1
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Caminati G, Procacci P. Mounting evidence of FKBP12 implication in neurodegeneration. Neural Regen Res 2020; 15:2195-2202. [PMID: 32594030 PMCID: PMC7749462 DOI: 10.4103/1673-5374.284980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/18/2020] [Accepted: 03/24/2020] [Indexed: 12/25/2022] Open
Abstract
Intrinsically disordered proteins, such as tau or α-synuclein, have long been associated with a dysfunctional role in neurodegenerative diseases. In Alzheimer's and Parkinson's' diseases, these proteins, sharing a common chemical-physical pattern with alternating hydrophobic and hydrophilic domains rich in prolines, abnormally aggregate in tangles in the brain leading to progressive loss of neurons. In this review, we present an overview linking the studies on the implication of the peptidyl-prolyl isomerase domain of immunophilins, and notably FKBP12, to a variety of neurodegenerative diseases, focusing on the molecular origin of such a role. The involvement of FKBP12 dysregulation in the aberrant aggregation of disordered proteins pinpoints this protein as a possible therapeutic target and, at the same time, as a predictive biomarker for early diagnosis in neurodegeneration, calling for the development of reliable, fast and cost-effective detection methods in body fluids for community-based screening campaigns.
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Affiliation(s)
- Gabriella Caminati
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
- Center for Colloid and Surface Science (CSGI), University of Florence, Sesto Fiorentino, Italy
| | - Piero Procacci
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
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2
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Zhu T, Li L, Feng L, Mo H, Ren M. Target of Rapamycin Regulates Genome Methylation Reprogramming to Control Plant Growth in Arabidopsis. Front Genet 2020; 11:186. [PMID: 32194640 PMCID: PMC7062917 DOI: 10.3389/fgene.2020.00186] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/17/2020] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is an indispensable epigenetic modification that dynamically regulates gene expression and genome stability during cell growth and development processes. The target of rapamycin (TOR) has emerged as a central regulator to regulate many fundamental cellular metabolic processes from protein synthesis to autophagy in all eukaryotic species. However, little is known about the functions of TOR in DNA methylation. In this study, the synergistic growth inhibition of Arabidopsis seedlings can be observed when DNA methylation inhibitor azacitidine was combined with TOR inhibitors. Global DNA methylation level was evaluated using whole-genome bisulfite sequencing (WGBS) under TOR inhibition. Hypomethylation level of whole genome DNA was observed in AZD-8055 (AZD), rapamycin (RAP) and AZD + RAP treated Arabidopsis seedlings. Based on functional annotation and KEGG pathway analysis of differentially methylated genes (DMGs), most of DMGs were enriched in carbon metabolism, biosynthesis of amino acids and other metabolic processes. Importantly, the suppression of TOR caused the change in DNA methylation of the genes associated with plant hormone signal transduction, indicating that TOR played an important role in modulating phytohormone signals in Arabidopsis. These observations are expected to shed light on the novel functions of TOR in DNA methylation and provide some new insights into how TOR regulates genome DNA methylation to control plant growth.
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Affiliation(s)
- Tingting Zhu
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China.,School of Life Sciences, Chongqing University, Chongqing, China
| | - Linxuan Li
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Li Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Huijuan Mo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Maozhi Ren
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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3
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Zhu T, Li L, Feng L, Mo H, Ren M. Target of Rapamycin Regulates Genome Methylation Reprogramming to Control Plant Growth in Arabidopsis. Front Genet 2020. [PMID: 32194640 DOI: 10.3389/fgene.2020.0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
DNA methylation is an indispensable epigenetic modification that dynamically regulates gene expression and genome stability during cell growth and development processes. The target of rapamycin (TOR) has emerged as a central regulator to regulate many fundamental cellular metabolic processes from protein synthesis to autophagy in all eukaryotic species. However, little is known about the functions of TOR in DNA methylation. In this study, the synergistic growth inhibition of Arabidopsis seedlings can be observed when DNA methylation inhibitor azacitidine was combined with TOR inhibitors. Global DNA methylation level was evaluated using whole-genome bisulfite sequencing (WGBS) under TOR inhibition. Hypomethylation level of whole genome DNA was observed in AZD-8055 (AZD), rapamycin (RAP) and AZD + RAP treated Arabidopsis seedlings. Based on functional annotation and KEGG pathway analysis of differentially methylated genes (DMGs), most of DMGs were enriched in carbon metabolism, biosynthesis of amino acids and other metabolic processes. Importantly, the suppression of TOR caused the change in DNA methylation of the genes associated with plant hormone signal transduction, indicating that TOR played an important role in modulating phytohormone signals in Arabidopsis. These observations are expected to shed light on the novel functions of TOR in DNA methylation and provide some new insights into how TOR regulates genome DNA methylation to control plant growth.
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Affiliation(s)
- Tingting Zhu
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Linxuan Li
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
| | - Li Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Huijuan Mo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Maozhi Ren
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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4
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Tang X, Xu P, Wang B, Luo J, Fu R, Huang K, Dai L, Lu J, Cao G, Peng H, Zhang L, Zhang Z, Chen Q. Identification of a Specific Gene Module for Predicting Prognosis in Glioblastoma Patients. Front Oncol 2019; 9:812. [PMID: 31508371 PMCID: PMC6718733 DOI: 10.3389/fonc.2019.00812] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/08/2019] [Indexed: 12/13/2022] Open
Abstract
Introduction: Glioblastoma (GBM) is the most common and malignant variant of intrinsic glial brain tumors. The poor prognosis of GBM has not significantly improved despite the development of innovative diagnostic methods and new therapies. Therefore, further understanding the molecular mechanism that underlies the aggressive behavior of GBM and the identification of appropriate prognostic markers and therapeutic targets is necessary to allow early diagnosis, to develop appropriate therapies and to improve prognoses. Methods: We used a weighted gene co-expression network analysis (WGCNA) to construct a gene co-expression network with 524 glioblastoma samples from The Cancer Genome Atlas (TCGA). A risk score was then constructed based on four module genes and the patients' overall survival (OS) rate. The prognostic and predictive accuracy of the risk score were verified in the GSE16011 cohort and the REMBRANDT cohort. Results: We identified a gene module (the green module) related to prognosis. Then, multivariate Cox analysis was performed on 4 hub genes to construct a Cox proportional hazards regression model from 524 glioblastoma patients. A risk score for predicting survival time was calculated with the following formula based on the top four genes in the green module: risk score = (0.00889 × EXPCLEC5A) + (0.0681 × EXPFMOD) + (0.1724 × EXPFKBP9) + (0.1557 × EXPLGALS8). The 5-year survival rate of the high-risk group (survival rate: 2.7%, 95% CI: 1.2–6.3%) was significantly lower than that of the low-risk group (survival rate: 8.8%, 95% CI: 5.5–14.1%). Conclusions: This study demonstrated the potential application of a WGCNA-based gene prognostic model for predicting the survival outcome of glioblastoma patients.
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Affiliation(s)
- Xiangjun Tang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China.,Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China.,Department of Neurosurgery, Affiliated Hospital of Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Pengfei Xu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bin Wang
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jie Luo
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Rui Fu
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Kuanming Huang
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Longjun Dai
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Junti Lu
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Gang Cao
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Hao Peng
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Li Zhang
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhaohui Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
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5
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Yaseen A, Audette GF. Structural flexibility in the Helicobacter pylori peptidyl-prolyl cis,trans-isomerase HP0175 is achieved through an extension of the chaperone helices. J Struct Biol 2018; 204:261-269. [PMID: 30179659 DOI: 10.1016/j.jsb.2018.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 08/08/2018] [Accepted: 08/31/2018] [Indexed: 01/19/2023]
Abstract
Helicobacter pylori infects the gastric epithelium of half the global population, where infections can persist into adenocarcinomas and peptic ulcers. H. pylori secretes several proteins that lend to its pathogenesis and survival including VacA, CagA, γ-glutamyltransferase and HP0175. HP0175, also known as HpCBF2, classified as a peptidyl-prolyl cis,trans-isomerase, has been shown to induce apoptosis through a cascade of mechanisms initiated though its interaction with toll like receptor 4 (TLR4). Here, we report the structure of apo-HP0175 at 2.09 Å with a single monomer in the asymmetric unit. Chromatographic, light scattering and mass spectrometric analysis of HP0175 in solution indicate that the protein is mainly monomeric under low salt conditions, while increasing ionic interactions facilitates protein dimerization. A comparison of the apo-HP0175 structure to that of the indole-2-carboxylic acid-bound form shows movement of the N- and C-terminal helices upon interaction of the catalytic residues in the binding pocket. Helix extension of the N/C chaperone domains between apo and I2CA-bound HP0175 supports previous findings in parvulin PPIases for their role in protein stabilization (and accommodation of variable protein lengths) of those undergoing catalysis.
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Affiliation(s)
- Ayat Yaseen
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
| | - Gerald F Audette
- Department of Chemistry, York University, Toronto M3J 1P3, Canada; Centre for Research of Biomolecular Interactions, York University, Toronto M3J 1P3, Canada.
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6
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Banafshe HR, Mohsenpour M, Ardjmand A. Effects Following Intracerebroventricular Injection of Immunosuppressant Cyclosporine A On Inhibitory Avoidance Learning and Memory in Mice. Galen Med J 2018; 7:e1044. [PMID: 34466427 PMCID: PMC8343945 DOI: 10.22086/gmj.v0i0.1044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/27/2018] [Accepted: 05/04/2018] [Indexed: 11/30/2022] Open
Abstract
Background: Protein phosphatase-2B or calcineurin (CN) is the main phosphatase and a critical regulator of cellular pathways for learning, memory, and plasticity. Cyclosporine A(CyA), a phosphatase and peptidyl-prolyl cis/trans isomerase inhibitor, is a common immune suppressant extensively used in tissue transplantation. To further clarify the role of CN in different stages of learning and memory, the aim of the present study was to evaluate the role of CyA in an inhibitory avoidance (IA) model in mice. Materials and Methods: Using intracerebroventricular (ICV) injection of different doses of CyA (0.5, 5, and 50 nM) at different periods (pre-/post-training and pre-test), the effect of the drug was evaluated in a step-down IA paradigm. The latency of step-down (sec) was considered a criterion for memory performance. Results: The pre-training injections of CyA (0.5, 5 nM), however not of 50 nM, impaired IA learning acquisition. The post-training injection of high-dose CyA (50 nM) impaired memory consolidation. The pre-test ICV CyA injection did not impair memory retrieval; the ICV injection of CyA caused no change in locomotion. Conclusion: These findings suggest that CyA selectively interferes with acquisition, retention, but not retrieval, of information processing in mice. Given the crucial role of CN in common signaling pathway of memory performance and cognition, it could be a probable therapeutic target in the treatment of a wide variety of neurological conditions involving memory.
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Affiliation(s)
- Hamid Reza Banafshe
- Physiology Research Center, Kashan University of Medical Sciences, Kashan, Iran.,Department of Pharmacology, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohsen Mohsenpour
- Physiology Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Abolfazl Ardjmand
- Physiology Research Center, Kashan University of Medical Sciences, Kashan, Iran.,Department of Physiology, Kashan University of Medical Sciences, Kashan, Iran
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7
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Posterior Reversible Encephalopathy Syndrome After Transplantation: a Review. Mol Neurobiol 2015; 53:6897-6909. [PMID: 26666662 DOI: 10.1007/s12035-015-9560-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 11/29/2015] [Indexed: 12/29/2022]
Abstract
Posterior reversible encephalopathy syndrome (PRES) is a rare neurological disease. Recently, an increase in the number of transplantations has led to more cases being associated with PRES than what was previously reported. Calcineurin inhibitors (CNIs) are major risk factors for PRES in posttransplantation patients. The mechanisms of the development of PRES remain to be unclear. The typical clinical symptoms of PRES include seizures, acute encephalopathy syndrome, and visual symptoms. The hyperintense signal on fluid-attenuated inversion recovery image is the characteristic of the imaging appearance in these patients. In addition, other abnormal signals distributed in multiple locations are also reported in some atypical cases. Unfortunately, PRES is often not recognized or diagnosed too late due to complicated differential diagnoses, such as ischemic stroke, progressive multifocal leukoencephalopathy, and neurodegenerative diseases. Thus, this review emphasizes the importance of considering the possibility of PRES when neurological disturbances appear after solid organ transplantation or hematopoietic cell transplantation. Moreover, this review demonstrates the molecular mechanisms of PRES associated with CNIs after transplantation, which aims to help clinicians further understand PRES in the transplantation era.
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8
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Labrador‐Garrido A, Cejudo‐Guillén M, Daturpalli S, Leal MM, Klippstein R, De Genst EJ, Villadiego J, Toledo‐Aral JJ, Dobson CM, Jackson SE, Pozo D, Roodveldt C. Chaperome screening leads to identification of Grp94/Gp96 and FKBP4/52 as modulators of the α‐synuclein‐elicited immune response. FASEB J 2015; 30:564-77. [DOI: 10.1096/fj.15-275131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/21/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Adahir Labrador‐Garrido
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER)SevilleSpain
- Department of Medical Biochemistry, Molecular Biology, and ImmunologySchool of MedicineUniversity of SevilleSevilleSpain
| | - Marta Cejudo‐Guillén
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER)SevilleSpain
- Department of Medical Biochemistry, Molecular Biology, and ImmunologySchool of MedicineUniversity of SevilleSevilleSpain
| | - Soumya Daturpalli
- Department of ChemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - María M. Leal
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER)SevilleSpain
| | - Rebecca Klippstein
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER)SevilleSpain
- Department of Medical Biochemistry, Molecular Biology, and ImmunologySchool of MedicineUniversity of SevilleSevilleSpain
| | - Erwin J. De Genst
- Department of ChemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Javier Villadiego
- Department of Medical Physiology and BiophysicsSchool of MedicineUniversity of SevilleSevilleSpain
- Institute of Biomedicine of Seville (IBiS)University Hospital Virgen del RocioConsejo Superior de Investigaciones Científicas (CSIC)University of SevilleSevilleSpain
- Centers for Networked Biomedical Research in Neurodegenerative Diseases (CIBERNED)SevilleSpain
| | - Juan J. Toledo‐Aral
- Department of Medical Physiology and BiophysicsSchool of MedicineUniversity of SevilleSevilleSpain
- Institute of Biomedicine of Seville (IBiS)University Hospital Virgen del RocioConsejo Superior de Investigaciones Científicas (CSIC)University of SevilleSevilleSpain
- Centers for Networked Biomedical Research in Neurodegenerative Diseases (CIBERNED)SevilleSpain
| | | | - Sophie E. Jackson
- Department of ChemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - David Pozo
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER)SevilleSpain
- Department of Medical Biochemistry, Molecular Biology, and ImmunologySchool of MedicineUniversity of SevilleSevilleSpain
| | - Cintia Roodveldt
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER)SevilleSpain
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9
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Cho KI, Orry A, Park SE, Ferreira PA. Targeting the cyclophilin domain of Ran-binding protein 2 (Ranbp2) with novel small molecules to control the proteostasis of STAT3, hnRNPA2B1 and M-opsin. ACS Chem Neurosci 2015; 6:1476-85. [PMID: 26030368 DOI: 10.1021/acschemneuro.5b00134] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cyclophilins are peptidyl cis-trans prolyl isomerases (PPIases), whose activity is typically inhibited by cyclosporine A (CsA), a potent immunosuppressor. Cyclophilins are also chaperones. Emerging evidence supports that cyclophilins present nonoverlapping PPIase and chaperone activities. The proteostasis of the disease-relevant substrates, signal transducer and activator of transcription 3 and 5 (STAT3/STAT5), heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1), and M-opsin, is regulated by nonoverlapping chaperone and PPIase activities of the cyclophilin domain (CY) of Ranbp2, a multifunctional and modular scaffold that controls nucleocytoplasmic shuttling and proteostasis of selective substrates. Although highly homologous, CY and the archetypal cyclophilin A (CyPA) present distinct catalytic and CsA-binding activities owing to unique structural features between these cylophilins. We explored structural idiosyncrasies between CY and CyPA to screen in silico nearly 9 million small molecules (SM) against the CY PPIase pocket and identify SMs with selective bioactivity toward STAT3, hnRNPA2B1, or M-opsin proteostasis. We found three classes of SMs that enhance the cytokine-stimulated transcriptional activity of STAT3 without changing latent and activated STAT3 levels, down-regulate hnRNPA2B1 or M-opsin proteostasis, or a combination of these. Further, a SM that suppresses hnRNPA2B1 proteostasis also inhibits strongly and selectively the PPIase activity of CY. This study unravels chemical probes for multimodal regulation of CY of Ranbp2 and its substrates, and this regulation likely results in the allosterism stemming from the interconversion of conformational substates of cyclophilins. The results also demonstrate the feasibility of CY in drug discovery against disease-relevant substrates controlled by Ranbp2, and they open new opportunities for therapeutic interventions.
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Affiliation(s)
- Kyoung-in Cho
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Andrew Orry
- MolSoft LLC, San Diego, California 92121, United States
| | - Se Eun Park
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Paulo A. Ferreira
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina 27710, United States
- Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, United States
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10
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Zaheer R, Klima CL, McAllister TA. Expeditious screening of candidate proteins for microbial vaccines. J Microbiol Methods 2015; 116:53-9. [PMID: 26149626 DOI: 10.1016/j.mimet.2015.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 06/26/2015] [Accepted: 06/27/2015] [Indexed: 11/18/2022]
Abstract
Advancements in high-throughput "omics" technologies have revolutionized the way vaccine candidates are identified. Now every surface expressed protein that an organism produces can be identified in silico and possibly made available for the rapid development of recombinant/subunit vaccines. However, evaluating the antigenicity of a large number of candidate proteins is an immense challenge, typically requiring cloning of several hundred candidates followed by immunogenicity screening. Here we report the development of a rapid, high-throughput method for screening candidate proteins for vaccines. This method involves utilizing a coupled, cell-free transcription-translation system to screen tagged proteins that are captured at the C-termini using appropriate ligand coated wells in 96 well ELISA plates. The template DNA for the cell-free expression is generated by two sequential PCRs and includes gene coding sequences, promoter, terminator, other necessary cis-acting elements and appropriate tag sequences. The process generates expressible candidate proteins containing two different peptide tags at the N- and the C-termini of the protein molecules. Proteins are screened in parallel for their quantity and immunoreactivity with N-terminal tag antibodies and antisera raised against the pathogen of interest, respectively. Normalization against the total detectable bound protein in the control wells allows for the identification of highly immunoreactive candidates. For this study we selected 30 representatives of >300 potential candidate proteins from Mannheimia haemolytica, a bacterial agent of pneumonia in feedlot cattle for expression with N-terminal Strep-II and C-terminal His(x6)-tag and evaluated their relative immunoreactivities using Strep-tactin-HRP and rabbit antisera generated against M. haemolytica. Using this system we were able to swiftly and quantitatively analyze and rank the suitability of proteins to identify potentially viable vaccine candidates, with the majority of the high ranking candidates being associated with virulence and pathogenicity. The system is adaptable to any bacterial target and presents an alternative to conventional laborious cloning, expression and screening procedures.
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Affiliation(s)
- Rahat Zaheer
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1 Canada
| | - Cassidy L Klima
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1 Canada
| | - Tim A McAllister
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1 Canada.
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11
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Microbial peptidyl-prolyl cis/trans isomerases (PPIases): virulence factors and potential alternative drug targets. Microbiol Mol Biol Rev 2015; 78:544-71. [PMID: 25184565 DOI: 10.1128/mmbr.00015-14] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Initially discovered in the context of immunomodulation, peptidyl-prolyl cis/trans isomerases (PPIases) were soon identified as enzymes catalyzing the rate-limiting protein folding step at peptidyl bonds preceding proline residues. Intense searches revealed that PPIases are a superfamily of proteins consisting of three structurally distinguishable families with representatives in every described species of prokaryote and eukaryote and, recently, even in some giant viruses. Despite the clear-cut enzymatic activity and ubiquitous distribution of PPIases, reports on solely PPIase-dependent biological roles remain scarce. Nevertheless, they have been found to be involved in a plethora of biological processes, such as gene expression, signal transduction, protein secretion, development, and tissue regeneration, underscoring their general importance. Hence, it is not surprising that PPIases have also been identified as virulence-associated proteins. The extent of contribution to virulence is highly variable and dependent on the pleiotropic roles of a single PPIase in the respective pathogen. The main objective of this review is to discuss this variety in virulence-related bacterial and protozoan PPIases as well as the involvement of host PPIases in infectious processes. Moreover, a special focus is given to Legionella pneumophila macrophage infectivity potentiator (Mip) and Mip-like PPIases of other pathogens, as the best-characterized virulence-related representatives of this family. Finally, the potential of PPIases as alternative drug targets and first tangible results are highlighted.
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12
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Noninvasive bioluminescence imaging of α-synuclein oligomerization in mouse brain using split firefly luciferase reporters. J Neurosci 2015; 34:16518-32. [PMID: 25471588 DOI: 10.1523/jneurosci.4933-13.2014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Alpha-synuclein (αSYN) aggregation plays a pivotal role in the pathogenesis of Parkinson's disease and other synucleinopathies. In this multistep process, oligomerization of αSYN monomers is the first step in the formation of fibrils and intracytoplasmic inclusions. Although αSYN oligomers are generally considered to be the culprit of these diseases, the methodology currently available to follow-up oligomerization in cells and in brain is inadequate. We developed a split firefly luciferase complementation system to visualize oligomerization of viral vector-encoded αSYN fusion proteins. αSYN oligomerization resulted in successful luciferase complementation in cell culture and in mouse brain. Oligomerization of αSYN was monitored noninvasively with bioluminescence imaging in the mouse striatum and substantia nigra up to 8 months after injection. Moreover, the visualized αSYN oligomers retained their toxic and aggregation properties in both model systems. Next, the effect of two small molecules, FK506 and (-)-epigallocatechin-3-gallate (EGCG), known to inhibit αSYN fibril formation, was investigated. FK506 inhibited the observed αSYN oligomerization both in cell culture and in mouse brain. In conclusion, the split firefly luciferase-αSYN complementation assay will increase our insight in the role of αSYN oligomers in synucleinopathies and opens new opportunities to evaluate potential αSYN-based neuroprotective therapies.
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13
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Mantovani F, Zannini A, Rustighi A, Del Sal G. Interaction of p53 with prolyl isomerases: Healthy and unhealthy relationships. Biochim Biophys Acta Gen Subj 2015; 1850:2048-60. [PMID: 25641576 DOI: 10.1016/j.bbagen.2015.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 01/17/2015] [Accepted: 01/19/2015] [Indexed: 01/11/2023]
Abstract
BACKGROUND The p53 protein family, comprising p53, p63 and p73, is primarily involved in preserving genome integrity and preventing tumor onset, and also affects a range of physiological processes. Signal-dependent modifications of its members and of other pathway components provide cells with a sophisticated code to transduce a variety of stress signaling into appropriate responses. TP53 mutations are highly frequent in cancer and lead to the expression of mutant p53 proteins that are endowed with oncogenic activities and sensitive to stress signaling. SCOPE OF REVIEW p53 family proteins have unique structural and functional plasticity, and here we discuss the relevance of prolyl-isomerization to actively shape these features. MAJOR CONCLUSIONS The anti-proliferative functions of the p53 family are carefully activated upon severe stress and this involves the interaction with prolyl-isomerases. In particular, stress-induced stabilization of p53, activation of its transcriptional control over arrest- and cell death-related target genes and of its mitochondrial apoptotic function, as well as certain p63 and p73 functions, all require phosphorylation of specific S/T-P motifs and their subsequent isomerization by the prolyl-isomerase Pin1. While these functions of p53 counteract tumorigenesis, under some circumstances their activation by prolyl-isomerases may have negative repercussions (e.g. tissue damage induced by anticancer therapies and ischemia-reperfusion, neurodegeneration). Moreover, elevated Pin1 levels in tumor cells may transduce deregulated phosphorylation signaling into activation of mutant p53 oncogenic functions. GENERAL SIGNIFICANCE The complex repertoire of biological outcomes induced by p53 finds mechanistic explanations, at least in part, in the association between prolyl-isomerases and the p53 pathway. This article is part of a Special Issue entitled Proline-directed foldases: Cell signaling catalysts and drug targets.
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Affiliation(s)
- Fiamma Mantovani
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Trieste, Italy; Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Trieste, Italy
| | - Alessandro Zannini
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Trieste, Italy; Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Trieste, Italy
| | - Alessandra Rustighi
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Trieste, Italy; Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Trieste, Italy
| | - Giannino Del Sal
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Trieste, Italy; Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Trieste, Italy.
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14
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Selective inhibitors of the FK506-binding protein 51 by induced fit. Nat Chem Biol 2014; 11:33-7. [PMID: 25436518 DOI: 10.1038/nchembio.1699] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 10/09/2014] [Indexed: 01/17/2023]
Abstract
The FK506-binding protein 51 (FKBP51, encoded by the FKBP5 gene) is an established risk factor for stress-related psychiatric disorders such as major depression. Drug discovery for FKBP51 has been hampered by the inability to pharmacologically differentiate against the structurally similar but functional opposing homolog FKBP52, and all known FKBP ligands are unselective. Here, we report the discovery of the potent and highly selective inhibitors of FKBP51, SAFit1 and SAFit2. This new class of ligands achieves selectivity for FKBP51 by an induced-fit mechanism that is much less favorable for FKBP52. By using these ligands, we demonstrate that selective inhibition of FKBP51 enhances neurite elongation in neuronal cultures and improves neuroendocrine feedback and stress-coping behavior in mice. Our findings provide the structural and functional basis for the development of mechanistically new antidepressants.
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15
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Brown CA, Schmidt C, Poulter M, Hummerich H, Klöhn PC, Jat P, Mead S, Collinge J, Lloyd SE. In vitro screen of prion disease susceptibility genes using the scrapie cell assay. Hum Mol Genet 2014; 23:5102-8. [PMID: 24833721 PMCID: PMC4159154 DOI: 10.1093/hmg/ddu233] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/10/2014] [Indexed: 11/29/2022] Open
Abstract
Prion diseases (transmissible spongiform encephalopathies) are fatal neurodegenerative diseases, including Creutzfeldt-Jakob disease in humans, scrapie in sheep and bovine spongiform encephalopathy in cattle. While genome-wide association studies in human and quantitative trait loci mapping in mice have provided evidence for multiple susceptibility genes, few of these have been confirmed functionally. Phenotyping mouse models is generally the method of choice. However, this is not a feasible option where many novel genes, without pre-existing models, would need to be tested. We have therefore developed and applied an in-vitro screen to triage and prioritize candidate modifier genes for more detailed future studies which is faster, far more cost effective and ethical relative to mouse bioassay models. An in vitro prion bioassay, the scrapie cell assay, uses a neuroblastoma-derived cell line (PK1) that is susceptible to RML prions and able to propagate prions at high levels. In this study, we have generated stable gene silencing and/or overexpressing PK1-derived cell lines to test whether perturbation of 14 candidate genes affects prion susceptibility. While no consistent differences were determined for seven genes, highly significant changes were detected for Zbtb38, Sorcs1, Stmn2, Hspa13, Fkbp9, Actr10 and Plg, suggesting that they play key roles in the fundamental processes of prion propagation or clearance. Many neurodegenerative diseases involve the accumulation of misfolded protein aggregates and 'prion-like' seeding and spread has been implicated in their pathogenesis. It is therefore expected that some of these prion-modifier genes may be of wider relevance in neurodegeneration.
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Affiliation(s)
- Craig A Brown
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Christian Schmidt
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Mark Poulter
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Holger Hummerich
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Peter-C Klöhn
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Parmjit Jat
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Simon Mead
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - John Collinge
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Sarah E Lloyd
- MRC Prion Unit and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
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16
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Li B, Jung HJ, Kim SM, Kim MJ, Jahng JW, Lee JH. Human periodontal ligament stem cells repair mental nerve injury. Neural Regen Res 2014; 8:2827-37. [PMID: 25206604 PMCID: PMC4146018 DOI: 10.3969/j.issn.1673-5374.2013.30.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/26/2013] [Indexed: 01/31/2023] Open
Abstract
Human periodontal ligament stem cells are easily accessible and can differentiate into Schwann cells. We hypothesized that human periodontal ligament stem cells can be used as an alternative source for the autologous Schwann cells in promoting the regeneration of injured peripheral nerve. To validate this hypothesis, human periodontal ligament stem cells (1 × 106) were injected into the crush-injured left mental nerve in rats. Simultaneously, autologous Schwann cells (1 × 106) and PBS were also injected as controls. Real-time reverse transcriptase polymerase chain reaction showed that at 5 days after injection, mRNA expression of low affinity nerve growth factor receptor was significantaly increased in the left trigeminal ganglion of rats with mental nerve injury. Sensory tests, histomorphometric evaluation and retrograde labeling demonstrated that at 2 and 4 weeks after injection, sensory function was significantly improved, the numbers of retrograde labeled sensory neurons and myelinated axons were significantly increased, and human periodontal ligament stem cells and autologous Schwann cells exhibited similar therapeutic effects. These findings suggest that transplantation of human periodontal ligament stem cells show a potential value in repair of mental nerve injury.
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Affiliation(s)
- Bohan Li
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Binzhou Medical College, Binzhou, Shandong Province, China
| | - Hun-Jong Jung
- Department of Occupation and Environment, Konkuk Postgraduate Medical School, Choong-Ju, Korea
| | - Soung-Min Kim
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Seoul National University, Seoul, Korea
| | - Myung-Jin Kim
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Seoul National University, Seoul, Korea
| | - Jeong Won Jahng
- Dental Research Institute, Seoul National University, Seoul, Korea
| | - Jong-Ho Lee
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Seoul National University, Seoul, Korea ; Dental Research Institute, Seoul National University, Seoul, Korea
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17
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Olivieri L, Gardebien F. Classical force field parameters for two high-affinity ligands of FKBP12. J Mol Graph Model 2014; 49:118-28. [PMID: 24657432 DOI: 10.1016/j.jmgm.2014.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 02/16/2014] [Accepted: 02/18/2014] [Indexed: 11/25/2022]
Abstract
FKBP12 is an important target in the treatment of transplant rejection and is also a promising target for cancer and neurodegenerative diseases. We determined for two ligands of nanomolar affinity the set of parameters in the CHARMM force field. The fitting procedure was based on reproducing the quantum chemistry data (distances, angles, and energies). Since the dynamical behavior of such ligands strongly depends on the dihedral angles, care was taken to derive the corresponding parameters. Moreover, since each of the central core region of these two ligands is similar to other known ligands or drugs of other proteins, part at least of these parameters could also be useful for these other ligands.
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Affiliation(s)
- Lilian Olivieri
- DSIMB, INSERM, U1134, Paris F-75015, France; Université de la Réunion, UMR_S 1134, Faculté des Sciences et Technologies, 15, avenue René Cassin, BP 7151, 97715 Saint Denis Messag Cedex 09, Réunion; Institut National de la Transfusion Sanguine, F-75015 Paris, France; Laboratory of Excellence GR-Ex
| | - Fabrice Gardebien
- DSIMB, INSERM, U1134, Paris F-75015, France; Université de la Réunion, UMR_S 1134, Faculté des Sciences et Technologies, 15, avenue René Cassin, BP 7151, 97715 Saint Denis Messag Cedex 09, Réunion; Institut National de la Transfusion Sanguine, F-75015 Paris, France; Laboratory of Excellence GR-Ex.
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18
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Montané MH, Menand B. ATP-competitive mTOR kinase inhibitors delay plant growth by triggering early differentiation of meristematic cells but no developmental patterning change. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4361-74. [PMID: 23963679 PMCID: PMC3808319 DOI: 10.1093/jxb/ert242] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The TOR (target of rapamycin) protein, a large phosphatidylinositol 3-kinase-like protein kinase (PIKK) that is conserved in eukaryotes and is a central regulator of growth and metabolism. The analysis of function of TOR in plant growth and development has been limited by the fact that plants are very poorly sensitive to rapamycin. As the kinase domain of TOR is highly conserved, this study analysed the dose-dependent effect of three sets of first- and second-generation ATP-competitive inhibitors (called asTORis for active-site TOR inhibitors) recently developed for the human TOR kinase on Arabidopsis thaliana growth. All six asTORis inhibited plant root growth in a dose-dependent manner, with 50% growth inhibitory doses (GI50) of <10 μM and <1 μM for the first- and second-generation inhibitors, respectively, similarly to the values in mammalian cells. A genetic approach further demonstrated that only asTORis inhibited root growth in an AtTOR gene-dosage-dependent manner. AsTORis decreased the length of: (i) the meristematic zone (MZ); (ii) the division zone in the MZ; (iii) epidermal cells in the elongation zone; and (iv) root hair cells. Whereas meristematic cells committed to early differentiation, the pattern of cell differentiation was not affected per se. AsTORis-induced root hair growth phenotype was shown to be specific by using other growth inhibitors blocking the cell cycle or translation. AsTORis dose-dependent inhibition of growth and root hairs was also observed in diverse groups of flowering plants, indicating that asTORis can be used to study the TOR pathway in other angiosperms, including crop plants.
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Affiliation(s)
- Marie-Hélène Montané
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, F-13009, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales, Marseille, F-13009, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et Biotechnologie, Marseille, F-13009, France
| | - Benoît Menand
- Aix-Marseille Université, Laboratoire de Génétique et Biophysique des Plantes, Marseille, F-13009, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7265 Biologie Végétale et Microbiologie Environnementales, Marseille, F-13009, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Environnementale et Biotechnologie, Marseille, F-13009, France
- * To whom correspondence should be addressed.
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19
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Hsp90-binding immunophilins as a potential new platform for drug treatment. Future Med Chem 2013; 5:591-607. [PMID: 23573975 DOI: 10.4155/fmc.13.7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Immunophilins are proteins that contain a PPIase domain as a family signature. Low-molecular-weight immunophilins were first described associated to immunosuppressive action and protein folding. Recent studies of other members of the family have led to the identification of their participation in basic processes such as protein-protein interactions, signal transduction cascades, cell differentiation, cell cycle progression, metabolic activity, apoptosis mechanisms, microorganisms infection, cancer, neurotrophism and neuroprotection, among several other physiological and pathophysiological processes. Due to all these emerging features, the development of specific ligands for immunophilins appears to have promising perspectives, in particular in the fields of cancer biology and neuroregeneration fields. We review the emerging role of immunophilins in protein transport, transcription regulation, malignancies development and neurotrophic action, in addition to a number of biological properties that transform these proteins in potential targets for novel therapeutic strategies.
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20
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Martina MR, Tenori E, Bizzarri M, Menichetti S, Caminati G, Procacci P. The precise chemical-physical nature of the pharmacore in FK506 binding protein inhibition: ElteX, a New class of nanomolar FKBP12 ligands. J Med Chem 2013; 56:1041-51. [PMID: 23301792 DOI: 10.1021/jm3015052] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Due to its central role in immunosuppression and cell proliferation and due to its specific peptidyl-prolyl-isomerase (PPI) function, the FKBP protein family is at the crossroad of several important metabolic pathways. Members of this family, and notably FK506 binding protein (FKBP12), are thought to be involved in neurodegenerative diseases such as Alzheimer disease, Parkinson disease, multiple sclerosis, amyotrophic lateral sclerosis, as well as in proliferation disorders and cancer. Using an interdisciplinary approach based on computational, synthetic, and experimental techniques, we show that the best potential binders for FKBP proteins optimally expose the two contiguous carbonyl oxygen in the proline-mimetic chain for FKBP docking and are characterized by the abundance of rigid quasi-cyclic structures stabilized in aqueous solution by intraligand hydrophobic interactions mimicking the macrolide structure of the natural FKBP binders FK506 and Rapamycin. These peculiar structural and chemical-physical features define at the same time an ElteX compound and the minimal pharmacore in the FKBP family, shedding new light on the isomerization mechanism of the PPI domain. On the basis of the above hypothesis, we have successfully designed and synthesized several nanomolar ElteX FKBP12 ligands. Among these, ElteN378 is a new low atomic weight ligand with affinity comparable to that of the macrolide Rapamycin.
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Affiliation(s)
- Maria Raffaella Martina
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
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