1
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Tsekrekou M, Giannakou M, Papanikolopoulou K, Skretas G. Protein aggregation and therapeutic strategies in SOD1- and TDP-43- linked ALS. Front Mol Biosci 2024; 11:1383453. [PMID: 38855322 PMCID: PMC11157337 DOI: 10.3389/fmolb.2024.1383453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 06/11/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with severe socio-economic impact. A hallmark of ALS pathology is the presence of aberrant cytoplasmic inclusions composed of misfolded and aggregated proteins, including both wild-type and mutant forms. This review highlights the critical role of misfolded protein species in ALS pathogenesis, particularly focusing on Cu/Zn superoxide dismutase (SOD1) and TAR DNA-binding protein 43 (TDP-43), and emphasizes the urgent need for innovative therapeutic strategies targeting these misfolded proteins directly. Despite significant advancements in understanding ALS mechanisms, the disease remains incurable, with current treatments offering limited clinical benefits. Through a comprehensive analysis, the review focuses on the direct modulation of the misfolded proteins and presents recent discoveries in small molecules and peptides that inhibit SOD1 and TDP-43 aggregation, underscoring their potential as effective treatments to modify disease progression and improve clinical outcomes.
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Affiliation(s)
- Maria Tsekrekou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Maria Giannakou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Katerina Papanikolopoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
- Institute for Bio-innovation, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
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2
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Han ISM, Thayer KM. Reconnaissance of Allostery via the Restoration of Native p53 DNA-Binding Domain Dynamics in Y220C Mutant p53 Tumor Suppressor Protein. ACS OMEGA 2024; 9:19837-19847. [PMID: 38737036 PMCID: PMC11079909 DOI: 10.1021/acsomega.3c08509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 05/14/2024]
Abstract
Allosteric regulation of protein dynamics infers a long-range deliberate propagation of information via micro- and macroscale interactions. The Y220C structural mutant is one of the most frequent cancerous p53 mutants. The mutation is distally located from the DNA-binding site of the p53 DNA-binding domain yet causes changes in DNA recognition. This system presents a unique opportunity to examine the allosteric control of mutated proteins under a drug design paradigm. We focus on the key case study of p53 Y220C mutation restoration by a series of new compounds suggested to have Y220C reactivation properties in comparison to our previous findings on the restorative potential of PK11000, a compound studied extensively for reactivation in vitro and in vivo. Previously, we implemented all-atom molecular dynamics (MD) simulations and our lab's techniques of MD-Sectors and MD-Markov state models on the wild type, the Y220C mutant, and Y220C with PK11000 to characterize the effector's restorative properties in terms of conformational dynamics and hydrogen bonding. In this study, we turn to probing the effects made by docking the battery of a new but less well-tested set of aminobenzothiazole derivative compounds reported by Baud et al., which show promise of Y220C rescue. We find that while complete and precise reconstitution of p53 WT molecular dynamics may not be observed as was the case with PK11000, dispersed local reconstitution of loop dynamics provides evidence of rescuing effects by aminobenzothiazole derivative N,2-dihydroxy-3,5-diiodo-4-(1H-pyrrol-1-yl)benzamide, Effector 22, like what we observed for PK11000. Generalizable insights into the mutation and allosteric reactivation of p53 by various effectors by reconstitution of WT dynamics observed in statistical conformational ensemble analysis and network inference are discussed, considering the development of allosteric drug design rooted in first principles.
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Affiliation(s)
- In Sub M. Han
- College of Integrated Sciences, Wesleyan University, Hall-Atwater Laboratories, Middletown, Connecticut 06459-0180, United States
| | - Kelly M. Thayer
- College of Integrated Sciences, Wesleyan University, Hall-Atwater Laboratories, Middletown, Connecticut 06459-0180, United States
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3
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Rahman A, Saikia B, Baruah A. In silico analysis of SOD1 aggregation inhibition modes of tertiary amine pyrazolone and pyrano coumarin ferulate as ALS drug candidates. Phys Chem Chem Phys 2023; 25:26833-26846. [PMID: 37782142 DOI: 10.1039/d3cp03978a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease, the familial form (fALS) of which is often cognate to mutations in the antioxidant enzyme Cu/Zn superoxide dismutase 1 (SOD1) leading to misfolding and aggregation. Two small molecules, a tertiary amine pyrazolone (TAP) and a pyrano coumarin ferulate (PCF) were suggested to be ALS drug candidates following experimental observation of their ability to inhibit SOD1 protein misfolding and aggregation. The present work aims at computational investigation of these experimentally proposed drug candidates to gain insight into their mechanism of SOD1 misfolding and aggregation inhibition. On the basis of molecular docking, molecular dynamics simulation, MM-PBSA and per-residue energy decomposition analysis, we examined the specific interactions of TAP and PCF with three probable binding sites of SOD1, namely, dimeric interface cavity, W32 and, UMP binding sites. Results suggest that the binding of TAP at W32 and at UMP sites are least probable due to absence of any favorable interaction. The binding of TAP to dimeric cavity is also unstable due to strong unfavorable interactions. In case of PCF, binding at the UMP site is least probable while binding at dimeric cavity is accompanied by unfavorable interactions. PCF, however, exhibits stable binding with the W32 binding site of SOD1 by stabilizing the solvent accessible hydrophobic residues, which otherwise would have acted as contact points for aggregation. Thus the results imply that compound PCF functions as an inhibitior of SOD1 misfolding/aggregation through direct interaction with the protein SOD1 at the W32 binding site. However, TAP is likely to act as an inhibitor through a different mechanism rather than direct interaction with the protein SOD1. These results apart from reinforcing previous experimental findings, shed light on the probable mechanism of action of the proposed drug candidates.
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Affiliation(s)
- Aziza Rahman
- Department of Chemistry, Dibrugarh University, Dibrugarh, Assam, 786004, India.
| | - Bondeepa Saikia
- Department of Chemistry, Dibrugarh University, Dibrugarh, Assam, 786004, India.
| | - Anupaul Baruah
- Department of Chemistry, Dibrugarh University, Dibrugarh, Assam, 786004, India.
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4
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Roy R, Paul S. Illustrating the Effect of Small Molecules Derived from Natural Resources on Amyloid Peptides. J Phys Chem B 2023; 127:600-615. [PMID: 36638829 DOI: 10.1021/acs.jpcb.2c07607] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The onset of amyloidogenic diseases is associated with the misfolding and aggregation of proteins. Despite extensive research, no effective therapeutics are yet available to treat these chronic degenerative diseases. Targeting the aggregation of disease-specific proteins is regarded as a promising new approach to treat these diseases. In the past few years, rapid progress in this field has been made in vitro, in vivo, and in silico to generate potential drug candidates, ranging from small molecules to polymers to nanoparticles. Small molecular probes, mostly those derived from natural sources, have been of particular interest among amyloid inhibitors. Here, we summarize some of the most important natural small molecular probes which can inhibit the aggregation of Aβ, hIAPP, and α-syn peptides and discuss how their binding efficacy and preference for the peptides vary with their structure and conformation. This provides a comprehensive idea of the crucial factors which should be incorporated into the future design of novel drug candidates useful for the treatment of amyloid diseases.
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Affiliation(s)
- Rituparna Roy
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam-781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam-781039, India
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5
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Rahman A, Saikia B, Gogoi CR, Baruah A. Advances in the understanding of protein misfolding and aggregation through molecular dynamics simulation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:31-48. [PMID: 36044970 DOI: 10.1016/j.pbiomolbio.2022.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Aberrant protein folding known as protein misfolding is counted as one of the striking factors of neurodegenerative diseases. The extensive range of pathologies caused by protein misfolding, aggregation and subsequent accumulation are mainly classified into either gain of function diseases or loss of function diseases. In order to seek for novel strategies for treatment and diagnosis of neurodegenerative diseases, insights into the mechanism of misfolding and aggregation is essential. A comprehensive knowledge on the factors influencing misfolding and aggregation is required as well. An extensive experimental study on protein aggregation is somewhat challenging due to the insoluble and noncrystalline nature of amyloid fibrils. Thus there has been a growing use of computational approaches including Monte Carlo simulation, docking simulation, molecular dynamics simulation in the study of protein misfolding and aggregation. The review presents a discussion on molecular dynamics simulation alone as to how it has emerged as a promising tool in the understanding of protein misfolding and aggregation in general, detailing upon three different aspects considering four misfold prone proteins in particular. It is noticeable that all four proteins considered in this review i.e prion, superoxide dismutase1, huntingtin and amyloid β are linked to chronic neurodegenerative diseases with debilitating effects. Initially the review elaborates on the factors influencing the misfolding and aggregation. Next, it addresses our current understanding of the amyloid structures and the associated aggregation mechanisms, finally, summarizing the contribution of this computational tool in the search for therapeutic strategies against the respective protein-deposition diseases.
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Affiliation(s)
- Aziza Rahman
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Bondeepa Saikia
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Chimi Rekha Gogoi
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India
| | - Anupaul Baruah
- Department of Chemistry, Dibrugarh University, Dibrugarh, 786004, Assam, India.
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6
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Sharma R, Kumari A, Kundu B, Grover A. Amyloid fibrillation of the glaucoma associated myocilin protein is inhibited by epicatechin gallate (ECG). RSC Adv 2022; 12:29469-29481. [PMID: 36320765 PMCID: PMC9562371 DOI: 10.1039/d2ra05061g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/18/2022] [Indexed: 11/05/2022] Open
Abstract
Inherited glaucoma is a recent addition to the inventory of diseases arising due to protein misfolding. Mutations in the olfactomedin (OLF) domain of myocilin are the most common genetic cause behind this disease. Disease associated variants of m-OLF are predisposed to misfold and aggregate in the trabecular meshwork (TM) tissue of the eye. In recent years, the nature of these aggregates was revealed to exhibit the hallmarks of amyloids. Amyloid aggregates are highly stable structures that are formed, often with toxic consequences in a number of debilitating diseases. In spite of its clinical relevance the amyloidogenic nature of m-OLF has not been studied adequately. Here we have studied the amyloid fibrillation of m-OLF and report ECG as an inhibitor against it. Using biophysical and biochemical assays, coupled with advanced microscopic evaluations we show that ECG binds and stabilizes native m-OLF and thus prevents its aggregation into amyloid fibrils. Furthermore, we have used REMD simulations to delineate the stabilizing effects of ECG on the structure of m-OLF. Collectively, we report ECG as a molecular scaffold for designing and testing of novel inhibitors against m-OLF amyloid fibrillation.
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Affiliation(s)
- Ritika Sharma
- School of Biotechnology, Jawaharlal Nehru UniversityNew Delhi-110067India+91-8130738032
| | - Anchala Kumari
- Indian Council of Medical Research, International Health DivisionNew Delhi-110029India
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology DelhiHauz KhasNew DelhiIndia – 110016
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru UniversityNew Delhi-110067India+91-8130738032
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7
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Chen Y, Cao H, He W, Zhang X, Xu R. tert-Butylhydroquinone-induced formation of high-molecular-weight p62: A novel mechanism in the activation of Nrf2-Keap1. Cell Biol Int 2022; 46:1345-1354. [PMID: 35830696 DOI: 10.1002/cbin.11849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 11/06/2022]
Abstract
The respiratory system is always exposed to air and is most vulnerable to attack by environmental free radicals. The nuclear factor E2-related factor 2-Kelch-like ECH-associated protein 1-antioxidant response element (Nrf2-Keap1-ARE) pathway and p62 are both involved in the oxidative stress response. However, the interplay between these two systems remains largely unknown. This study shows that treatment of L2 cells with tert-Butylhydroquinone (tBHQ) generates a high-molecular-weight (HMW) form of p62, leading to activation of the Nrf2-Keap1-ARE pathway. The levels of HMW-p62 increased as the tBHQ concentration increased, with concomitant decreases seen in the classical form of p62. Moreover, small interfering RNA targeting p62 increases Keap1 protein levels and inactivates the Nrf2-Keap1-ARE pathway. These results demonstrate that the Nrf2-Keap1 pathway is partially regulated by p62. tBHQ-induced HMW-p62 production may be a novel mechanism in the activation of the Nrf2-Keap1-ARE pathway.
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Affiliation(s)
- Yunfang Chen
- Department of Oncology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Guangdong, China.,Department of Oncology, The First Affiliated Hospital, Southern University of Science and Technology, Shenzen, China
| | - Hua Cao
- Department of Oncology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Guangdong, China.,Department of Oncology, The First Affiliated Hospital, Southern University of Science and Technology, Shenzen, China
| | - Wan He
- Department of Oncology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Guangdong, China.,Department of Oncology, The First Affiliated Hospital, Southern University of Science and Technology, Shenzen, China
| | - Xi Zhang
- Department of Oncology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Guangdong, China.,Department of Oncology, The First Affiliated Hospital, Southern University of Science and Technology, Shenzen, China
| | - Ruilian Xu
- Department of Oncology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Guangdong, China.,Department of Oncology, The First Affiliated Hospital, Southern University of Science and Technology, Shenzen, China
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8
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Hatstat AK, Pupi MD, Reinhart MC, McCafferty DG. Small Molecule Improvement of Trafficking Defects in Models of Neurodegeneration. ACS Chem Neurosci 2021; 12:3972-3984. [PMID: 34652126 DOI: 10.1021/acschemneuro.1c00524] [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: 11/30/2022] Open
Abstract
Disrupted cellular trafficking and transport processes are hallmarks of many neurodegenerative disorders (NDs). Recently, efforts have been made toward developing and implementing experimental platforms to identify small molecules that may help restore normative trafficking functions. There have been a number of successes in targeting endomembrane trafficking with the identification of compounds that restore cell viability through rescue of protein transport and trafficking. Here, we describe some of the experimental platforms implemented for small molecule screening efforts for rescue of trafficking defects in neurodegeneration. A survey of phenotypically active small molecules identified to date is provided, including a summary of medicinal chemistry efforts and insights into putative targets and mechanisms of action. In particular, emphasis is put on ligands that demonstrate activity in more than one model of neurodegeneration as retention of phenotypic activity across ND models suggests conservation of biological targets across NDs.
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Affiliation(s)
- A. Katherine Hatstat
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Michael D. Pupi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Michaela C. Reinhart
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Dewey G. McCafferty
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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9
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Sharma R, Srivastava T, Pandey AR, Mishra T, Gupta B, Reddy SS, Singh SP, Narender T, Tripathi A, Chandramouli B, Sashidhara KV, Priya S, Kumar N. Identification of Natural Products as Potential Pharmacological Chaperones for Protein Misfolding Diseases. ChemMedChem 2021; 16:2146-2156. [PMID: 33760394 DOI: 10.1002/cmdc.202100147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 01/12/2023]
Abstract
Defective protein folding and accumulation of misfolded proteins is associated with neurodegenerative, cardiovascular, secretory, and metabolic disorders. Efforts are being made to identify small-molecule modulators or structural-correctors for conformationally destabilized proteins implicated in various protein aggregation diseases. Using a metastable-reporter-based primary screen, we evaluated pharmacological chaperone activity of a diverse class of natural products. We found that a flavonoid glycoside (C-10, chrysoeriol-7-O-β-D-glucopyranoside) stabilizes metastable proteins, prevents its aggregation, and remodels the oligomers into protease-sensitive species. Data was corroborated with additional secondary screen with disease-specific pathogenic protein. In vitro and cell-based experiments showed that C-10 inhibits α-synuclein aggregation which is implicated in synucleinopathies-related neurodegeneration. C-10 interferes in its structural transition into β-sheeted fibrils and mitigates α-synuclein aggregation-associated cytotoxic effects. Computational modeling suggests that C-10 binds to unique sites in α-synuclein which may interfere in its aggregation amplification. These findings open an avenue for comprehensive SAR development for flavonoid glycosides as pharmacological chaperones for metastable and aggregation-prone proteins implicated in protein conformational diseases.
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Affiliation(s)
- Richa Sharma
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Tulika Srivastava
- CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | - Alka Raj Pandey
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | - Tripti Mishra
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Bhagyashri Gupta
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | | | - Suriya P Singh
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Tadigoppula Narender
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | - Aradhya Tripathi
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | | | - Koneni V Sashidhara
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | - Smriti Priya
- CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
| | - Niti Kumar
- CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201 002, India
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10
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He S, He X, Liu L, Zhang W, Yu L, Deng Z, Feiyi Z, Mo S, Fan Y, Zhao X, Wang L, Wang C, Zhang S. The Structural Understanding of Transthyretin Misfolding and the Inspired Drug Approaches for the Treatment of Heart Failure Associated With Transthyretin Amyloidosis. Front Pharmacol 2021; 12:628184. [PMID: 33679409 PMCID: PMC7930814 DOI: 10.3389/fphar.2021.628184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/13/2021] [Indexed: 01/15/2023] Open
Abstract
Substantial controversies exist in the exploration of the molecular mechanism of heart failure (HF) and pose challenges to the diagnosis of HF and the discovery of specific drugs for the treatment. Recently, cardiac transthyretin (TTR) amyloidosis is becoming recognized as one of major causes of underdiagnosed HF. The investigation and modulation of TTR misfolding and amyloidal aggregation open up a new revenue to reveal the molecular mechanisms of HF and provide new possibilities for the treatment of HF. The aim of this review is to briefly introduce the recent advances in the study of TTR native and misfolding structures, discuss the correlation between the genotype and phenotype of cardiac TTR amyloidosis, and summarize the therapeutic applications of TTR structural stabilizers in the treatment of TTR amyloidosis-associated HF.
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Affiliation(s)
- Shan He
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xinyue He
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhun Deng
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhang Feiyi
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Institute for Advanced Materials, Jiangsu University, Zhenjiang, China
| | - Shanshan Mo
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Fan
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xinyue Zhao
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Lun Wang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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11
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Internalization of α-synuclein oligomers into SH-SY5Y cells. Biophys J 2021; 120:877-885. [PMID: 33515601 DOI: 10.1016/j.bpj.2020.12.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/09/2020] [Accepted: 12/30/2020] [Indexed: 11/20/2022] Open
Abstract
Aggregates of misfolded α-synuclein are a distinctive feature of Parkinson's disease. Small oligomers of α-synuclein are thought to be an important neurotoxic agent, and α-synuclein aggregates exhibit prion-like behavior, propagating misfolding between cells. α-Synuclein is internalized by both passive diffusion and active uptake mechanisms, but how uptake varies with the size of the oligomer is less clear. We explored how α-synuclein internalization into live SH-SY5Y cells varied with oligomer size by comparing the uptake of fluorescently labeled monomers to that of engineered tandem dimers and tetramers. We found that these α-synuclein constructs were internalized primarily through endocytosis. Oligomer size had little effect on their internalization pathway, whether they were added individually or together. Measurements of co-localization of the α-synuclein constructs with fluorescent markers for early endosomes and lysosomes showed that most of the α-synuclein entered endocytic compartments, in which they were probably degraded. Treatment of the cells with the Pitstop inhibitor suggested that most of the oligomers were internalized by the clathrin-mediated pathway.
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12
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Kellici TF, Pilka ES, Bodkin MJ. Small-molecule modulators of serine protease inhibitor proteins (serpins). Drug Discov Today 2020; 26:442-454. [PMID: 33259801 DOI: 10.1016/j.drudis.2020.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/11/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023]
Abstract
Serine protease inhibitors (serpins) are a large family of proteins that regulate and control crucial physiological processes, such as inflammation, coagulation, thrombosis and thrombolysis, and immune responses. The extraordinary impact that these proteins have on numerous crucial pathways makes them an attractive target for drug discovery. In this review, we discuss recent advances in research on small-molecule modulators of serpins, examine their mode of action, analyse the structural data from crystallised protein-ligand complexes, and highlight the potential obstacles and possible therapeutic perspectives. The application of in silico methods for rational drug discovery is also summarised. In addition, we stress the need for continued research in this field.
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13
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Heydari Dokoohaki M, Zolghadr AR, Klein A. Impact of the chemical structure on the distribution of neuroprotective N-alkyl-9H-carbazoles at octanol/water interfaces. NEW J CHEM 2020. [DOI: 10.1039/c9nj04251b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
All-atom molecular dynamics (MD) simulations were performed on distribution and agglomeration dynamics of neuroprotective N-(3-anilinopropyl)-9H-carbazoles at octanol/water interfaces.
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Affiliation(s)
| | | | - Axel Klein
- Department of Chemistry
- Shiraz University
- Shiraz
- Iran
- Department für Chemie
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14
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Renal response to an oral protein load in patients with central diabetes insipidus before and after treatment with vasopressin. J Nephrol 2019; 32:411-415. [PMID: 30778919 DOI: 10.1007/s40620-018-00575-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/18/2018] [Indexed: 10/27/2022]
Abstract
AIM Different factors have been hypothesized to play a role in the cascade of events associated with the protein-induced glomerular response. However, scant data are available on the possible functional effect of vasopressin (VP) on the glomerular filtration rate (GFR) in humans with central diabetes insipidus (CDI), which was the aim of the present study. METHOD Renal function was studied under fasting conditions (baseline) and after a meat meal in 16 patients with CDI before and after treatment with desmopressin (DDAVP) and in 16 control subjects. GFR was measured by the inulin method. RESULTS At baseline, the GFR was lower in patients with CDI. Treatment with DDAVP resulted in an insignificant increase in GFR, which was not statistically different from untreated patients. After an acute oral protein load, the GFR increased, peaking at 45 min post meal in controls, and at 135 min post meal in treated and untreated CDI patients. CONCLUSION After a meat meal, the peak GFR response is delayed in CDI patients suggesting that VP might indirectly affect tubule-glomerular feedback.
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15
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Sevšek A, Sastre Toraño J, Quarles van Ufford L, Moret EE, Pieters RJ, Martin NI. Orthoester functionalized N-guanidino derivatives of 1,5-dideoxy-1,5-imino-d-xylitol as pH-responsive inhibitors of β-glucocerebrosidase. MEDCHEMCOMM 2017; 8:2050-2054. [PMID: 30108721 PMCID: PMC6072142 DOI: 10.1039/c7md00480j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/09/2017] [Indexed: 01/14/2023]
Abstract
Alkylated guanidino derivatives of 1,5-dideoxy-1,5-imino-d-xylitol bearing an orthoester moiety were prepared using a concise synthetic protocol. Inhibition assays with a panel of glycosidases revealed that one of the compounds prepared displays potent inhibition against human β-glucocerebrosidase (GBA) at pH 7.0 with IC50 values in the low nanomolar range. Notably, a significant drop in inhibitory activity is observed when the same compound is tested at pH 5.2. This pH sensitive activity is due to degradation of the orthoester functionality at lower pH accompanied by loss of the alkyl group. This approach provides a degree of control in tuning enzyme inhibition based on the local pH. Compounds like those here described may serve as tools for studying various lysosomal storage disorders such as Gaucher disease. In this regard, the most active compound was also evaluated as a potential pharmacological chaperone by assessing its effect on GBA activity in an assay employing fibroblasts from Gaucher patients.
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Affiliation(s)
- Alen Sevšek
- Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands . ;
| | - Javier Sastre Toraño
- Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands . ;
| | - Linda Quarles van Ufford
- Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands . ;
| | - Ed E Moret
- Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands . ;
| | - Roland J Pieters
- Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands . ;
| | - Nathaniel I Martin
- Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands . ;
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16
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Zhang W, Chen X, Yan Z, Chen Y, Cui Y, Chen B, Huang C, Zhang W, Yin X, He QY, He F, Wang T. Detergent-Insoluble Proteome Analysis Revealed Aberrantly Aggregated Proteins in Human Preeclampsia Placentas. J Proteome Res 2017; 16:4468-4480. [PMID: 28965414 DOI: 10.1021/acs.jproteome.7b00352] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Preeclampsia (PE) is a placenta disease, featured by hypertension, proteinuria, and other multiorgan dysfunctions, and its etiology is unclear. We and others have shown that intensive endoplasmic reticulum (ER) stress and unfolded protein response (UPR) occur in the PE placenta. In this study, we isolated detergent-insoluble proteins (DIPs) from human placenta tissues, which were enriched with protein aggregates, to characterize the placenta UPR in PE. With data-independent acquisition (DIA) mass spectrometry, we identified 2066 DIPs across all normal (n = 10) and PE (n = 10) placenta samples, among which 110 and 108 DIPs were significantly up- and down-regulated in PE, respectively. Per clustering analysis, differential DIPs could generally distinguish PE from normal placentas. We verified the MS quantitation of endoglin and vimentin by immunoblotting. In addition, we observed that PE placenta tissues have remarkably more endoglin in the cytoplasm. Furthermore, we found that DIPs were evenly distributed across different chromosomes and could be enriched in diversified gene ontology terms, while differential DIPs avoided to distribute on X-chromosome. Significantly up-regulated DIPs in PE were focused on the top functions of lipid metabolism, while 23 of these DIPs could form the top network regulating cellular movement, development, growth, and proliferation. Our results implicate that human PE placentas have disease-relevant differential DIPs, which reflect aberrantly aggregated proteins of placental tissues. The mass spectrometry proteomics data have been deposited to ProteomeXchange consortium with the data set identifier PXD006654, and iProX database (accession number: IPX0000948000).
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Affiliation(s)
- Wanling Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Xing Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Ziqi Yan
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Yang Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Yizhi Cui
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | | | | | | | - Xingfeng Yin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | | | - Tong Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
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17
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Matis I, Delivoria DC, Mavroidi B, Papaevgeniou N, Panoutsou S, Bellou S, Papavasileiou KD, Linardaki ZI, Stavropoulou AV, Vekrellis K, Boukos N, Kolisis FN, Gonos ES, Margarity M, Papadopoulos MG, Efthimiopoulos S, Pelecanou M, Chondrogianni N, Skretas G. An integrated bacterial system for the discovery of chemical rescuers of disease-associated protein misfolding. Nat Biomed Eng 2017; 1:838-852. [DOI: 10.1038/s41551-017-0144-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/06/2017] [Indexed: 01/31/2023]
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18
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Shamsi TN, Athar T, Parveen R, Fatima S. A review on protein misfolding, aggregation and strategies to prevent related ailments. Int J Biol Macromol 2017; 105:993-1000. [PMID: 28743576 DOI: 10.1016/j.ijbiomac.2017.07.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 07/13/2017] [Accepted: 07/18/2017] [Indexed: 01/28/2023]
Abstract
This review aims to highlight the fundamental mechanism of protein misfolding leading to protein aggregation and associated diseases. It also aims to anticipate novel therapeutic strategies with which to prevent or treat these highly debilitating conditions linked to these pathologies. The failure of a protein to correctly fold de novo or to remain correctly folded can have profound consequences on a living system especially when the cellular quality control processes fail to eliminate the rogue proteins. The core cause of over 20 different human diseases which have now been designated as 'conformational diseases' including neurodegenerative diseases such as Alzheimer's disease (AD), Huntington's disease (HD) and Parkinson's disease (PD) etc. A comprehensive study on protein misfolding, aggregation, and the outcomes of the effects of cytotoxic aggregates will lead to understand the aggregation-mediated cell toxicity and serves as a foundation for future research in development of promising therapies and drugs. This review has also shed light on the mechanism of protein misfolding which leads to its aggregation and hence the neurodegeneration. From these considerations, one could also envisage the possibility that protein aggregation may be exploited by nature to perform specific physiological functions in differing biological contexts.
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Affiliation(s)
- Tooba Naz Shamsi
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India.
| | - Teeba Athar
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India.
| | - Romana Parveen
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India.
| | - Sadaf Fatima
- Department of Biotechnology, Jamia Millia Islamia, New Delhi 110025, India.
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19
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Proteins behaving badly. Substoichiometric molecular control and amplification of the initiation and nature of amyloid fibril formation: lessons from and for blood clotting. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 123:16-41. [DOI: 10.1016/j.pbiomolbio.2016.08.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/14/2016] [Accepted: 08/19/2016] [Indexed: 02/08/2023]
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20
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Yuste-Checa P, Brasil S, Gámez A, Underhaug J, Desviat LR, Ugarte M, Pérez-Cerdá C, Martinez A, Pérez B. Pharmacological Chaperoning: A Potential Treatment for PMM2-CDG. Hum Mutat 2016; 38:160-168. [PMID: 27774737 DOI: 10.1002/humu.23138] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 10/17/2016] [Indexed: 12/22/2022]
Abstract
The congenital disorder of glycosylation (CDG) due to phosphomannomutase 2 deficiency (PMM2-CDG), the most common N-glycosylation disorder, is a multisystem disease for which no effective treatment is available. The recent functional characterization of disease-causing mutations described in patients with PMM2-CDG led to the idea of a therapeutic strategy involving pharmacological chaperones (PC) to rescue PMM2 loss-of-function mutations. The present work describes the high-throughput screening, by differential scanning fluorimetry, of 10,000 low-molecular-weight compounds from a commercial library, to search for possible PCs for the enzyme PMM2. This exercise identified eight compounds that increased the thermal stability of PMM2. Of these, four compounds functioned as potential PCs that significantly increased the stability of several destabilizing and oligomerization mutants and also increased PMM activity in a disease model of cells overexpressing PMM2 mutations. Structural analysis revealed one of these compounds to provide an excellent starting point for chemical optimization since it passed tests based on a number of pharmacochemical quality filters. The present results provide the first proof-of-concept of a possible treatment for PMM2-CDG and describe a promising chemical structure as a starting point for the development of new therapeutic agents for this severe orphan disease.
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Affiliation(s)
- Patricia Yuste-Checa
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Sandra Brasil
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Alejandra Gámez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Jarl Underhaug
- Department of Biomedicine and KG Jebsen Center for Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Lourdes R Desviat
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Celia Pérez-Cerdá
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
| | - Aurora Martinez
- Department of Biomedicine and KG Jebsen Center for Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid/Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, Madrid, Spain
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21
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Caenorhabditis elegans as a model system to study post-translational modifications of human transthyretin. Sci Rep 2016; 6:37346. [PMID: 27869126 PMCID: PMC5116746 DOI: 10.1038/srep37346] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/27/2016] [Indexed: 12/27/2022] Open
Abstract
The visceral protein transthyretin (TTR) is frequently affected by oxidative post-translational protein modifications (PTPMs) in various diseases. Thus, better insight into structure-function relationships due to oxidative PTPMs of TTR should contribute to the understanding of pathophysiologic mechanisms. While the in vivo analysis of TTR in mammalian models is complex, time- and resource-consuming, transgenic Caenorhabditis elegans expressing hTTR provide an optimal model for the in vivo identification and characterization of drug-mediated oxidative PTPMs of hTTR by means of matrix assisted laser desorption/ionization - time of flight - mass spectrometry (MALDI-TOF-MS). Herein, we demonstrated that hTTR is expressed in all developmental stages of Caenorhabditis elegans, enabling the analysis of hTTR metabolism during the whole life-cycle. The suitability of the applied model was verified by exposing worms to D-penicillamine and menadione. Both drugs induced substantial changes in the oxidative PTPM pattern of hTTR. Additionally, for the first time a covalent binding of both drugs with hTTR was identified and verified by molecular modelling.
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22
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Kumar V, Sami N, Kashav T, Islam A, Ahmad F, Hassan MI. Protein aggregation and neurodegenerative diseases: From theory to therapy. Eur J Med Chem 2016; 124:1105-1120. [DOI: 10.1016/j.ejmech.2016.07.054] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 12/23/2022]
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23
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Peacock H, Luo J, Yamashita T, Luccarelli J, Thompson S, Hamilton AD. Non-covalent S···O interactions control conformation in a scaffold that disrupts islet amyloid polypeptide fibrillation. Chem Sci 2016; 7:6435-6439. [PMID: 28451100 PMCID: PMC5363787 DOI: 10.1039/c6sc00756b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/09/2016] [Indexed: 12/23/2022] Open
Abstract
Conformationally-constrained molecules that selectively recognise the surfaces of proteins have the potential to direct the path of protein folding. Such molecules are of therapeutic interest because the misfolding of proteins, especially that which results in fibrillation and aggregation, is strongly correlated with numerous diseases. Here we report the novel use of S···O interactions as a conformational control element in a new class of non-peptidic scaffold that mimics key elements of protein surfaces. These molecules disrupt the fibrillation of islet amyloid polypeptide (IAPP), a process that is implicated in the pathology of type II diabetes.
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Affiliation(s)
- Hayden Peacock
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; Tel: +44 (0) 1865 275978
| | - Jinghui Luo
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; Tel: +44 (0) 1865 275978
| | - Tohru Yamashita
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; Tel: +44 (0) 1865 275978
| | - James Luccarelli
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; Tel: +44 (0) 1865 275978
| | - Sam Thompson
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; Tel: +44 (0) 1865 275978
| | - Andrew D Hamilton
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; Tel: +44 (0) 1865 275978
- Department of Chemistry , New York University , New York , New York 10003 , USA .
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Abstract
Highly sophisticated mechanisms that modulate protein structure and function, which involve synthesis and degradation, have evolved to maintain cellular homeostasis. Perturbations in these mechanisms can lead to protein dysfunction as well as deleterious cell processes. Therefore in recent years the etiology of a great number of diseases has been attributed to failures in mechanisms that modulate protein structure. Interconnections among metabolic and cell signaling pathways are critical for homeostasis to converge on mechanisms associated with protein folding as well as for the preservation of the native structure of proteins. For instance, imbalances in secretory protein synthesis pathways lead to a condition known as endoplasmic reticulum (ER) stress which elicits the adaptive unfolded protein response (UPR). Therefore, taking this into consideration, a key part of this paper is developed around the protein folding phenomenon, and cellular mechanisms which support this pivotal condition. We provide an overview of chaperone protein function, UPR via, spatial compartmentalization of protein folding, proteasome role, autophagy, as well as the intertwining between these processes. Several diseases are known to have a molecular etiology in the malfunction of mechanisms responsible for protein folding and in the shielding of native structure, phenomena which ultimately lead to misfolded protein accumulation. This review centers on our current knowledge about pathways that modulate protein folding, and cell responses involved in protein homeostasis.
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25
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Iakovleva I, Begum A, Pokrzywa M, Walfridsson M, Sauer-Eriksson AE, Olofsson A. The flavonoid luteolin, but not luteolin-7-O-glucoside, prevents a transthyretin mediated toxic response. PLoS One 2015; 10:e0128222. [PMID: 26020516 PMCID: PMC4447256 DOI: 10.1371/journal.pone.0128222] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 04/24/2015] [Indexed: 01/08/2023] Open
Abstract
Transthyretin (TTR) is a homotetrameric plasma protein with amyloidogenic properties that has been linked to the development of familial amyloidotic polyneuropathy (FAP), familial amyloidotic cardiomyopathy, and senile systemic amyloidosis. The in vivo role of TTR is associated with transport of thyroxine hormone T4 and retinol-binding protein. Loss of the tetrameric integrity of TTR is a rate-limiting step in the process of TTR amyloid formation, and ligands with the ability to bind within the thyroxin binding site (TBS) can stabilize the tetramer, a feature that is currently used as a therapeutic approach for FAP. Several different flavonoids have recently been identified that impair amyloid formation. The flavonoid luteolin shows therapeutic potential with low incidence of unwanted side effects. In this work, we show that luteolin effectively attenuates the cytotoxic response to TTR in cultured neuronal cells and rescues the phenotype of a Drosophila melanogaster model of FAP. The plant-derived luteolin analogue cynaroside has a glucoside group in position 7 of the flavone A-ring and as opposed to luteolin is unable to stabilize TTR tetramers and thus prevents a cytotoxic effect. We generated high-resolution crystal-structures of both TTR wild type and the amyloidogenic mutant V30M in complex with luteolin. The results show that the A-ring of luteolin, in contrast to what was previously suggested, is buried within the TBS, consequently explaining the lack of activity from cynaroside. The flavonoids represent an interesting group of drug candidates for TTR amyloidosis. The present investigation shows the potential of luteolin as a stabilizer of TTR in vivo. We also show an alternative orientation of luteolin within the TBS which could represent a general mode of binding of flavonoids to TTR and is of importance concerning the future design of tetramer stabilizing drugs.
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Affiliation(s)
- Irina Iakovleva
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Afshan Begum
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Malin Walfridsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | | | - Anders Olofsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- * E-mail:
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26
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Lepage ML, Mirloup A, Ripoll M, Stauffert F, Bodlenner A, Ziessel R, Compain P. Design, synthesis and photochemical properties of the first examples of iminosugar clusters based on fluorescent cores. Beilstein J Org Chem 2015; 11:659-67. [PMID: 26124868 PMCID: PMC4464267 DOI: 10.3762/bjoc.11.74] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/17/2015] [Indexed: 12/24/2022] Open
Abstract
The synthesis and photophysical properties of the first examples of iminosugar clusters based on a BODIPY or a pyrene core are reported. The tri- and tetravalent systems designed as molecular probes and synthesized by way of Cu(I)-catalysed azide-alkyne cycloadditions are fluorescent analogues of potent pharmacological chaperones/correctors recently reported in the field of Gaucher disease and cystic fibrosis, two rare genetic diseases caused by protein misfolding.
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Affiliation(s)
- Mathieu L Lepage
- Laboratoire de Synthèse Organique et Molécules Bioactives (SYBIO), Université de Strasbourg/CNRS (UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), 25 rue Becquerel, 67087 Strasbourg, France
| | - Antoine Mirloup
- Institut de Chimie et Procédés pour l’Energie, l’Environnement et la Santé (ICPEES), Laboratoire de Chimie Organique et Spectroscopie Avancées (LCOSA), Université de Strasbourg/CNRS (UMR 7515), Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), 25 rue Becquerel, 67087 Strasbourg, France
| | - Manon Ripoll
- Laboratoire de Synthèse Organique et Molécules Bioactives (SYBIO), Université de Strasbourg/CNRS (UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), 25 rue Becquerel, 67087 Strasbourg, France
| | - Fabien Stauffert
- Laboratoire de Synthèse Organique et Molécules Bioactives (SYBIO), Université de Strasbourg/CNRS (UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), 25 rue Becquerel, 67087 Strasbourg, France
| | - Anne Bodlenner
- Laboratoire de Synthèse Organique et Molécules Bioactives (SYBIO), Université de Strasbourg/CNRS (UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), 25 rue Becquerel, 67087 Strasbourg, France
| | - Raymond Ziessel
- Institut de Chimie et Procédés pour l’Energie, l’Environnement et la Santé (ICPEES), Laboratoire de Chimie Organique et Spectroscopie Avancées (LCOSA), Université de Strasbourg/CNRS (UMR 7515), Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), 25 rue Becquerel, 67087 Strasbourg, France
| | - Philippe Compain
- Laboratoire de Synthèse Organique et Molécules Bioactives (SYBIO), Université de Strasbourg/CNRS (UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), 25 rue Becquerel, 67087 Strasbourg, France
- Institut Universitaire de France, 103 Bd Saint-Michel, 75005 Paris, France
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27
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A system biology study of BALF from patients affected by idiopathic pulmonary fibrosis (IPF) and healthy controls. Proteomics Clin Appl 2014; 8:932-50. [DOI: 10.1002/prca.201400001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 06/03/2014] [Accepted: 08/26/2014] [Indexed: 12/23/2022]
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28
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Robinson LZ, Reixach N. Quantification of quaternary structure stability in aggregation-prone proteins under physiological conditions: the transthyretin case. Biochemistry 2014; 53:6496-510. [PMID: 25245430 PMCID: PMC4204887 DOI: 10.1021/bi500739q] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The quaternary structure stability
of proteins is typically studied
under conditions that accelerate their aggregation/unfolding processes
on convenient laboratory time scales. Such conditions include high
temperature or pressure, chaotrope-mediated unfolding, or low or high
pH. These approaches have the limitation of being nonphysiological
and that the concentration of the protein in solution is changing
as the reactions proceed. We describe a methodology to define the
quaternary structure stability of the amyloidogenic homotetrameric
protein transthyretin (TTR) under physiological conditions. This methodology
expands from a described approach based on the measurement of the
rate of subunit exchange of TTR with a tandem flag-tagged (FT2) TTR counterpart. We demonstrate that subunit exchange of
TTR with FT2·TTR can be analyzed and quantified using
a semi-native polyacrylamide gel electrophoresis technique. In addition,
we biophysically characterized two FT2·TTR variants
derived from wild-type and the amyloidogenic variant Val122Ile TTR,
both of which are associated with cardiac amyloid deposition late
in life. The FT2·TTR variants have similar amyloidogenic
potential and similar thermodynamic and kinetic stabilities compared
to those of their nontagged counterparts. We utilized the methodology
to study the potential of the small molecule SOM0226, a repurposed
drug under clinical development for the prevention and treatment of
the TTR amyloidoses, to stabilize TTR. The results enabled us to characterize
the binding energetics of SOM0226 to TTR. The described technique
is well-suited to study the quaternary structure of other human aggregation-prone
proteins under physiological conditions.
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Affiliation(s)
- Lei Z Robinson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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29
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Abstract
For a protein to function appropriately, it must first achieve its proper conformation and location within the crowded environment inside the cell. Multiple chaperone systems are required to fold proteins correctly. In addition, degradation pathways participate by destroying improperly folded proteins. The intricacy of this multisystem process provides many opportunities for error. Furthermore, mutations cause misfolded, nonfunctional forms of proteins to accumulate. As a result, many pathological conditions are fundamentally rooted in the protein-folding problem that all cells must solve to maintain their function and integrity. Here, to illustrate the breadth of this phenomenon, we describe five examples of protein-misfolding events that can lead to disease: improper degradation, mislocalization, dominant-negative mutations, structural alterations that establish novel toxic functions, and amyloid accumulation. In each case, we will highlight current therapeutic options for battling such diseases.
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Affiliation(s)
- Julie S Valastyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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30
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Tao YX, Conn PM. Chaperoning G protein-coupled receptors: from cell biology to therapeutics. Endocr Rev 2014; 35:602-47. [PMID: 24661201 PMCID: PMC4105357 DOI: 10.1210/er.2013-1121] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 03/14/2014] [Indexed: 12/13/2022]
Abstract
G protein-coupled receptors (GPCRs) are membrane proteins that traverse the plasma membrane seven times (hence, are also called 7TM receptors). The polytopic structure of GPCRs makes the folding of GPCRs difficult and complex. Indeed, many wild-type GPCRs are not folded optimally, and defects in folding are the most common cause of genetic diseases due to GPCR mutations. Both general and receptor-specific molecular chaperones aid the folding of GPCRs. Chemical chaperones have been shown to be able to correct the misfolding in mutant GPCRs, proving to be important tools for studying the structure-function relationship of GPCRs. However, their potential therapeutic value is very limited. Pharmacological chaperones (pharmacoperones) are potentially important novel therapeutics for treating genetic diseases caused by mutations in GPCR genes that resulted in misfolded mutant proteins. Pharmacoperones also increase cell surface expression of wild-type GPCRs; therefore, they could be used to treat diseases that do not harbor mutations in GPCRs. Recent studies have shown that indeed pharmacoperones work in both experimental animals and patients. High-throughput assays have been developed to identify new pharmacoperones that could be used as therapeutics for a number of endocrine and other genetic diseases.
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Affiliation(s)
- Ya-Xiong Tao
- Department of Anatomy, Physiology, and Pharmacology (Y.-X.T.), College of Veterinary Medicine, Auburn University, Auburn, Alabama 36849-5519; and Departments of Internal Medicine and Cell Biology (P.M.C.), Texas Tech University Health Science Center, Lubbock, Texas 79430-6252
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31
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Multitarget ligands and theranostics: sharpening the medicinal chemistry sword against prion diseases. Future Med Chem 2014; 6:1017-29. [DOI: 10.4155/fmc.14.56] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Prion diseases (PrDs) are fatal neurodegenerative disorders, for which no effective therapeutic and diagnostic tools exist. The main pathogenic event has been identified as the misfolding of a disease-associated prion protein. Nevertheless, pathogenesis seems to involve an intricate array of concomitant processes. Thus, it may be unlikely that drugs acting on single targets can effectively control PrDs. In addition, diagnosis occurs late in the disease process, by which point it is difficult to determine a successful therapeutic intervention. In this context, multitarget ligands (MTLs) and theranostic ligands (TLs) emerge for their potential to effectively cure and diagnose PrDs. In this review, we discuss the medicinal chemistry challenges of identifying novel MTLs and TLs against PrDs, and envision their impact on prion drug discovery.
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32
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Compain P, Decroocq C, Joosten A, de Sousa J, Rodríguez-Lucena D, Butters TD, Bertrand J, Clément R, Boinot C, Becq F, Norez C. Rescue of functional CFTR channels in cystic fibrosis: a dramatic multivalent effect using iminosugar cluster-based correctors. Chembiochem 2013; 14:2050-8. [PMID: 24038832 DOI: 10.1002/cbic.201300312] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Indexed: 12/23/2022]
Abstract
Cystic fibrosis is caused by a mutation in the gene for the cystic fibrosis transmembrane conductance regulator (CFTR) protein. N-butyl 1-deoxynojirimycin (N-Bu DNJ), a clinical candidate for the treatment of cystic fibrosis, is able to act as a CFTR corrector by overcoming the processing defect of the mutant protein. To explore the potential of multivalency on CFTR correction activity, a library of twelve DNJ click clusters with valencies ranging from 3 to 14 were synthesized. Significantly, the trivalent analogues were found to be up to 225-fold more potent than N-Bu DNJ and up to 1000-fold more potent than the corresponding monovalent models. These results provide the first description of a multivalent effect for correcting protein folding defects in cells and should have application for the treatment of a number of protein folding disorders. Preliminary mechanistic studies indicated that CFTR correction activity enhancement was not due to a multivalent effect in ER-glucosidase inhibition or to a different mode of action of the multivalent iminosugars.
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Affiliation(s)
- Philippe Compain
- Laboratoire de Synthèse Organique et Molécules Bioactives, Université de Strasbourg et CNRS (UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087 Strasbourg (France); Institut Universitaire de France, 103 Bd Saint-Michel, 75005 Paris (France).
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33
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Prell T, Lautenschläger J, Grosskreutz J. Calcium-dependent protein folding in amyotrophic lateral sclerosis. Cell Calcium 2013; 54:132-43. [DOI: 10.1016/j.ceca.2013.05.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/16/2013] [Accepted: 05/18/2013] [Indexed: 12/25/2022]
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34
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Jenkinson SF, Best D, Saville AW, Mui J, Martínez RF, Nakagawa S, Kunimatsu T, Alonzi DS, Butters TD, Norez C, Becq F, Blériot Y, Wilson FX, Weymouth-Wilson AC, Kato A, Fleet GWJ. C-branched iminosugars: α-glucosidase inhibition by enantiomers of isoDMDP, isoDGDP, and isoDAB-L-isoDMDP compared to miglitol and miglustat. J Org Chem 2013; 78:7380-97. [PMID: 23688199 DOI: 10.1021/jo4005487] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The Ho crossed aldol condensation provides access to a series of carbon branched iminosugars as exemplified by the synthesis of enantiomeric pairs of isoDMDP, isoDGDP, and isoDAB, allowing comparison of their biological activities with three linear isomeric natural products DMDP, DGDP, and DAB and their enantiomers. L-IsoDMDP [(2S,3S,4R)-2,4-bis(hydroxymethyl)pyrrolidine-3,4-diol], prepared in 11 steps in an overall yield of 45% from d-lyxonolactone, is a potent specific competitive inhibitor of gut disaccharidases [K(i) 0.081 μM for rat intestinal maltase] and is more effective in the suppression of hyperglycaemia in a maltose loading test than miglitol, a drug presently used in the treatment of late onset diabetes. The partial rescue of the defective F508del-CFTR function in CF-KM4 cells by L-isoDMDP is compared with miglustat and isoLAB in an approach to the treatment of cystic fibrosis.
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Affiliation(s)
- Sarah F Jenkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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35
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Vuong QV, Siposova K, Nguyen TT, Antosova A, Balogova L, Drajna L, Imrich J, Li MS, Gazova Z. Binding of Glyco-Acridine Derivatives to Lysozyme Leads to Inhibition of Amyloid Fibrillization. Biomacromolecules 2013; 14:1035-43. [DOI: 10.1021/bm301891q] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Quan Van Vuong
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward,
Thu Duc District, Ho Chi Minh
City, Vietnam
| | - Katarina Siposova
- Department of Biophysics, Institute of Experimental
Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
| | - Trang Truc Nguyen
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward,
Thu Duc District, Ho Chi Minh
City, Vietnam
| | - Andrea Antosova
- Department of Biophysics, Institute of Experimental
Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
| | | | | | | | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental
Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
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36
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Denny RA, Gavrin LK, Saiah E. Recent developments in targeting protein misfolding diseases. Bioorg Med Chem Lett 2013; 23:1935-44. [PMID: 23454013 DOI: 10.1016/j.bmcl.2013.01.089] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/18/2013] [Accepted: 01/21/2013] [Indexed: 10/27/2022]
Abstract
Protein misfolding is an emerging field that crosses multiple therapeutic areas and causes many serious diseases. As the biological pathways of protein misfolding become more clearly elucidated, small molecule approaches in this arena are gaining increased attention. This manuscript will survey current small molecules from the literature that are known to modulate misfolding, stabilization or proteostasis. Specifically, the following targets and approaches will be discussed: CFTR, glucocerebrosidase, modulation of toxic oligomers, serum amyloid P (SAP) sections and HSF1 activators.
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Affiliation(s)
- Rajiah Aldrin Denny
- BioTherapeutics Chemistry, Pfizer Worldwide Medicinal Chemistry, 200 CambridgePark Drive, Cambridge, MA 02140, USA
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37
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Jellinger KA. The relevance of metals in the pathophysiology of neurodegeneration, pathological considerations. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2013; 110:1-47. [PMID: 24209432 DOI: 10.1016/b978-0-12-410502-7.00002-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neurodegenerative disorders are featured by a variety of pathological conditions that share similar critical processes, such as oxidative stress, free radical activity, proteinaceous aggregations, mitochondrial dysfunctions, and energy failure. They are mediated or triggered by an imbalance of metal ions leading to changes of critical biological systems and initiating a cascade of events finally leading to neurodegeneration and cell death. Their causes are multifactorial, and although the source of the shift in oxidative homeostasis is still unclear, current evidence points to changes in the balance of redox transition metals, especially iron, copper, and other trace metals. They are present at elevated levels in Alzheimer disease, Parkinson disease, multisystem atrophy, etc., while in other neurodegenerative disorders, copper, zinc, aluminum, and manganese are involved. This chapter will review the recent advances of the role of metals in the pathogenesis and pathophysiology of major neurodegenerative diseases and discuss the use of chelating agents as potential therapies for metal-related disorders.
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