligation assays (PLAs). Binding also occurred in vitro, as measured by isothermal titration calorimetry (ITC) and fluorescence, with a low micromolar affinity (~1 μM). AlphaFold2-multimer (AF2) results indicate that PADI4's catalytic domain interacts with the Arg53 of RYBP docking into its active site. As RYBP sensitizes cells to PARP (Poly (ADP-ribose) polymerase) inhibitors, we applied them in combination with an enzymatic inhibitor of PADI4 observing a change in cell proliferation, and the hampering of the interaction of both proteins. This study unveils for the first time the possible citrullination of an IDP, and suggests that this new interaction, whether it involves or not citrullination of RYBP, might have implications in cancer development and progression.
Collapse
Affiliation(s)
- Salomé Araujo-Abad
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Centro de Biotecnología, Universidad Nacional de Loja, Avda. Pío Jaramillo Alvarado s/n, 110111 Loja, Ecuador
| | - María Fuentes-Baile
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche, Alicante, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - J Fernando Bazán
- ħ Bioconsulting, LLC, Stillwater, MN, USA; Unit for Structural Biology, Vlaams Instituut voor Biotechnologie-UGent Center for Inflammation Research, Technologiepark 71, 9052 Ghent, Belgium
| | | | - Miguel Saceda
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche, Alicante, Spain
| | - Eduardo Fernández
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Centro de Investigación Biomédica en Red CIBER-BBN, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Calle Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Olga Abian
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrián Velazquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche, Alicante, Spain.
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) - Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
| |
Collapse
|
10
|
Araujo-Abad S, Neira JL, Rizzuti B, García-Morales P, de Juan Romero C, Santofimia-Castaño P, Iovanna J. Intrinsically Disordered Chromatin Protein NUPR1 Binds to the Enzyme PADI4. J Mol Biol 2023; 435:168033. [PMID: 36858171 DOI: 10.1016/j.jmb.2023.168033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
The nuclear protein 1 (NUPR1) is an intrinsically disordered protein involved in stress-mediated cellular conditions. Its paralogue nuclear protein 1-like (NUPR1L) is p53-regulated, and its expression down-regulates that of the NUPR1 gene. Peptidyl-arginine deiminase 4 (PADI4) is an isoform of a family of enzymes catalyzing arginine to citrulline conversion; it is also involved in stress-mediated cellular conditions. We characterized the interaction between NUPR1 and PADI4 in vitro, in silico, and in cellulo. The interaction of NUPR1 and PADI4 occurred with a dissociation constant of 18 ± 6 μM. The binding region of NUPR1, mapped by NMR, was a hydrophobic polypeptide patch surrounding the key residue Ala33, as pinpointed by: (i) computational results; and, (ii) site-directed mutagenesis of residues of NUPR1. The association between PADI4 and wild-type NUPR1 was also assessed in cellulo by using proximity ligation assays (PLAs) and immunofluorescence (IF), and it occurred mainly in the nucleus. Moreover, binding between NUPR1L and PADI4 also occurred in vitro with an affinity similar to that of NUPR1. Molecular modelling provided information on the binding hot spot for PADI4. This is an example of a disordered partner of PADI4, whereas its other known interacting proteins are well-folded. Altogether, our results suggest that the NUPR1/PADI4 complex could have crucial functions in modulating DNA-repair, favoring metastasis, or facilitating citrullination of other proteins.
Collapse
Affiliation(s)
- Salomé Araujo-Abad
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Centro de Biotecnología, Universidad Nacional de Loja, Avda. Pío Jaramillo Alvarado s/n, Loja, 110111 Loja, Ecuador
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Bruno Rizzuti
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
| | | | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche (Alicante), Spain
| | - Patricia Santofimia-Castaño
- Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France.
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille, INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
| |
Collapse
|
11
|
Zhang C, Zhang J, Zhang Y, Song Z, Bian J, Yi H, Ma Z. Identifying neutrophil-associated subtypes in ulcerative colitis and confirming neutrophils promote colitis-associated colorectal cancer. Front Immunol 2023; 14:1095098. [PMID: 36845139 PMCID: PMC9950623 DOI: 10.3389/fimmu.2023.1095098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Background Ulcerative colitis (UC) is a chronic inflammatory disease of the intestinal mucosa, the incidence of which has increased worldwide. There is still a lack of clear understanding of the pathogenesis of ulcerative colitis that ultimately leads to colitis-associated colorectal cancer. Method We download UC transcriptome data from the GEO database and pass the limma package in order to identify differentially expressed genes. Gene Set Enrichment Analysis (GSEA) was used to identify potential biological pathways. We identified immune cells associated with UC by CIBERSORT and Weighted co-expression network analysis (WGCNA). We used validation cohorts and mouse models to verify the expression of the hub genes and the role of neutrophils. Result We identified 65 differentially expressed genes in UC samples and healthy controls. GSEA, KEGG, and GO analyses displayed that DEGs were enriched in immune-related pathways. CIBERSORT analysis revealed increased infiltration of neutrophils in UC tissues. The red module, obtained by WGCNA analysis, was considered to be the most relevant module for neutrophils.Based on neutrophil-associated differentially expressed genes, UC patients were classified into two subtypes of neutrophil infiltration. We discovered that the highly neutrophil-infiltrated subtype B of UC patients had a higher risk of developing CAC. Five genes were identified as biomarkers by searching for DEGs between distinct subtypes. Finally, using the mouse model, we determined the expression of these five genes in the control, DSS, and AOM/DSS groups. The degree of neutrophil infiltration in mice and the percentage of MPO and pSTAT3 expression in neutrophils were analyzed by flow cytometry. In the AOM/DSS model, MPO and pSTAT3 expressions were significantly increased. Conclusions These findings suggested neutrophils might promote the conversion of UC into CAC. These findings improve our understanding of the pathogenesis of CAC and provide new and more effective insights into the prevention and treatment of CAC.
Collapse
Affiliation(s)
- Chen Zhang
- Colorectal & Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiantao Zhang
- Colorectal & Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Yanli Zhang
- Central Laboratory, First Hospital of Jilin University, Changchun, Jilin, China
- Echocardiography Department, First Hospital of Jilin University, Changchun, Jilin, China
| | - Zian Song
- Colorectal & Anal Surgery Department, General Surgery Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jing Bian
- Department of Respiratory Medicine, First Affiliated Hospital of Jilin University, Changchun, Jilin, China
| | - Huanfa Yi
- Central Laboratory, First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhanchuan Ma
- Central Laboratory, First Hospital of Jilin University, Changchun, Jilin, China
| |
Collapse
|
12
|
Neira JL, Rizzuti B, Araujo-Abad S, Abian O, Fárez-Vidal ME, Velazquez-Campoy A, de Juan Romero C. The armadillo-repeat domain of Plakophilin 1 binds to human enzyme PADI4. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140868. [PMID: 36372391 DOI: 10.1016/j.bbapap.2022.140868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/10/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022]
Abstract
Plakophilin 1 (PKP1), a member of the armadillo repeat family of proteins, is a key structural component of cell-cell adhesion scaffolds, although it can also be found in other cell locations, including the cytoplasm and the nucleus. PADI4 (peptidyl-arginine deiminase 4) is one of the human isoforms of a family of enzymes engaged in the conversion of arginine to citrulline, and is present in monocytes, macrophages, granulocytes, and in several types of cancer cells. It is the only family member observed both within the nucleus and the cytoplasm under ordinary conditions. We studied the binding of the armadillo domain of PKP1 (ARM-PKP1) with PADI4, by using several biophysical methods, namely fluorescence, far-ultraviolet (far-UV) circular dichroism (CD), isothermal titration calorimetry (ITC), and molecular simulations; furthermore, binding was also tested by Western-blot (WB) analyses. Our results show that there was binding between the two proteins, with a dissociation constant in the low micromolar range (∼ 1 μM). Molecular modelling provided additional information on the possible structure of the binding complex, and especially on the binding hot-spot predicted for PADI4. This is the first time that the interaction between these two proteins has been described and studied. Our findings could be of importance to understand the development of tumors, where PKP1 and PADI4 are involved. Moreover, our findings pave the way to describe the formation of neutrophil extracellular traps (NETs), whose construction is modulated by PADI4, and which mediate the proteolysis of cell-cell junctions where PKP1 intervenes.
Collapse
Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Bruno Rizzuti
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Salome Araujo-Abad
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Centro de Biotecnología, Universidad Nacional de Loja, Avda. Pío Jaramillo Alvarado s/n, Loja, 110111 Loja, Ecuador
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - María Esther Fárez-Vidal
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain; Instituto de Investigación Biomédica IBS, Granada, Spain; Complejo Hospitalario Universitario de Granada, Universidad de Granada, 18071 Granada, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems - Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche (Alicante), Spain.
| |
Collapse
|
13
|
Pan Z, Xie X, Chen Y, Pan S, Wu Z, Yang C, Liang J, Zhang M, Wang Q, Chen J, Zhou L, Luo X. Huang Qin Decoction inhibits the initiation of experimental colitis associated carcinogenesis by controlling the PAD4 dependent NETs. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 107:154454. [PMID: 36155218 DOI: 10.1016/j.phymed.2022.154454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/27/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Colorectal cancer is associated with ulcerative colitis (UC). The infiltration of neutrophils is the main cause of DNA damage produced by inflammation in the intestinal epithelium. Under the action of peptidyl arginine deaminase 4 (PAD4), neutrophils dissociate chromatin and form neutrophil extracellular traps (NETs), which can aggravate tissue inflammation and encourage tumor development. Although Huang Qin Decoction (HQD) was found to be useful in treating UC and was used to gradually prevent and treat digestive tract cancers, the underlying reasons were unclear. METHODS To demonstrate HQD could inhibits the initiation of colitis associated carcinogenesis by controlling NETs related inflammation, we first performed an AOM/DSS-generated colitis-associated carcinogenesis model to assess the efficacy of HQD in reducing neutrophil infiltration and anti-tumor activity. Then, using network pharmacology research, we investigated the potential mechanisms underlying those medicinal effects, as demonstrated by the detection of NETs aggregation and PAD4 expression changes in the colon. RESULTS HQD substantially reduced the number of colon cancers and the expression of Ki67, restored the level of intestinal tight junction protein occludin and ZO-1, and relieved the intestinal inflammation caused by TNF-α, IL-1β. At the same time, it inhibited neutrophil infiltration in the colon and improved the immunosurveillance of CD8+T cells. The potential mechanisms of HQD intervention against UC and UC with neoplasia (UCN) were studied using network pharmacology, and 156 conjunct genes as well as numerous inflammation-related pathways were identified. Protein-protein interaction (PPI) analysis indicated that HQD inhibition of intestinal tumors might be related to the deactivation of PAD4, which was verified by the down-regulation of NETs, MPO-DNA complex levels, and PAD4 expression after HQD treatment. CONCLUSION Huang Qin Decoction inhibits the initiation of colitis associated carcinogenesis by controlling PAD4-dependent neutrophil extracellular traps.
Collapse
Affiliation(s)
- Zengfeng Pan
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No. 232 Outer Ring Road, Panyu District, Guangzhou, Guang Dong 510006, China
| | - Xuting Xie
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No. 232 Outer Ring Road, Panyu District, Guangzhou, Guang Dong 510006, China
| | - Yunliang Chen
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No. 232 Outer Ring Road, Panyu District, Guangzhou, Guang Dong 510006, China
| | - Simin Pan
- The First School of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Zhiyun Wu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No. 232 Outer Ring Road, Panyu District, Guangzhou, Guang Dong 510006, China
| | - Caiyi Yang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No. 232 Outer Ring Road, Panyu District, Guangzhou, Guang Dong 510006, China
| | - Junjie Liang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No. 232 Outer Ring Road, Panyu District, Guangzhou, Guang Dong 510006, China
| | - Meilin Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No. 232 Outer Ring Road, Panyu District, Guangzhou, Guang Dong 510006, China
| | - Qing Wang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No. 232 Outer Ring Road, Panyu District, Guangzhou, Guang Dong 510006, China
| | - Jinyan Chen
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Lian Zhou
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No. 232 Outer Ring Road, Panyu District, Guangzhou, Guang Dong 510006, China.
| | - Xia Luo
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No. 232 Outer Ring Road, Panyu District, Guangzhou, Guang Dong 510006, China.
| |
Collapse
|
14
|
Zhu D, Lu Y, Wang Y, Wang Y. PAD4 and Its Inhibitors in Cancer Progression and Prognosis. Pharmaceutics 2022; 14:2414. [PMID: 36365233 PMCID: PMC9699117 DOI: 10.3390/pharmaceutics14112414] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/28/2022] [Accepted: 11/06/2022] [Indexed: 07/24/2023] Open
Abstract
The systemic spread of malignancies and the risk of cancer-associated thrombosis are major clinical challenges in cancer therapy worldwide. As an important post-translational modification enzyme, peptidyl arginine deiminase 4 (PAD4) could mediate the citrullination of protein in different components (including nucleus and cytoplasm, etc.) of a variety of cells (tumor cells, neutrophils, macrophages, etc.), thus participating in gene regulation, neutrophil extracellular trap (NET) and macrophage extracellular trap (MET). Thereby, PAD4 plays an important role in enhancing the growth of primary tumors and facilitating the distant metastasis of cancer cells. In addition, it is related to the formation of cancer-associated thrombosis. Therefore, the development of PAD4-specific inhibitors may be a promising strategy for treating cancer, and it may improve patient prognosis. In this review, we describe PAD4 involvement in gene regulation, protein citrullination, and NET formation. We also discuss its potential role in cancer and cancer-associated thrombosis, and we summarize the development and application of PAD4 inhibitors.
Collapse
Affiliation(s)
- Di Zhu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, China
| | - Yu Lu
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, China
| | - Yanming Wang
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yuji Wang
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences of Capital Medical University, Beijing 100069, China
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, Beijing 100069, China
| |
Collapse
|
15
|
Gu W, Zhang M, Gao F, Niu Y, Sun L, Xia H, Li W, Zhang Y, Guo Z, Du G. Berberine regulates PADI4-related macrophage function to prevent lung cancer. Int Immunopharmacol 2022; 110:108965. [PMID: 35764017 DOI: 10.1016/j.intimp.2022.108965] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 12/14/2022]
Abstract
Coptis chinensis Franch (CCF) has been widely used by Chinese old herbalist doctor to treat internal and external diseases including malignant sore and cancer. Berberine (BBR) is a major bioactive compound in CCF and may exert anti-tumor and anti-inflammatory effects like CCF. However, the prevention effect of berberine against lung cancer and its relevance of anti-inflammation property to cancer-preventing effect are still obscure. Protein arginine deaminase 4 (PAD4) played an important role in macrophage related inflammatory response, the purpose of this study was to identify whether berberine can prevent lung cancer and explore its effect on PADI4-related macrophage function. In vitro, PADI4 overexpression affects cell-activated state in macrophages. PADI4 overexpressed macrophages promote epithelial-mesenchymal transition (EMT) of A549 lung cancer cells and inhibit cell apoptosis. Berberine at the experiment dose had no effect on cell viability of U937-derived macrophages, but could significantly inhibit PADI4 expression to reverse the macrophage-activated state and the lung cancer -promoting effect of PADI4-overexpressed macrophages. Unlike GSK484, berberine had a little effect on the PADI4 citrullination activity at the experimental doses, its IC50 for PADI4 inhibition is 45.07 μM (44.03-46.12 μM). In the mouse lung carcinogenetic model, PADI4 expression was directly related to the number of lung nodules. Berberine had the similar role to GSK484 in reducing the number of lung tumor nodules with the improved lung pathology in a dose-dependent manner and significantly inhibited PADI4 expression. Further, we found that PADI4 overexpression could inhibit IRF5 expression, up-regulate CD163 and CD206 and down-regulate CD86 in macrophages, which could be reversed by berberine. Our results suggest that berberine may regulate PADI4-related macrophage function to prevent lung cancer.
Collapse
Affiliation(s)
- Wenwen Gu
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng 475004, Henan, China
| | - Mengdi Zhang
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng 475004, Henan, China
| | - Fan Gao
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng 475004, Henan, China
| | - Yuji Niu
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng 475004, Henan, China
| | - Luyao Sun
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng 475004, Henan, China
| | - Haojie Xia
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng 475004, Henan, China
| | - Wenwen Li
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng 475004, Henan, China
| | - Yaru Zhang
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng 475004, Henan, China
| | - Zhenzhen Guo
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng 475004, Henan, China.
| | - Gangjun Du
- Institute of Pharmacy, Pharmaceutical College of Henan University, Kaifeng 475004, Henan, China; School of Pharmacy and Chemical Engineering, Zhengzhou University of Industry Technology, Xinzheng, Henan Province 451150, China.
| |
Collapse
|