1
|
Yuce M, Ates B, Yasar NI, Sungur FA, Kurkcuoglu O. A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of E. coli ribosome. J Mol Graph Model 2024; 131:108817. [PMID: 38976944 DOI: 10.1016/j.jmgm.2024.108817] [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: 03/22/2024] [Revised: 05/08/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
Abstract
The global antibiotic resistance problem necessitates fast and effective approaches to finding novel inhibitors to treat bacterial infections. In this study, we propose a computational workflow to identify plausible high-affinity compounds from FDA-approved, investigational, and experimental libraries for the decoding center on the small subunit 30S of the E. coli ribosome. The workflow basically consists of two molecular docking calculations on the intact 30S, followed by molecular dynamics (MD) simulations coupled with MM-GBSA calculations on a truncated ribosome structure. The parameters used in the molecular docking suits, Glide and AutoDock Vina, as well as in the MD simulations with Desmond were carefully adjusted to obtain expected interactions for the ligand-rRNA complexes. A filtering procedure was followed, considering a fingerprint based on aminoglycoside's binding site on the 30S to obtain seven hit compounds either with different clinical usages or aminoglycoside derivatives under investigation, suggested for in vitro studies. The detailed workflow developed in this study promises an effective and fast approach for the estimation of binding free energies of large protein-RNA and ligand complexes.
Collapse
Affiliation(s)
- Merve Yuce
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
| | - Beril Ates
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
| | - Nesrin Isil Yasar
- Istanbul Technical University, Computational Science and Engineering Division, Informatics Institute, Istanbul, 34469, Turkey.
| | - Fethiye Aylin Sungur
- Istanbul Technical University, Computational Science and Engineering Division, Informatics Institute, Istanbul, 34469, Turkey.
| | - Ozge Kurkcuoglu
- Istanbul Technical University, Department of Chemical Engineering, Istanbul, 34469, Turkey.
| |
Collapse
|
2
|
Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight. Molecules 2021; 26:molecules26041079. [PMID: 33670773 PMCID: PMC7922218 DOI: 10.3390/molecules26041079] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Folate receptor alpha (FRα) is known as a biological marker for many cancers due to its overexpression in cancerous epithelial tissue. The folic acid (FA) binding affinity to the FRα active site provides a basis for designing more specific targets for FRα. Heterocyclic rings have been shown to interact with many receptors and are important to the metabolism and biological processes within the body. Nineteen FA analogs with substitution with various heterocyclic rings were designed to have higher affinity toward FRα. Molecular docking was used to study the binding affinity of designed analogs compared to FA, methotrexate (MTX), and pemetrexed (PTX). Out of 19 FA analogs, analogs with a tetrazole ring (FOL03) and benzothiophene ring (FOL08) showed the most negative binding energy and were able to interact with ASP81 and SER174 through hydrogen bonds and hydrophobic interactions with amino acids of the active site. Hence, 100 ns molecular dynamics (MD) simulations were carried out for FOL03, FOL08 compared to FA, MTX, and PTX. The root mean square deviation (RMSD) and root mean square fluctuation (RMSF) of FOL03 and FOL08 showed an apparent convergence similar to that of FA, and both of them entered the binding pocket (active site) from the pteridine part, while the glutamic part was stuck at the FRα pocket entrance during the MD simulations. Molecular mechanics Poisson-Boltzmann surface accessible (MM-PBSA) and H-bond analysis revealed that FOL03 and FOL08 created more negative free binding and electrostatic energy compared to FA and PTX, and both formed stronger H-bond interactions with ASP81 than FA with excellent H-bond profiles that led them to become bound tightly in the pocket. In addition, pocket volume calculations showed that the volumes of active site for FOL03 and FOL08 inside the FRα pocket were smaller than the FA–FRα system, indicating strong interactions between the protein active site residues with these new FA analogs compared to FA during the MD simulations.
Collapse
|
3
|
Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019; 119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200122, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
4
|
Ouyang J, Sun F, Feng W, Xie Y, Ren L, Chen Y. Antimicrobial Activity of Galangin and Its Effects on Murein Hydrolases of Vancomycin-Intermediate Staphylococcus aureus (VISA) Strain Mu50. Chemotherapy 2017; 63:20-28. [PMID: 29145175 DOI: 10.1159/000481658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/19/2017] [Indexed: 11/19/2022]
Abstract
Backgroud: Antibiotic treatment for infections caused by vancomycin-intermediate Staphylococcus aureus (VISA) strains is challenging, and only a few effective and curative methods have been developed to combat these strains. This study aimed to investigate the antimicrobial activity of galangin against S. aureus and its effects on the murein hydrolases of VISA strain Mu50. This is the first report on these effects of galangin, and it may help to improve the treatment for VISA infections by demonstrating the effective use of galangin. METHODS Firstly, the minimum inhibitory concentration (MIC) and growth curve were used to investigate the antimicrobial activity of galangin against S. aureus. Secondly, transmission electron microscopy (TEM) was used to observe morphological changes of VISA strain Mu50. Thirdly, Triton X-100-induced autolysis and cell wall hydrolysis assays were performed to determine the activities of the murein hydrolases of Mu50. Finally, fluorescence real-time quantitative PCR was used to investigate the expression of the murein hydrolase-related Mu50 genes. RESULTS The results indicated that the MIC of galangin was 32 μg/mL against ATCC25293, N315, and Mu50, and galangin could significantly suppress the bacterial growth (p < 0.05) with concentrations of 4, 8 and 16 μg/mL, compared with control group (0 μg/mL). To explore the possible reasons of bacteriostatic effects of galangin, we observed morphological changes using TEM which showed that the division of Mu50 daughter cells treated with galangin was obviously inhibited. Considering the vital role of murein hydrolases in cellular division, assays were performed, and galangin markedly decreased Triton X-100-induced autolysis and cell wall hydrolysis. Galangin also significantly inhibited the expression of the murein hydrolase genes (atl, lytM, and lytN) and their regulatory genes (cidR, cidA, and cidB). CONCLUSIONS Our findings indicated that galangin can effectively inhibit murein hydrolase activity as well as the growth of VISA strain Mu50.
Collapse
Affiliation(s)
- Jing Ouyang
- Department of Pharmacy, Chongqing Public Health Medical Center, Chongqing, China
| | | | | | | | | | | |
Collapse
|
5
|
Pavlova A, Parks JM, Oyelere AK, Gumbart JC. Toward the rational design of macrolide antibiotics to combat resistance. Chem Biol Drug Des 2017; 90:641-652. [DOI: 10.1111/cbdd.13004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/03/2017] [Accepted: 04/08/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Anna Pavlova
- School of Physics Georgia Institute of Technology Atlanta GA USA
| | - Jerry M. Parks
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
| | - Adegboyega K. Oyelere
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology Atlanta GA USA
| | - James C. Gumbart
- School of Physics Georgia Institute of Technology Atlanta GA USA
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology Atlanta GA USA
| |
Collapse
|
6
|
Makarov GI, Makarova TM, Sumbatyan NV, Bogdanov AA. Investigation of Ribosomes Using Molecular Dynamics Simulation Methods. BIOCHEMISTRY (MOSCOW) 2017; 81:1579-1588. [PMID: 28260485 DOI: 10.1134/s0006297916130010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ribosome as a complex molecular machine undergoes significant conformational changes while synthesizing a protein molecule. Molecular dynamics simulations have been used as complementary approaches to X-ray crystallography and cryoelectron microscopy, as well as biochemical methods, to answer many questions that modern structural methods leave unsolved. In this review, we demonstrate that all-atom modeling of ribosome molecular dynamics is particularly useful in describing the process of tRNA translocation, atomic details of behavior of nascent peptides, antibiotics, and other small molecules in the ribosomal tunnel, and the putative mechanism of allosteric signal transmission to functional sites of the ribosome.
Collapse
Affiliation(s)
- G I Makarov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | | | | | | |
Collapse
|
7
|
Pavlova A, Gumbart JC. Parametrization of macrolide antibiotics using the force field toolkit. J Comput Chem 2015; 36:2052-63. [PMID: 26280362 DOI: 10.1002/jcc.24043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/25/2015] [Accepted: 07/03/2015] [Indexed: 01/09/2023]
Abstract
Macrolides are an important class of antibiotics that target the bacterial ribosome. Computer simulations of macrolides are limited as specific force field parameters have not been previously developed for them. Here, we determine CHARMM-compatible force field parameters for erythromycin, azithromycin, and telithromycin, using the force field toolkit (ffTK) plugin in VMD. Because of their large size, novel approaches for parametrizing them had to be developed. Two methods for determining partial atomic charges, from interactions with TIP3P water and from the electrostatic potential, as well as several approaches for fitting the dihedral parameters were tested. The performance of the different parameter sets was evaluated by molecular dynamics simulations of the macrolides in ribosome, with a distinct improvement in maintenance of key interactions observed after refinement of the initial parameters. Based on the results of the macrolide tests, recommended procedures for parametrizing very large molecules using ffTK are given.
Collapse
Affiliation(s)
- Anna Pavlova
- School of Physics and School of Chemistry, Georgia Institute of Technology, Atlanta, 30332, Georgia
| | - James C Gumbart
- School of Physics and School of Chemistry, Georgia Institute of Technology, Atlanta, 30332, Georgia
| |
Collapse
|
8
|
Villarino N, Brown SA, Martín-Jiménez T. The role of the macrolide tulathromycin in veterinary medicine. Vet J 2013; 198:352-7. [DOI: 10.1016/j.tvjl.2013.07.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 07/26/2013] [Accepted: 07/29/2013] [Indexed: 10/26/2022]
|
9
|
Shishkina A, Makarov G, Tereshchenkov A, Korshunova G, Sumbatyan N, Golovin A, Svetlov M, Bogdanov A. Conjugates of amino acids and peptides with 5-o-mycaminosyltylonolide and their interaction with the ribosomal exit tunnel. Bioconjug Chem 2013; 24:1861-9. [PMID: 24090034 DOI: 10.1021/bc400236n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During protein synthesis the nascent polypeptide chain (NC) extends through the ribosomal exit tunnel (NPET). Also, the large group of macrolide antibiotics binds in the nascent peptide exit tunnel. In some cases interaction of NC with NPET leads to the ribosome stalling, a significant event in regulation of translation. In other cases NC-ribosome interactions lead to pauses in translation that play an important role in cotranslational folding of polypeptides emerging from the ribosome. The precise mechanism of NC recognition in NPET as well as factors that determine NC conformation in the ribosomal tunnel are unknown. A number of derivatives of the macrolide antibiotic 5-O-mycaminosyltylonolide (OMT) containing N-acylated amino acid or peptide residues were synthesized in order to study potential sites of NC-NPET interactions. The target compounds were prepared by conjugation of protected amino acids and peptides with the C23 hydroxyl group of the macrolide. These OMT derivatives showed high although varying abilities to inhibit the firefly luciferase synthesis in vitro. Three glycil-containing derivatives appeared to be strong inhibitors of translation, more potent than parental OMT. Molecular dynamics (MD) simulation of complexes of tylosin, OMT, and some of OMT derivatives with the large ribosomal subunit of E. coli illuminated a plausible reason for the high inhibitory activity of Boc-Gly-OMT. In addition, the MD study detected a new putative site of interaction of the nascent polypeptide chain with the NPET walls.
Collapse
Affiliation(s)
- Anna Shishkina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Leninskie Gory, 1, bldg 40, 119992 Moscow, Russia
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Tan X, Song Z. Continuous, quantitative monitoring of roxithromycin in human saliva by flow injection chemiluminescence analysis. APPLIED SPECTROSCOPY 2013; 67:54-58. [PMID: 23317671 DOI: 10.1366/12-06644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Human saliva quantitative monitoring of roxithromycin (ROX) at picomolar-level by flow injection (FI) chemiluminescence (CL) analysis is described for the first time, to our knowledge. Monitoring was based on the CL intensity from luminol-BSA reaction, which can be quenched in the presence of ROX, with the decreasing CL intensity linearly proportional to the logarithm of the ROX concentration, ranging from 0.6 to 1000 pmol·L(-1). The detection limit of the proposed method for the determination of ROX was as low as 0.2 pmol·L(-1) (3σ), and the relative standard deviations were less than 4.0% (n = 7). A complete analytical process, including sampling and washing for ROX determination, conducted at a flow rate of 2.0 mL·min(-1), was performed completely within 30 s, yielding a sample efficiency of 120 h(-1). The proposed method was successfully applied to the determination of ROX in human saliva and serum samples with recoveries from 90.9% to 110.1%. The continuous monitoring of ROX in human saliva after oral intake showed that the total elimination ratio was 87.1% during 24 h, and the pharmacokinetic parameters were 0.97 ± 0.18 h(-1) for the absorption rate constant K(a), 0.082 ± 0.010 h(-1) for the elimination rate constant K(e), and 8.56 ± 1.11 h for the elimination half-life time t(1/2). It was also found that ROX in human saliva and urine simultaneously reached the maximum at 2 h with the concentration correlate ratio of 0.97.
Collapse
Affiliation(s)
- Xijuan Tan
- Key Laboratory of Synthetic and Natural Functional Molecule, Chemistry of Ministry of Education, College of Chemistry and Material Science, Northwest University, Xi'an 710069, China
| | | |
Collapse
|
11
|
Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012; 2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
Collapse
Affiliation(s)
- B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- School of Chemistry, National University of Ireland, Galway, Ireland
| |
Collapse
|
12
|
Darré L, Tek A, Baaden M, Pantano S. Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk. J Chem Theory Comput 2012; 8:3880-94. [DOI: 10.1021/ct3001816] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Leonardo Darré
- Institut Pasteur de Montevideo,
Mataojo 2020, CP 11400, Uruguay
| | - Alex Tek
- Laboratoire de Biochimie Théorique,
CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité. 13
rue Pierre et Marie Curie, 75005, Paris, France
- Université Pierre et Marie
Curie, UPMC Sorbonne Universités, 4 place Jussieu 75005 Paris,
France
| | - Marc Baaden
- Laboratoire de Biochimie Théorique,
CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité. 13
rue Pierre et Marie Curie, 75005, Paris, France
| | - Sergio Pantano
- Institut Pasteur de Montevideo,
Mataojo 2020, CP 11400, Uruguay
| |
Collapse
|
13
|
Yu L, Hong Y, Li L, Jin Y, Zheng M, Jiang H, Zeng S. Enantioselective drug–protein interaction between mexiletine and plasma protein. J Pharm Pharmacol 2012; 64:792-801. [DOI: 10.1111/j.2042-7158.2012.01487.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abstract
Objectives
This study examined the interaction of mexiletine enantiomers with human plasma, human serum albumin (HSA), and human α1-acid glycoprotein (hAGP), and characterized the binding modes of mexiletine enantiomers with hAGP in the molecular level.
Methods
Enantiomer separation of mexiletine was performed using precolumn derivatization chiral HPLC. The ultrafiltration technique was used to separate the free mexiletine in plasma matrix. Molecular dynamics simulations and free energy calculations were assessed using molecular mechanics and the generalized Born surface area method.
Key findings
Significant differences in enantioselective binding to human plasma were observed (R > S). The hAGP–mexiletine binding profile exhibited similar enantioselectivity (R > S) to that in human plasma, whereas HSA–mexiletine interaction was S > R at pH 7.4. Moreover, the results of comparative studies indicated that mexiletine had the highest binding affinity for F1-S, a variant of hAGP. Based on the computational studies, residues such as Arg90, Leu79, Ser89 and Phe89 showed an energy difference of more than −0.35 kcal/mol between the enantiomers.
Conclusions
hAGP may be one of the key proteins leading to the enantioselective protein bindings of mexiletine in human plasma (R > S). The residues Arg90, Leu79, Ser89 and Phe89 of hAGP may have important roles in the observed enantioselectivity.
Collapse
Affiliation(s)
- Lushan Yu
- Department of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yanjun Hong
- Department of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Li Li
- Department of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yingxiu Jin
- Department of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Su Zeng
- Department of Pharmaceutical Analysis and Drug Metabolism, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
14
|
Zhang J, Chen F, Li W, Xiong Q, Yang M, Zheng P, Li C, Pei J, Ge F. 14-3-3ζ interacts with stat3 and regulates its constitutive activation in multiple myeloma cells. PLoS One 2012; 7:e29554. [PMID: 22279540 PMCID: PMC3261159 DOI: 10.1371/journal.pone.0029554] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 11/30/2011] [Indexed: 12/18/2022] Open
Abstract
The 14-3-3 proteins are a family of regulatory signaling molecules that interact with other proteins in a phosphorylation-dependent manner and function as adapter or scaffold proteins in signal transduction pathways. One family member, 14-3-3ζ, is believed to function in cell signaling, cycle control, and apoptotic death. A systematic proteomic analysis done in our laboratory has identified signal transducers and activators of transcription 3 (Stat3) as a novel 14-3-3ζ interacting protein. Following our initial finding, in this study, we provide evidence that 14-3-3ζ interacts physically with Stat3. We further demonstrate that phosphorylation of Stat3 at Ser727 is vital for 14-3-3ζ interaction and mutation of Ser727 to Alanine abolished 14-3-3ζ/Stat3 association. Inhibition of 14-3-3ζ protein expression in U266 cells inhibited Stat3 Ser727 phosphorylation and nuclear translocation, and decreased both Stat3 DNA binding and transcriptional activity. Moreover, 14-3-3ζ is involved in the regulation of protein kinase C (PKC) activity and 14-3-3ζ binding to Stat3 protects Ser727 dephosphorylation from protein phosphatase 2A (PP2A). Taken together, our findings support the model that multiple signaling events impinge on Stat3 and that 14-3-3ζ serves as an essential coordinator for different pathways to regulate Stat3 activation and function in MM cells.
Collapse
Affiliation(s)
- Jia Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fangjin Chen
- Center for Theoretical Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wenliang Li
- School of Science and Technology, Tokai University, Tokyo, Japan
| | - Qian Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Mingkun Yang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Peng Zheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chongyang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jianfeng Pei
- Center for Theoretical Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- * E-mail: (JP); (FG)
| | - Feng Ge
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (JP); (FG)
| |
Collapse
|
15
|
LING BAOPING, ZHANG RUI, WANG ZHIGUO, LIU YONGJUN, LIU CHENGBU. STUDY ON THE INTERACTIONS OF Smac MIMETICS WITH XIAP-BIR3 DOMAIN BY DOCKING AND MOLECULAR DYNAMICS SIMULATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633610005980] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Upon receiving an apoptotic stimulus, the mature mitochondrial protein second mitochondria-derived activator of caspases (Smac)/direct IAP-binding protein with low PI (DIABLO), which could be released from mitochondria into the cytosol together with cytochrome C , specifically binds to inhibitor of apoptosis proteins (IAPs) and relieves the inhibitory effect of caspase, thus promotes cell death. Some artificial small molecules (called Smac mimetics) can mimic the N-terminal four residues Ala1-Val2-Pro3-Ile4 (AVPI) sequence of mitochondrial protein Smac, and competitively bind to X-linked inhibitor of apoptosis protein baculoviral IAP repeats (XIAP-BIR3) domain with caspase-9, which leads to the removal of the inhibition of caspase-9 by XIAP and induce apoptosis. To gain an insight into the nature of XIAP-BIR3 domain recognizing Smac mimetics, we used docking and molecular dynamics simulations methods to study four representative Smac mimetics. The docking results show that the orientations of these backbones of ligands are identical with that of AVPI in the binding pocket. Each ligand corresponds to two competitive conformations, which are called extended and bended conformations. The results of molecular dynamics simulations show that the extended conformation is more stable, and the calculations of energy decomposition reveal that the residue Thr308 makes the strongest interaction with XIAP-BIR3. In addition, Asp309, Glu314, and Trp323 are indispensable for XIAP-BIR3 recognizing and binding Smac mimetics.
Collapse
Affiliation(s)
- BAOPING LING
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, P. R. China
| | - RUI ZHANG
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, P. R. China
| | - ZHIGUO WANG
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, P. R. China
| | - YONGJUN LIU
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, P. R. China
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, P. R. China
| | - CHENGBU LIU
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, P. R. China
| |
Collapse
|
16
|
Xu P, Chen XZ, Liu L, Jin ZP, Lei PS. A new series of macrolide derivatives with 4″-O-saccharide substituents. Bioorg Med Chem Lett 2010; 20:5527-31. [DOI: 10.1016/j.bmcl.2010.07.072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 06/23/2010] [Accepted: 07/16/2010] [Indexed: 10/19/2022]
|