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Chen Y, Guo P, Dong Z. The role of histone acetylation in transcriptional regulation and seed development. PLANT PHYSIOLOGY 2024; 194:1962-1979. [PMID: 37979164 DOI: 10.1093/plphys/kiad614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/09/2023] [Accepted: 10/29/2023] [Indexed: 11/20/2023]
Abstract
Histone acetylation is highly conserved across eukaryotes and has been linked to gene activation since its discovery nearly 60 years ago. Over the past decades, histone acetylation has been evidenced to play crucial roles in plant development and response to various environmental cues. Emerging data indicate that histone acetylation is one of the defining features of "open chromatin," while the role of histone acetylation in transcription remains controversial. In this review, we briefly describe the discovery of histone acetylation, the mechanism of histone acetylation regulating transcription in yeast and mammals, and summarize the research progress of plant histone acetylation. Furthermore, we also emphasize the effect of histone acetylation on seed development and its potential use in plant breeding. A comprehensive knowledge of histone acetylation might provide new and more flexible research perspectives to enhance crop yield and stress resistance.
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Affiliation(s)
- Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Peiguo Guo
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
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2
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Akhilesh, Baidya ATK, Uniyal A, Das B, Kumar R, Tiwari V. Structure-based virtual screening and molecular dynamics simulation for the identification of sphingosine kinase-2 inhibitors as potential analgesics. J Biomol Struct Dyn 2022; 40:12472-12490. [PMID: 34519252 DOI: 10.1080/07391102.2021.1971559] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Neuropathic pain is due to an injury or disease of the somatosensory nervous system, which accounts for a significant economical and health burden to society. Due to poor understanding of their underlying mechanisms, the available treatments merely provide symptomatic relief and precipitates a variety of adverse effects. This suggests that there is an unmet medical need that must be addressed with effective strategies for the development of novel therapeutics. Sphingosine kinase 2 (SphK2) is an oncogenic lipid kinase that has emerged as a promising target for chronic pain and other diseases. In the present study, we have explored the structure-based virtual high-throughput screening of the Nuclei of Bioassays, Ecophysiology, and Biosynthesis of Natural Products Database (NuBBE) to identify potent natural products as inhibitors of SphK2. A molecular docking study was performed to calculate binding affinities and specificity to identify potential leads against SphK2. Initially, hits were selected by the implementation of absorption, distribution, metabolism, excretion and toxicity properties, Lipinski rule, and PAINS filters. The top-scoring hits also exhibiting an optimal ADMET profile were subjected to MM/GBSA free binding free energy calculation and molecular dynamics simulation. The results from molecular dynamics simulation revealed a stable ligand -SphK2 complex with protein and ligand RMSD within reasonable limits. Overall, we identified compounds, NuBBE_972 and NuBBE_1107 as potential inhibitors of SphK2 with optimal pharmacokinetic properties which have the potential to be developed as novel therapeutics for the management of chronic pain.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akhilesh
- Neuroscience & Pain Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Anurag T K Baidya
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Ankit Uniyal
- Neuroscience & Pain Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Bhanuranjan Das
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Rajnish Kumar
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India.,Department of Neuroscience Care and Society, Division of Neurogeriatrics, Karolinska Institute, Solna, Sweden
| | - Vinod Tiwari
- Neuroscience & Pain Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
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3
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He L, Liu Y, Xu J, Li J, Cheng G, Cai J, Dang J, Yu M, Wang W, Duan W, Liu K. Inhibitory Effects of Myriocin on Non-Enzymatic Glycation of Bovine Serum Albumin. Molecules 2022; 27:molecules27206995. [PMID: 36296589 PMCID: PMC9607541 DOI: 10.3390/molecules27206995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/12/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
Advanced glycation end products (AGEs) are the compounds produced by non-enzymatic glycation of proteins, which are involved in diabetic-related complications. To investigate the potential anti-glycation activity of Myriocin (Myr), a fungal metabolite of Cordyceps, the effect of Myr on the formation of AGEs resulted from the glycation of bovine serum albumin (BSA) and the interaction between Myr and BSA were studied by multiple spectroscopic techniques and computational simulations. We found that Myr inhibited the formation of AGEs at the end stage of glycation reaction and exhibited strong anti-fibrillation activity. Spectroscopic analysis revealed that Myr quenched the fluorescence of BSA in a static process, with the possible formation of a complex (approximate molar ratio of 1:1). The binding between BSA and Myr mainly depended on van der Waals interaction, hydrophobic interactions and hydrogen bond. The synchronous fluorescence and UV-visible (UV-vis) spectra results indicated that the conformation of BSA altered in the presence of Myr. The fluorescent probe displacement experiments and molecular docking suggested that Myr primarily bound to binding site 1 (subdomain IIA) of BSA. These findings demonstrate that Myr is a potential anti-glycation agent and provide a theoretical basis for the further functional research of Myr in the prevention and treatment of AGEs-related diseases.
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Affiliation(s)
- Libo He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yang Liu
- Department of Central Laboratory, The First People’s Hospital of Huzhou, First Affiliated Hospital of Huzhou University, Huzhou 313000, China
| | - Junling Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jingjing Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Guohua Cheng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jiaxiu Cai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jinye Dang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Meng Yu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Weiyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wei Duan
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
| | - Ke Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Correspondence:
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Workman AS. Comparative analyses and molecular videography of MD simulations on WT human SOD1. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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Zhang Z, Liu L, Li H, Zhang S, Fu X, Zhai X, Yang N, Shen J, Li R, Li D. Exogenous Melatonin Promotes the Salt Tolerance by Removing Active Oxygen and Maintaining Ion Balance in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 12:787062. [PMID: 35173749 PMCID: PMC8841648 DOI: 10.3389/fpls.2021.787062] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/17/2021] [Indexed: 05/16/2023]
Abstract
Melatonin (MT) is a small molecule indole hormone that plays an important role in the regulation of biological processes and abiotic stress resistance. Previous studies have confirmed that MT promotes the normal development of plants under stress by mediating physiological regulation mechanisms. However, the physiological mechanism of exogenous MT regulating seed germination and seedling growth of wheat under salt stress is still unclear. In this study, NaCl stress decreased germination rate and inhibited seedling growth of wheat, but shoot length, root length, and plant weight of SM15 did not change significantly. The addition of 300 μM MT in the cultivation solution directly promoted the germination rate of SM15 and ZM18, and lateral root production, but decreased the germination rate of JM22 and inhibited the length of germ and radicle of three varieties under salt stress. For wheat seedling, application of MT could increase proline content, soluble protein, soluble sugar, Ca2+ content, and vital amino acid content in leaves to keep high water content, low level of H2O2 content, and low [K+]/[Na+] ratio. MT increased root vigor and [K+]/[Na+] ratio and decreased H2O2 content in root induced by salt stress. In conclusion, MT enhanced salt tolerance in wheat seeds and seedlings by regulating the synthesis of soluble protein and sugar, ion compartmentation in roots and leaves, enhancement of enzymatic systems, and changes in amino acid levels. Salt resistance varied with different varieties under the same environmental condition. SM15 was a higher salt-resistant variety and JM22 was a salt-sensitive one. In wheat production, the application of exogenous MT should consider the differences among varieties of wheat during the sowing and seedling stages.
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Affiliation(s)
- Zhihui Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Liantao Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hongye Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaocong Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xiaoyi Fu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Xiuzhen Zhai
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Na Yang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jiaming Shen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Ruiqi Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Dongxiao Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, China
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High-Throughput Docking and Molecular Dynamics Simulations towards the Identification of Potential Inhibitors against Human Coagulation Factor XIIa. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2020:2852051. [PMID: 32549905 PMCID: PMC7261338 DOI: 10.1155/2020/2852051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/22/2020] [Accepted: 04/07/2020] [Indexed: 11/17/2022]
Abstract
Human coagulation factor XIIa (FXIIa) is a trypsin-like serine protease that is involved in pathologic thrombosis. As a potential target for designing safe anticoagulants, FXIIa has received a great deal of interest in recent years. In the present study, we employed virtual high-throughput screening of 500,064 compounds within Enamine database to acquire the most potential inhibitors of FXIIa. Subsequently, 18 compounds with significant binding energy (from -65.195 to -15.726 kcal/mol) were selected, and their ADMET properties were predicted to select representative inhibitors. Three compounds (Z1225120358, Z432246974, and Z146790068) exhibited excellent binding affinity and druggability. MD simulation for FXIIa-ligand complexes was carried out to reveal the stability and inhibition mechanism of these three compounds. Through the inhibition of activated factor XIIa assay, we tested the activity of five compounds Z1225120358, Z432246974, Z45287215, Z30974175, and Z146790068, with pIC50 values of 9.3∗10−7, 3.0∗10−5, 7.8∗10−7, 8.7∗10−7, and 1.3∗10−6 M, respectively; the AMDET properties of Z45287215 and Z30974175 show not well but have better inhibition activity. We also found that compounds Z1225120358, Z45287215, Z30974175, and Z146790068 could be more inhibition of FXIIa than Z432246974. Collectively, compounds Z1225120358, Z45287215, Z30974175, and Z146790068 were anticipated to be promising drug candidates for inhibition of FXIIa.
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Esfandi B, Atabati M. Sequential Dihedral Angles (SDAs): A Method for Evaluating the 3D Structure of Proteins. Protein J 2021; 40:1-7. [PMID: 33442828 DOI: 10.1007/s10930-020-09961-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2020] [Indexed: 11/29/2022]
Abstract
One of the most important steps in modeling three-dimensional (3D) structures of proteins is the evaluation of the constructed models. The present study suggests that the correctness of a structure may be tested by using the characteristics of sequential dihedral angles (SDAs) between adjacent alpha-carbons (Cα) in the main chains of proteins. From our studies on protein structures in the protein data bank (PDB), the SDAs between the Cα in the main chains are limited in their values. In addition, the sum of the absolute values of the three sequential dihedral angles (SDAs) can never be 0 degree. Moreover, 48 degrees is the lowest value existing for the sum of the absolute values of three sequential dihedral angles (SDAs). Thus, the SDAs between the alpha-carbons along the main chains of proteins may be a useful parameter for evaluating anomalies in protein structures.
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Affiliation(s)
- Babak Esfandi
- School of Chemistry, Damghan University, Damghan, Iran
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8
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Wang W, Zhang Q, Xiong X, Zheng Y, Yang W, Du L. Investigation on the influence of galloyl moiety to the peptidyl prolyl cis/trans isomerase Pin1: A spectral and computational analysis. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Li D, Batchelor WD, Zhang D, Miao H, Li H, Song S, Li R. Analysis of melatonin regulation of germination and antioxidant metabolism in different wheat cultivars under polyethylene glycol stress. PLoS One 2020; 15:e0237536. [PMID: 32790719 PMCID: PMC7425870 DOI: 10.1371/journal.pone.0237536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
Melatonin is effective in enhancing various abiotic stress resistances of plants. However, its underlying mechanisms in drought-resistance in winter wheat (Triticum aestivum L.) is not clear. The goal of this work was to investigate the effect of melatonin on seed germination and to evaluate leaf antioxidant physiology for two wheat varieties. Experiments included 20% PEG, melatonin plus 20% PEG and a control using two contrasting wheat varieties (JM22– drought sensitive and HG35– drought resistant). Melatonin levels were 0, 1, 10, 100 and 300 μmol L-1. Results revealed that 300 μmol L-1 of melatonin alleviated the negative effect of water stress on germination and increased radicle length, radicle number, and plumule length of the germinated seeds. Principal component analysis showed a significant change in amino acid content during germination and this change was dependent on melatonin concentration and the variety. Lysine (Lys) content in wheat seeds under the PEG plus 300 μmol L-1 melatonin treatment increased compared with that of the seeds under PEG alone. There was a significant and positive correlation between Lys content and morphological index of germination. During seedling growth, soluble protein was involved in osmotic adjustment and superoxide dismutase (SOD) activity was increased to mitigate the damage in the cytomembrane of JM 22 leaf under 300 μmol L-1 melatonin plus PEG treatment. The effect of melatonin was dependent on SOD activity increasing significantly for HG35—a drought resistant variety. The results of this work lays a foundation for further studies to determine if melatonin can be economically used to mitigate the impact of dry planting conditions on wheat productivity in North China Plain.
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Affiliation(s)
- Dongxiao Li
- College of Agronomy, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, China
| | - William D. Batchelor
- Biosystems Engineering Department, Auburn University, Auburn, Alabama, United States of America
| | - Di Zhang
- College of Agronomy, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Hanxiao Miao
- College of Agronomy, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Hongye Li
- College of Agronomy, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Shijia Song
- Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Ruiqi Li
- College of Agronomy, State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, Hebei Province, China
- * E-mail:
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10
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Zsidó BZ, Hetényi C. Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome. Int J Mol Sci 2020; 21:ijms21114134. [PMID: 32531926 PMCID: PMC7311975 DOI: 10.3390/ijms21114134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Development of valid structure–activity relationships (SARs) is a key to the elucidation of pathomechanisms of epigenetic diseases and the development of efficient, new drugs. The present review is based on selected methodologies and applications supplying molecular structure, binding affinity and biological activity data for the development of new SARs. An emphasis is placed on emerging trends and permanent challenges of new discoveries of SARs in the context of proteins as epigenetic drug targets. The review gives a brief overview and classification of the molecular background of epigenetic changes, and surveys both experimental and theoretical approaches in the field. Besides the results of sophisticated, cutting edge techniques such as cryo-electron microscopy, protein crystallography, and isothermal titration calorimetry, examples of frequently used assays and fast screening techniques are also selected. The review features how different experimental methods and theoretical approaches complement each other and result in valid SARs of the epigenome.
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Zhang Q, Sang F, Qian J, Lyu S, Wang W, Wang Y, Li Q, Du L. Identification of novel potential PI3Kα inhibitors for cancer therapy. J Biomol Struct Dyn 2020; 39:3721-3732. [DOI: 10.1080/07391102.2020.1771421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Qingyan Zhang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Feng Sang
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jieyu Qian
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - ShaoLi Lyu
- Department of Ecology and Resource Engineering, Hetao College, Bayannur, Inner Mongolia, PR of China
| | - Wang Wang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ying Wang
- The Department of Anesthesiology, the First Affiliated of Henan University, Kaifeng, China
| | - Qiang Li
- Department of Acquired Immune Deficiency Syndrome Treatment and Research Center, The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
- Henan Key Laboratory of Viral Diseases Prevention and Treatment of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - LinFang Du
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Lyu S, Wang W. Spectroscopic methodologies and computational simulation studies on the characterization of the interaction between human serum albumin and astragalin. J Biomol Struct Dyn 2020; 39:2959-2970. [DOI: 10.1080/07391102.2020.1758213] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- ShaoLi Lyu
- Department of Ecology and Resource Engineering, Hetao College, Bayannur, Inner Mongolia, PR of China
| | - Wang Wang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR of China
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Bendahou MA, Arrouchi H, Lakhlili W, Allam L, Aanniz T, Cherradi N, Ibrahimi A, Boutarbouch M. Computational Analysis of IDH1, IDH2, and TP53 Mutations in Low-Grade Gliomas Including Oligodendrogliomas and Astrocytomas. Cancer Inform 2020; 19:1176935120915839. [PMID: 32313423 PMCID: PMC7160765 DOI: 10.1177/1176935120915839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
Introduction: The emergence of new omics approaches, such as genomic algorithms to identify
tumor mutations and molecular modeling tools to predict the
three-dimensional structure of proteins, has facilitated the understanding
of the dynamic mechanisms involved in the pathogenesis of low-grade gliomas
including oligodendrogliomas and astrocytomas. Methods: In this study, we targeted known mutations involved in low-grade gliomas,
starting with the sequencing of genomic regions encompassing exon 4 of
isocitrate dehydrogenase 1 (IDH1) and isocitrate
dehydrogenase 2 (IDH2) and the four exons (5-6 and 7-8) of
TP53 from 32 samples, followed by computational
analysis to study the impact of these mutations on the structure and
function of 3 proteins IDH1, IDH2, and
p53. Results: We obtain a mutation that has an effect on the catalytic site of the protein
IDH1 as R132H and on the catalytic site of the protein
IDH2 as R172M. Other mutations at p53
have been identified as K305N, which is a pathogenic mutation; R175 H, which
is a benign mutation; and R158G, which disrupts the structural conformation
of the tumor suppressor protein. Conclusion: In low-grade gliomas, mutations in IDH1, IDH2, and
TP53 may be the key to tumor progression because they
have an effect on the function of the protein such as mutations R132H in
IDH1 and R172M in IDH2, which change
the function of the enzyme alpha-ketoglutarate, or R158G in
TP53, which affects the structure of the generated
protein, thus their importance in understanding gliomagenesis and for more
accurate diagnosis complementary to the anatomical pathology tests.
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Affiliation(s)
- Mohammed Amine Bendahou
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Housna Arrouchi
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Wiame Lakhlili
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Loubna Allam
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Tarik Aanniz
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Nadia Cherradi
- Department of Pathological Anatomy, Hospital of Specialties, CHU Ibn Sina, Rabat, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory (MedBiotech), BioInova Research Center, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
| | - Mahjouba Boutarbouch
- Department of Neurosurgery, Hospital of Specialties, CHU Ibn Sina, Rabat, Medical and Pharmacy School, Mohammed V University Rabat, Morocco
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Kwiatos N, Jędrzejczak-Krzepkowska M, Krzemińska A, Delavari A, Paneth P, Bielecki S. Evolved Fusarium oxysporum laccase expressed in Saccharomyces cerevisiae. Sci Rep 2020; 10:3244. [PMID: 32094483 PMCID: PMC7039978 DOI: 10.1038/s41598-020-60204-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/14/2020] [Indexed: 02/06/2023] Open
Abstract
Fusarium oxysporum laccase was functionally expressed in Saccharomyces cerevisiae and engineered towards higher expression levels and higher reactivity towards 2,6-dimethoxyphenol, that could be used as a mediator for lignin modification. A combination of classical culture optimization and protein engineering led to around 30 times higher activity in the culture supernatant. The winner mutant exhibited three times lower Km, four times higher kcat and ten times higher catalytic efficiency than the parental enzyme. The strategy for laccase engineering was composed of a combination of random methods with a rational approach based on QM/MM MD studies of the enzyme complex with 2,6-dimethoxyphenol. Laccase mediator system with 2,6-dimethoxyphenol caused fulvic acids release from biosolubilized coal.
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Affiliation(s)
- Natalia Kwiatos
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Marzena Jędrzejczak-Krzepkowska
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Agnieszka Krzemińska
- Institute of Physics, Lodz University of Technology, Wólczańska 219, 90-924, Lodz, Poland
| | | | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wróblewskiego 15, 93-590, Lodz, Poland
| | - Stanisław Bielecki
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland.
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15
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Ji M, Ding Y, Li X, Mao N, Chen J. Computational investigation of a ternary model of SnoN-SMAD3-SMAD4 complex. Comput Biol Chem 2019; 83:107159. [PMID: 31743832 DOI: 10.1016/j.compbiolchem.2019.107159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/28/2019] [Accepted: 11/03/2019] [Indexed: 12/18/2022]
Abstract
The transforming growth factor β (TGFβ) plays an essential role in the regulation of cellular processes such as cell proliferation, migration, differentiation, and apoptosis by association with SMAD transcriptional factors that are regulated by the transcriptional regulator SnoN. The crystal structure of SnoN-SMAD4 reveals that SnoN can adopt two binding modes, the open and closed forms, at the interfaces of SMAD4 subunits. Accumulating evidence indicates that SnoN can interact with both SMAD3 and SMAD4 to form a ternary SnoN-SMAD3-SMAD4 complex in the TGFβ signaling pathway. However, how the interaction of SnoN with the SMAD3 and SMAD4 remains unclear. Here, molecular dynamics (MD) simulations and molecular modeling methods were performed to figure out this issue. The simulations reveal that SnoNopen exists in two, open and semi-closed, conformations. Molecular modeling and MD simulation studies suggest that the SnoNclosed form interferes with the SMAD3-SMAD4 protein; in contract, the SnoNopen can form a stable SnoN-SMAD3-SMAD4 complex. These mechanistic mechanisms may help elucidate the detailed engagement of SnoN with two SMAD3 and SMAD4 transcriptional factors in the regulation of TGFβ signaling pathway.
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Affiliation(s)
- Mingfei Ji
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China
| | - Yelei Ding
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, 200433, China.
| | - Ningfang Mao
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, 200433, China.
| | - Jie Chen
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China.
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Insight into the structural stability of wild-type and histidine mutants in Pin1 by experimental and computational methods. Sci Rep 2019; 9:8413. [PMID: 31182777 PMCID: PMC6557836 DOI: 10.1038/s41598-019-44926-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/28/2019] [Indexed: 01/21/2023] Open
Abstract
Pin1, a polypeptide proline isomerase parvulin, plays a key role in Alzheimer’s disease (AD), common tumors and cancers. Two conservative histidine residues, His59 and His157, are important for maintaining the stability of the PPIase domain. Hence multiple spectral and computational techniques were performed to investigate the potential mechanism of two histidine residues. Thermal denaturation indicated that both residues His59 and His157 are not sensitive to the lower temperatures, while residue His59 is more sensitive to the higher temperatures than residue His157. Acidic denaturation suggested that influences of both residues His59 and His157 to acidic stability were the difference from Pin1-WT. ANS and RLS spectra hinted that there was no significant effect on hydrophobic change and aggregation by histidine mutations. The GndHCl-induced denaturation implied that residues His59 and His157 contributed the most to the chemical stability. MD simulations revealed that residues His59 and His157 mutations resulted in that the hydrogen bond network of the dual histidine motif was destroyed wholly. In summary, these histidine residues play an important role in maintaining the structural stability of the PPIase domain.
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17
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In Silico Investigation of the Anti-Tumor Mechanisms of Epigallocatechin-3-Gallate. Molecules 2019; 24:molecules24071445. [PMID: 30979098 PMCID: PMC6480119 DOI: 10.3390/molecules24071445] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/06/2019] [Accepted: 04/09/2019] [Indexed: 12/15/2022] Open
Abstract
The EGCG, an important component of polyphenol in green tea, is well known due to its numerous health benefits. We employed the reverse docking method for the identification of the putative targets of EGCG in the anti-tumor target protein database and these targets were further uploaded to public databases in order to understand the underlying pharmacological mechanisms and search for novel EGCG-associated targets. Similarly, the pharmacological linkage between tumor-related proteins and EGCG was manually constructed in order to provide greater insight into the molecular mechanisms through a systematic integration with applicable bioinformatics. The results indicated that the anti-tumor mechanisms of EGCG may involve 12 signaling transduction pathways and 33 vital target proteins. Moreover, we also discovered four novel putative target proteins of EGCG, including IKBKB, KRAS, WEE1 and NTRK1, which are significantly related to tumorigenesis. In conclusion, this work may provide a useful perspective that will improve our understanding of the pharmacological mechanism of EGCG and identify novel potential therapeutic targets.
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