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Luo Z, Li P, Zhang D, Zhu J, Wang W, Zhao W, Li P, Yuan G. A Novel Antimicrobial Mechanism of Azalomycin F Acting on Lipoteichoic Acid Synthase and Cell Envelope. Molecules 2024; 29:856. [PMID: 38398608 PMCID: PMC10893547 DOI: 10.3390/molecules29040856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Lipoteichoic acid (LTA) plays an essential role in bacterial growth and resistance to antibiotics, and LTA synthetase (LtaS) was considered as an attractive target for combating Gram-positive infections. Azalomycin F, a natural guanidyl-containing polyhydroxy macrolide, can target the LTA of Staphylococcus aureus. Using various technologies including enzyme-linked immunosorbent assay, transmission electron microscope, proteomics, and parallel reaction monitoring, here, the experimental results indicated that azalomycin F can accelerate the LTA release and disrupt the cell envelope, which would also lead to the feedback upregulation on the expressions of LtaS and other related enzymes. Simultaneously, the reconstituted enzyme activity evaluations showed that azalomycin F can significantly inhibit the extracellular catalytic domain of LtaS (eLtaS), while this was vague for LtaS embedded in the liposomes. Subsequently, the fluorescence analyses for five incubation systems containing azalomycin F and eLtaS or the LtaS-embedded liposome indicated that azalomcyin F can spontaneously bind to the active center of LtaS. Combining the mass spectroscopy analyses and the molecular dockings, the results further indicated that this interaction involves the binding sites of substrates and the LTA prolongation, especially the residues Lys299, Phe353, Trp354 and His416. All these suggested that azalomycin F has multiple antibacterial mechanisms against S. aureus. It can not only inhibit LTA biosynthesis through the interactions of its guanidyl side chain with the active center of LtaS but also disrupt the cell envelope through the synergistic effect of accelerating the LTA release, damaging the cell membrane, and electrostatically interacting with LTA. Simultaneously, these antibacterial mechanisms exhibit a synergistic inhibition effect on S. aureus cells, which would eventually cause the cellular autolysis.
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Affiliation(s)
- Zilong Luo
- Biotechnological Engineering Center for Pharmaceutical Research and Development, Jiangxi Agricultural University, Nanchang 330045, China
| | - Pingyi Li
- Biotechnological Engineering Center for Pharmaceutical Research and Development, Jiangxi Agricultural University, Nanchang 330045, China
| | - Duoduo Zhang
- Biotechnological Engineering Center for Pharmaceutical Research and Development, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jianping Zhu
- Laboratory of Natural Medicine and Microbiological Drug, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Wan Wang
- School of Basic Medicine, Nanchang Medical College, Nanchang 330006, China
| | - Wenjia Zhao
- Biotechnological Engineering Center for Pharmaceutical Research and Development, Jiangxi Agricultural University, Nanchang 330045, China
| | - Peibo Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ganjun Yuan
- Biotechnological Engineering Center for Pharmaceutical Research and Development, Jiangxi Agricultural University, Nanchang 330045, China
- Laboratory of Natural Medicine and Microbiological Drug, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
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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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Younus S, Vinod Chandra SS, Nair ASS. Docking and dynamic simulation study of Crizotinib and Temozolomide drug with Glioblastoma and NSCLC target to identify better efficacy of the drug. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00323-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Abstract
Background
Crizotinib and Temozolomide are the two major chemotherapy drugs used for the treatment of cancers. Crizotinib is used as a target chemotherapy drug in many cancers. It mainly binds on the ATP binding regions of receptor tyrosine kinases (RTKs) targets and inhibits protein phosphorylation, which has already been reported. Temozolomide drug is known as the alkylating agent. Its mechanism of action is the methylation of DNA and thereby inhibiting DNA replication. However, the Temozolomide drug with protein level interaction of Glioblastoma Multiforme (GBM) and Non-small-cell lung carcinoma (NSCLC) of RTKs targets has not been reported so far. In the proposed work, we investigated the molecular level interaction of the Temozolomide drug in C-MET, C-ROS1, and ALK RTKs targets of GBM and NSCLC using an in silico study. We performed comparative analysis studies in both drugs' docked complexes based on their drug properties and complex energy (CE) to identify the better efficacy of the drug.
Results
From the docking studies,
we could identify that the Temozolomide drug bounded protein complexes showed the least complex energy. The most stable complexes were identified from these docking studies by Molecular Dynamic simulation. In the proposed study, we found that the docked complex attained a stable conformation and least energy via solid hydrogen bond interactions between the amino acid residues and the drug at the binding sites of the proteins. The least energy and the hydrogen bond interaction of Temozolomide drug with the amino acid residues of the protein complexes of C-MET, C-ROS1 and ALK protein with their id name are: 2WGJ is − 11305.0830 (PRO1158, MET1160), 3ZBF is − 11,659.6814 (MET2029, GLU2027), and 2XP2 is − 11,734.7565 (ARG1275, ASP 1160, GLU1167).
Conclusion
Our studies revealed that the Temozolomide drug bounded protein complex showed the least energy when compared to Crizotinib. So it will give better interaction on the binding sites of proteins and thereby provide better inhibition in the treatment of target therapy of GBM and NSCLC.
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Zhu GF, Lyu SL, Liu Y, Ma C, Wang W. Spectroscopic and computational studies on the binding interaction between gallic acid and Pin1. LUMINESCENCE 2021; 36:2014-2021. [PMID: 34490991 DOI: 10.1002/bio.4138] [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: 03/20/2021] [Revised: 07/22/2021] [Accepted: 08/30/2021] [Indexed: 11/06/2022]
Abstract
Gallic acid (GA) is a natural ingredient in functional foods, which has various health-promoting and antitumour effects. Peptidyl-prolyl cis/trans isomerase Pin1 plays an important role in preventing the development of some malignant tumours. However, whether there was an interaction between Pin1 and GA remains unknown. In this work, the binding information of GA and Pin1 was investigated systematically using multiple spectral and computational methods. GA bound to Pin1 directly with moderate binding affinity in the order of 104 mol/L, therefore decreasing the activity of Pin1. Also, the binding process of GA to Pin1 was driven through weak van der Waals forces, hydrogen bonds, and electrostatic forces. In addition, the important residues Lys63, Arg68, and Arg69 played a significant role in maintaining the binding stability between Pin1 and GA. Interestingly, GA reduced the activity of Pin1 by affecting its conformational characteristics. Our present work showed that GA binds to Pin1 and inhibits its activity, affecting its structural and functional properties, which may contribute to the therapy of Pin1-related diseases.
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Affiliation(s)
- Guo Fei Zhu
- Institute of Food and Drug Manufacturing Engineering, Guizhou Institute of Technology, Guiyang, China
| | - Shao Li Lyu
- Department of Ecology and Resource Engineering, Hetao College, Inner Mongolia, Bayannur, China
| | - Yang Liu
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chao Ma
- Institute of Food and Drug Manufacturing Engineering, Guizhou Institute of Technology, Guiyang, China
| | - Wang Wang
- 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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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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Maggio J, Cabrera M, Armando R, Chinestrad P, Pifano M, Menna PL, Gomez DE, Gómez DLM. Rational design of PIN1 inhibitors for cancer treatment based on conformational diversity analysis and docking based virtual screening. J Biomol Struct Dyn 2021; 40:5858-5867. [PMID: 33463409 DOI: 10.1080/07391102.2021.1874531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The parvulin PIN1 (peptidyl-prolyl cis-trans isomerase NIMA-interacting 1), is the only enzyme capable of isomerizing prolines of phospho-Serine/Threonine-Proline motifs. PIN1 binds to a subset of proteins and plays an essential role in regulating protein function post-phosphorylation control. Furthermore, the activity of PIN1 regulates the outcome of the signalling of proline-directed kinases (e.g. MAPK, CDK, or GSK3) and thus regulates cell proliferation and cell survival. For these reasons, PIN1 inhibitors are interesting since they may have therapeutic implications for cancer. Several authors have already reported that the non-structural point mutation Trp34Ala prevents PIN1 from interacting with its downstream effector proteins. In this work, we characterized PIN1 structurally, intending to explore new inhibition targets for the rational design of pharmacological activity compounds. Through a conformational diversity analysis of PIN1, we identified and characterized a highly specific druggable pocket around the residue Trp34. This pocket was used in a high-throughput docking screening of 450,000 drug-like compounds, and the top 10 were selected for re-docking studies on the previously used conformers. Finally, we evaluated the binding of each compound by thermal shift assay and found four molecules with a high affinity for PIN1 and potential inhibitory activity. Through this strategy, we achieved novel drug candidates with the ability to interfere with the phosphorylation-dependent actions of PIN1 and with potential applications in the treatment of cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Julián Maggio
- Departamento de Ciencia y Tecnología, Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Maia Cabrera
- Departamento de Ciencia y Tecnología, Laboratorio de Farmacología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Romina Armando
- Departamento de Ciencia y Tecnología, Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Patricio Chinestrad
- Departamento de Ciencia y Tecnología, Laboratorio de Farmacología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Marina Pifano
- Departamento de Ciencia y Tecnología, Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Pablo Lorenzano Menna
- Departamento de Ciencia y Tecnología, Laboratorio de Farmacología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Daniel E Gomez
- Departamento de Ciencia y Tecnología, Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Diego L Mengual Gómez
- Departamento de Ciencia y Tecnología, Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, Bernal, Argentina
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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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8
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Scheuplein NJ, Bzdyl NM, Kibble EA, Lohr T, Holzgrabe U, Sarkar-Tyson M. Targeting Protein Folding: A Novel Approach for the Treatment of Pathogenic Bacteria. J Med Chem 2020; 63:13355-13388. [PMID: 32786507 DOI: 10.1021/acs.jmedchem.0c00911] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Infectious diseases are a major cause of morbidity and mortality worldwide, exacerbated by increasing antibiotic resistance in many bacterial species. The development of drugs with new modes of action is essential. A leading strategy is antivirulence, with the aim to target bacterial proteins that are important in disease causation and progression but do not affect growth, resulting in reduced selective pressure for resistance. Immunophilins, a superfamily of peptidyl-prolyl cis-trans isomerase (PPIase) enzymes have been shown to be important for virulence in a broad-spectrum of pathogenic bacteria. This Perspective will provide an overview of the recent advances made in understanding the role of each immunophilin family, cyclophilins, FK506 binding proteins (FKBPs), and parvulins in bacteria. Inhibitor design and medicinal chemistry strategies for development of novel drugs against bacterial FKBPs will be discussed. Furthermore, drugs against human cyclophilins and parvulins will be reviewed in their current indication as antiviral and anticancer therapies.
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Affiliation(s)
- Nicolas J Scheuplein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Nicole M Bzdyl
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 6009 Perth, Australia
| | - Emily A Kibble
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 6009 Perth, Australia.,School of Veterinary and Life Sciences, Murdoch University, 6150 Murdoch, Australia
| | - Theresa Lohr
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 6009 Perth, Australia
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Nakatsu Y, Matsunaga Y, Ueda K, Yamamotoya T, Inoue Y, Inoue MK, Mizuno Y, Kushiyama A, Ono H, Fujishiro M, Ito H, Okabe T, Asano T. Development of Pin1 Inhibitors and their Potential as Therapeutic Agents. Curr Med Chem 2020; 27:3314-3329. [PMID: 30394205 DOI: 10.2174/0929867325666181105120911] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 12/26/2022]
Abstract
The prolyl isomerase Pin1 is a unique enzyme, which isomerizes the cis-trans conformation between pSer/pThr and proline and thereby regulates the function, stability and/or subcellular distribution of its target proteins. Such regulations by Pin1 are involved in numerous physiological functions as well as the pathogenic mechanisms underlying various diseases. Notably, Pin1 deficiency or inactivation is a potential cause of Alzheimer's disease, since Pin1 induces the degradation of Tau. In contrast, Pin1 overexpression is highly correlated with the degree of malignancy of cancers, as Pin1 controls a number of oncogenes and tumor suppressors. Accordingly, Pin1 inhibitors as anti-cancer drugs have been developed. Interestingly, recent intensive studies have demonstrated Pin1 to be responsible for the onset or development of nonalcoholic steatosis, obesity, atherosclerosis, lung fibrosis, heart failure and so on, all of which have been experimentally induced in Pin1 deficient mice. In this review, we discuss the possible applications of Pin1 inhibitors to a variety of diseases including malignant tumors and also introduce the recent advances in Pin1 inhibitor research, which have been reported.
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Affiliation(s)
- Yusuke Nakatsu
- Department of Medical Science, Graduate School of Medicine, Hiroshima University, Hiroshima City, Hiroshima 734-8553, Japan
| | - Yasuka Matsunaga
- Department of Medical Science, Graduate School of Medicine, Hiroshima University, Hiroshima City, Hiroshima 734-8553, Japan
| | - Koji Ueda
- Department of Medical Science, Graduate School of Medicine, Hiroshima University, Hiroshima City, Hiroshima 734-8553, Japan
| | - Takeshi Yamamotoya
- Department of Medical Science, Graduate School of Medicine, Hiroshima University, Hiroshima City, Hiroshima 734-8553, Japan
| | - Yuki Inoue
- Department of Medical Science, Graduate School of Medicine, Hiroshima University, Hiroshima City, Hiroshima 734-8553, Japan
| | - Masa-Ki Inoue
- Department of Medical Science, Graduate School of Medicine, Hiroshima University, Hiroshima City, Hiroshima 734-8553, Japan
| | - Yu Mizuno
- Department of Medical Science, Graduate School of Medicine, Hiroshima University, Hiroshima City, Hiroshima 734-8553, Japan
| | - Akifumi Kushiyama
- The Division of Diabetes and Metabolism, Institute for Adult Diseases, Asahi Life Foundation, Chuo-ku, Tokyo 103-0002, Japan
| | - Hiraku Ono
- Department of Clinical Cell Biology, Chiba University Graduate School of Medicine, Chiba City, Chiba 260-8677, Japan
| | - Midori Fujishiro
- The Division of Diabetes and Metabolic Diseases, Nihon University School of Medicine, Itabashi, Tokyo 173-8610, Japan
| | - Hisanaka Ito
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Takayoshi Okabe
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomoichiro Asano
- Department of Medical Science, Graduate School of Medicine, Hiroshima University, Hiroshima City, Hiroshima 734-8553, Japan
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Elmezayen AD, Yelekçi K. Homology modeling and in silico design of novel and potential dual-acting inhibitors of human histone deacetylases HDAC5 and HDAC9 isozymes. J Biomol Struct Dyn 2020; 39:6396-6414. [PMID: 32715940 DOI: 10.1080/07391102.2020.1798812] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDACs) are a group of enzymes that have prominent and crucial effect on various biological systems, mainly by their suppressive effect on transcription. Searching for inhibitors targeting their respective isoforms without affecting other targets is greatly needed. Some histone deacetylases have no crystal structures, such as HDAC5 and HDAC9. Lacking proper and suitable crystal structure is obstructing the designing of appropriate isoform selective inhibitors. Here in this study, we constructed human HDAC5 and HDAC9 protein models using human HDAC4 (PDB:2VQM_A) as a template by the means of homology modeling approach. Based on the Z-score of the built models, model M0014 of HDAC5 and model M0020 of HDAC9 were selected. The models were verified by MODELLER and validated using the Web-based PROCHECK server. All selected known inhibitors displayed reasonable binding modes and equivalent predicted Ki values in comparison to the experimental binding affinities (Ki/IC50). The known inhibitor Rac26 showed the best binding affinity for HDAC5, while TMP269 showed the best binding affinity for HDAC9. The best two compounds, CHEMBL2114980 and CHEMBL217223, had relatively similar inhibition constants against HDAC5 and HDAC9. The built models and their complexes were subjected to molecular dynamic simulations (MD) for 100 ns. Examining the MD simulation results of all studied structures, including the RMSD, RMSF, radius of gyration and potential energy suggested the stability and reliability of the built models. Accordingly, the results obtained in this study could be used for designing de novo inhibitors against HDAC5 and HDAC9. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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11
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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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12
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Wang W, Xi L, Xiong X, Li X, Zhang Q, Yang W, Du L. 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] [Key Words] [MESH Headings] [Grants] [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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Affiliation(s)
- Wang Wang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Lei Xi
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Xiuhong Xiong
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Xue Li
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Qingyan Zhang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Wentao Yang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China
| | - Linfang Du
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, P.R. China.
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13
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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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14
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Safarizadeh H, Garkani-Nejad Z. Investigation of MI-2 analogues as MALT1 inhibitors to treat of diffuse large B-Cell lymphoma through combined molecular dynamics simulation, molecular docking and QSAR techniques and design of new inhibitors. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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15
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Molecular Targets of Epigallocatechin-Gallate (EGCG): A Special Focus on Signal Transduction and Cancer. Nutrients 2018; 10:nu10121936. [PMID: 30563268 PMCID: PMC6315581 DOI: 10.3390/nu10121936] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/30/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022] Open
Abstract
Green tea is a beverage that is widely consumed worldwide and is believed to exert effects on different diseases, including cancer. The major components of green tea are catechins, a family of polyphenols. Among them, epigallocatechin-gallate (EGCG) is the most abundant and biologically active. EGCG is widely studied for its anti-cancer properties. However, the cellular and molecular mechanisms explaining its action have not been completely understood, yet. EGCG is effective in vivo at micromolar concentrations, suggesting that its action is mediated by interaction with specific targets that are involved in the regulation of crucial steps of cell proliferation, survival, and metastatic spread. Recently, several proteins have been identified as EGCG direct interactors. Among them, the trans-membrane receptor 67LR has been identified as a high affinity EGCG receptor. 67LR is a master regulator of many pathways affecting cell proliferation or apoptosis, also regulating cancer stem cells (CSCs) activity. EGCG was also found to be interacting directly with Pin1, TGFR-II, and metalloproteinases (MMPs) (mainly MMP2 and MMP9), which respectively regulate EGCG-dependent inhibition of NF-kB, epithelial-mesenchimal transaction (EMT) and cellular invasion. EGCG interacts with DNA methyltransferases (DNMTs) and histone deacetylases (HDACs), which modulates epigenetic changes. The bulk of this novel knowledge provides information about the mechanisms of action of EGCG and may explain its onco-suppressive function. The identification of crucial signalling pathways that are related to cancer onset and progression whose master regulators interacts with EGCG may disclose intriguing pharmacological targets, and eventually lead to novel combined treatments in which EGCG acts synergistically with known drugs.
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16
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Zhao ML, Wang W, Nie H, Cao SS, Du LF. In silico structure prediction and inhibition mechanism studies of AtHDA14 as revealed by homology modeling, docking, molecular dynamics simulation. Comput Biol Chem 2018; 75:120-130. [PMID: 29775968 DOI: 10.1016/j.compbiolchem.2018.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/03/2018] [Accepted: 05/06/2018] [Indexed: 12/14/2022]
Abstract
Histone deacetylases (HDACs) play a significant role in the epigenetic mechanism by catalyzing deacetylation of lysine on histone in both animals and plants. HDACs involved in growth, development and response to stresses in plants. Arabidopsis thaliana histone deacetylase 14 (AtHDA14) is found to localize in the mitochondria and chloroplasts, and it involved in photosynthesis and melatonin biosynthesis. However, its mechanism of action was still unknowns so far. Therefore, in this study, we constructed AtHDA14 protein model using homology modeling method, validated using PROCHECK and presented using Ramachandran plots. We also performed virtual screening of AtHDA14 by docking with small molecule drugs and predicted their ADMET properties to select representative inhibitors. MD simulation for representative AtHDA14-ligand complexes was carried out to further research and reveal their stability and inhibition mechanism. Meanwhile, MM/PBSA method was utilized to obtain more valuable information about the residues energy contribution. Moreover, compared with four candidate inhibitors, we also found that compound 645533 and 6918837 might be a more potent AtHDA14 inhibitor than TSA (444732) and SAHA (5311). Therefore, compound 6445533 and 6918837 was anticipated to be a promising drug candidate for inhibition of AtHDA14.
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Affiliation(s)
- Ming-Lang Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Wang Wang
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Hu Nie
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Sha-Sha Cao
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Lin-Fang Du
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, PR China.
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17
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Matena A, Rehic E, Hönig D, Kamba B, Bayer P. Structure and function of the human parvulins Pin1 and Par14/17. Biol Chem 2018; 399:101-125. [PMID: 29040060 DOI: 10.1515/hsz-2017-0137] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Parvulins belong to the family of peptidyl-prolyl cis/trans isomerases (PPIases) assisting in protein folding and in regulating the function of a broad variety of proteins in all branches of life. The human representatives Pin1 and Par14/17 are directly involved in processes influencing cellular maintenance and cell fate decisions such as cell-cycle progression, metabolic pathways and ribosome biogenesis. This review on human parvulins summarizes the current knowledge of these enzymes and intends to oppose the well-studied Pin1 to its less well-examined homolog human Par14/17 with respect to structure, catalytic and cellular function.
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Affiliation(s)
- Anja Matena
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Edisa Rehic
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Dana Hönig
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Bianca Kamba
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
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