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Convertino M, Reddy A, Liu Y, Munoz-Zanzi C. Eco-epidemiological scaling of Leptospirosis: Vulnerability mapping and early warning forecasts. Sci Total Environ 2021; 799:149102. [PMID: 34388889 DOI: 10.1016/j.scitotenv.2021.149102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/29/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Infectious disease epidemics are plaguing the world and a lot of research is focused on the development of models to reproduce disease dynamics for eco-environmental and biological investigation, and disease management. Leptospirosis is an example of a neglected zoonosis strongly mediated by ecohydrological dynamics with emerging endemic and epidemic patterns worldwide in both animal and human populations. By accounting for large heterogeneities of affected areas we show how exponential endemics and scale-free epidemics are largely predictable and linked to common socio-environmental features via scaling laws with different exponents that inform about vulnerability factors. This led to the development of a novel pattern-oriented integrated model that can be used as an early-warning signal (EWS) tool for endemic-epidemic regime classification, risk determinant attribution, and near real-time forecast of outbreaks. Forecasts are grounded on expected outbreak recurrence time dependent on exceedance probabilities and statistical EWS that sense outbreak onset. A stochastic spatially-explicit model is shown to comprehensively predict outbreak dynamics (early sensing, timing, magnitude, decay, and eco-environmental determinants) and derive a spreading factor characterizing endemics and epidemics, where average over maximum rainfall is the critical factor characterizing disease transitions. Dynamically, case cross-correlation considering neighboring communities senses 2-weeks in advance outbreaks. Eco-environmental scaling relationships highlight how predicted host suitability and topographic index can be used as epidemiological footprints to effectively distinguish and control Leptospirosis regimes and areas dependent on hydro-climatological dynamics as the main trigger. The spatio-temporal scale-invariance of epidemics - underpinning persistent criticality and neutrality or independence among areas - is emphasized by the high accuracy in reproducing sequence and magnitude of cases via reliable surveillance. Further investigations of robustness and universality of eco-environmental determinants are required; nonetheless a comprehensive and computationally simple EWS method for the full characterization of Leptospirosis is provided. The tool is extendable to other climate-sensitive zoonoses to define vulnerability factors and predict outbreaks useful for optimal disease risk prevention and control.
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Affiliation(s)
- M Convertino
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School (Tsinghua SIGS), Tsinghua University, Shenzhen, China.
| | - A Reddy
- UnitedHealth Group, Minneapolis, MN, USA
| | - Y Liu
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene and Tropical Medicine, UK
| | - C Munoz-Zanzi
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota Twin-Cities, Minneapolis, MN, USA
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Muralidharan A, Samoshkin A, Convertino M, Piltonen MH, Gris P, Wang J, Jiang C, Klares R, Linton A, Ji RR, Maixner W, Dokholyan NV, Mogil JS, Diatchenko L. Identification and characterization of novel candidate compounds targeting 6- and 7-transmembrane μ-opioid receptor isoforms. Br J Pharmacol 2021; 178:2709-2726. [PMID: 33782947 PMCID: PMC10697213 DOI: 10.1111/bph.15463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND AND PURPOSE The μ-opioid receptor (μ receptor) is the primary target for opioid analgesics. The 7-transmembrane (TM) and 6TM μ receptor isoforms mediate inhibitory and excitatory cellular effects. Here, we developed compounds selective for 6TM- or 7TM-μ receptors to further our understanding of the pharmacodynamic properties of μ receptors. EXPERIMENTAL APPROACH We performed virtual screening of the ZINC Drug Now library of compounds using in silico 7TM- and 6TM-μ receptor structural models and identified potential compounds that are selective for 6TM- and/or 7TM-μ receptors. Subsequently, we characterized the most promising candidate compounds in functional in vitro studies using Be2C neuroblastoma transfected cells, behavioural in vivo pain assays using various knockout mice and in ex vivo electrophysiology studies. KEY RESULTS Our virtual screen identified 30 potential candidate compounds. Subsequent functional in vitro cellular assays shortlisted four compounds (#5, 10, 11 and 25) that demonstrated 6TM- or 7TM-μ receptor-dependent NO release. In in vivo pain assays these compounds also produced dose-dependent hyperalgesic responses. Studies using mice that lack specific opioid receptors further established the μ receptor-dependent nature of identified novel ligands. Ex vivo electrophysiological studies on spontaneous excitatory postsynaptic currents in isolated spinal cord slices also validated the hyperalgesic properties of the most potent 6TM- (#10) and 7TM-μ receptor (#5) ligands. CONCLUSION AND IMPLICATIONS Our novel compounds represent a new class of ligands for μ receptors and will serve as valuable research tools to facilitate the development of opioids with significant analgesic efficacy and fewer side-effects.
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Affiliation(s)
- Arjun Muralidharan
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Psychology, McGill University, Montreal, Quebec, Canada
| | - Alexander Samoshkin
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Anesthesia, McGill University, Montreal, Quebec, Canada
| | - Marino Convertino
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Marjo Hannele Piltonen
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Faculty of Dentistry, McGill University, Montreal, Quebec, Canada
| | - Pavel Gris
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Faculty of Dentistry, McGill University, Montreal, Quebec, Canada
| | - Jian Wang
- Department of Pharmacology, and Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Changyu Jiang
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Richard Klares
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Anesthesia, McGill University, Montreal, Quebec, Canada
- Faculty of Dentistry, McGill University, Montreal, Quebec, Canada
| | - Alexander Linton
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Anesthesia, McGill University, Montreal, Quebec, Canada
- Faculty of Dentistry, McGill University, Montreal, Quebec, Canada
| | - Ru-Rong Ji
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - William Maixner
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Pharmacology, and Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Jeffrey S. Mogil
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Psychology, McGill University, Montreal, Quebec, Canada
- Department of Anesthesia, McGill University, Montreal, Quebec, Canada
| | - Luda Diatchenko
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Anesthesia, McGill University, Montreal, Quebec, Canada
- Faculty of Dentistry, McGill University, Montreal, Quebec, Canada
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Zhu C, Han Q, Samoshkin A, Convertino M, Linton A, Faison EM, Ji RR, Diatchenko L, Dokholyan NV. Stabilization of μ-opioid receptor facilitates its cellular translocation and signaling. Proteins 2019; 87:878-884. [PMID: 31141214 DOI: 10.1002/prot.25751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/09/2019] [Accepted: 05/26/2019] [Indexed: 01/01/2023]
Abstract
The G protein-coupled μ-opioid receptor (μ-OR) mediates the majority of analgesia effects for morphine and other pain relievers. Despite extensive studies of its structure and activation mechanisms, the inherently low maturation efficiency of μ-OR represents a major hurdle to understanding its function. Here we computationally designed μ-OR mutants with altered stability to probe the relationship between cell-surface targeting, signal transduction, and agonist efficacy. The stabilizing mutation T315Y enhanced μ-OR trafficking to the plasma membrane and significantly promoted the morphine-mediated inhibition of downstream signaling. In contrast, the destabilizing mutation R165Y led to intracellular retention of μ-OR and reduced the response to morphine stimulation. These findings suggest that μ-OR stability is an important factor in regulating receptor signaling and provide a viable avenue to improve the efficacy of analgesics.
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Affiliation(s)
- Cheng Zhu
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pharmacology, Penn State University College of Medicine, Hershey, Pennsylvania
| | - Qingjian Han
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina.,Department of Neurobiology, Duke University Medical Center, Durham, North Carolina
| | - Alexander Samoshkin
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada.,School of the Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Marino Convertino
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alexander Linton
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
| | - Edgar M Faison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ru-Rong Ji
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina.,Department of Neurobiology, Duke University Medical Center, Durham, North Carolina
| | - Luda Diatchenko
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pharmacology, Penn State University College of Medicine, Hershey, Pennsylvania.,Department of Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania.,Department of Biomedical Engineering, Penn State University, Pennsylvania.,Department of Chemistry, Penn State University, Pennsylvania
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Luo J, Samanta S, Convertino M, Dokholyan NV, Deiters A. Front Cover: Reversible and Tunable Photoswitching of Protein Function through Genetic Encoding of Azobenzene Amino Acids in Mammalian Cells (ChemBioChem 20/2018). Chembiochem 2018. [DOI: 10.1002/cbic.201800570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ji Luo
- University of Pittsburgh; Department of Chemistry; Pittsburgh PA 15260 USA
| | - Subhas Samanta
- University of Pittsburgh; Department of Chemistry; Pittsburgh PA 15260 USA
| | - Marino Convertino
- University of North Carolina at Chapel Hill; Department of Biochemistry and Biophysics; Chapel Hill NC 27599 USA
| | - Nikolay V. Dokholyan
- University of North Carolina at Chapel Hill; Department of Biochemistry and Biophysics; Chapel Hill NC 27599 USA
| | - Alexander Deiters
- University of Pittsburgh; Department of Chemistry; Pittsburgh PA 15260 USA
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Luo J, Samanta S, Convertino M, Dokholyan NV, Deiters A. Reversible and Tunable Photoswitching of Protein Function through Genetic Encoding of Azobenzene Amino Acids in Mammalian Cells. Chembiochem 2018; 19:2178-2185. [PMID: 30277634 DOI: 10.1002/cbic.201800226] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 12/30/2022]
Abstract
The genetic encoding of three different azobenzene phenylalanines with different photochemical properties was achieved in human cells by using an engineered pyrrolysyl tRNA/tRNA synthetase pair. In order to demonstrate reversible light control of protein function, azobenzenes were site-specifically introduced into firefly luciferase. Computational strategies were applied to guide the selection of potential photoswitchable sites that lead to a reversibly controlled luciferase enzyme. In addition, the new azobenzene analogues provide enhanced thermal stability, high photoconversion, and responsiveness to visible light. These small-molecule photoswitches can reversibly photocontrol protein function with excellent spatiotemporal resolution, and preferred sites for incorporation can be computationally determined, thus providing a new tool for investigating biological processes.
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Affiliation(s)
- Ji Luo
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA, 15260, USA
| | - Subhas Samanta
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA, 15260, USA
| | - Marino Convertino
- University of North Carolina at Chapel Hill, Department of Biochemistry and Biophysics, Chapel Hill, NC, 27599, USA
| | - Nikolay V Dokholyan
- University of North Carolina at Chapel Hill, Department of Biochemistry and Biophysics, Chapel Hill, NC, 27599, USA
| | - Alexander Deiters
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA, 15260, USA
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Han Q, Liu D, Convertino M, Wang Z, Jiang C, Kim YH, Luo X, Zhang X, Nackley A, Dokholyan NV, Ji RR. miRNA-711 Binds and Activates TRPA1 Extracellularly to Evoke Acute and Chronic Pruritus. Neuron 2018; 99:449-463.e6. [PMID: 30033153 DOI: 10.1016/j.neuron.2018.06.039] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/04/2018] [Accepted: 06/25/2018] [Indexed: 01/02/2023]
Abstract
Increasing evidence suggests that extracellular miRNAs may serve as biomarkers of diseases, but the physiological relevance of extracellular miRNA is unclear. We find that intradermal cheek injection of miR-711 induces TRPA1-depedent itch (scratching) without pain (wiping) in naive mice. Extracellular perfusion of miR-711 induces TRPA1 currents in both Trpa1-expressing heterologous cells and native sensory neurons through the core sequence GGGACCC. Computer simulations reveal that the core sequence binds several residues at the extracellular S5-S6 loop of TRPA1, which are critical for TRPA1 activation by miR-711 but not allyl isothiocyanate. Intradermal inoculation of human Myla cells induces lymphoma and chronic itch in immune-deficient mice, associated with increased serum levels of miR-711, secreted from cancer cells. Lymphoma-induced chronic itch is suppressed by miR-711 inhibitor and a blocking peptide that disrupts the miR-711/TRPA1 interaction. Our findings demonstrated an unconventional physiological role of extracellular naked miRNAs as itch mediators and ion channel modulators.
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Affiliation(s)
- Qingjian Han
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Di Liu
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Marino Convertino
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Zilong Wang
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Changyu Jiang
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Yong Ho Kim
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Xin Luo
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Xin Zhang
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Andrea Nackley
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Ru-Rong Ji
- Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
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Lagarias P, Vrontaki E, Lambrinidis G, Stamatis D, Convertino M, Ortore G, Mavromoustakos T, Klotz KN, Kolocouris A. Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode. J Chem Inf Model 2018; 58:794-815. [PMID: 29485875 DOI: 10.1021/acs.jcim.7b00455] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An intense effort is made by pharmaceutical and academic research laboratories to identify and develop selective antagonists for each adenosine receptor (AR) subtype as potential clinical candidates for "soft" treatment of various diseases. Crystal structures of subtypes A2A and A1ARs offer exciting opportunities for structure-based drug design. In the first part of the present work, Maybridge HitFinder library of 14400 compounds was utilized to apply a combination of structure-based against the crystal structure of A2AAR and ligand-based methodologies. The docking poses were rescored by CHARMM energy minimization and calculation of the desolvation energy using Poisson-Boltzmann equation electrostatics. Out of the eight selected and tested compounds, five were found positive hits (63% success). Although the project was initially focused on targeting A2AAR, the identified antagonists exhibited low micromolar or micromolar affinity against A2A/A3, ARs, or A3AR, respectively. Based on these results, 19 compounds characterized by novel chemotypes were purchased and tested. Sixteen of them were identified as AR antagonists with affinity toward combinations of the AR family isoforms (A2A/A3, A1/A3, A1/A2A/A3, and A3). The second part of this work involves the performance of hundreds of molecular dynamics (MD) simulations of complexes between the ARs and a total of 27 ligands to resolve the binding interactions of the active compounds, which were not achieved by docking calculations alone. This computational work allowed the prediction of stable and unstable complexes which agree with the experimental results of potent and inactive compounds, respectively. Of particular interest is that the 2-amino-thiophene-3-carboxamides, 3-acylamino-5-aryl-thiophene-2-carboxamides, and carbonyloxycarboximidamide derivatives were found to be selective and possess a micromolar to low micromolar affinity for the A3 receptor.
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Affiliation(s)
- Panagiotis Lagarias
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Eleni Vrontaki
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - George Lambrinidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Dimitrios Stamatis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Marino Convertino
- Department of Biochemistry & Biophysics , University of North Carolina at Chapel Hill , 120 Mason Farm Road , Chapel Hill , North Carolina 27599 , United States
| | - Gabriella Ortore
- Department of Pharmacy , University of Pisa , 56126 Pisa , Italy
| | - Thomas Mavromoustakos
- Division of Organic Chemistry, Department of Chemistry, School of Science , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Karl-Norbert Klotz
- Institute of Pharmacology and Toxicology , University of Würzburg Versbacher Str. 9 , 97078 Würzburg , Germany
| | - Antonios Kolocouris
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
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Gualdani R, Cavalluzzi MM, Tadini-Buoninsegni F, Convertino M, Gailly P, Stary-Weinzinger A, Lentini G. Molecular Insights into hERG Potassium Channel Blockade by Lubeluzole. Cell Physiol Biochem 2018; 45:2233-2245. [PMID: 29550817 DOI: 10.1159/000488169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/01/2017] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND/AIMS Lubeluzole is a benzothiazole derivative that has shown neuroprotective properties in preclinical models of ischemic stroke. However, clinical research on lubeluzole is now at a standstill, since lubeluzole seems to be associated with the acquired long QT syndrome and ventricular arrhythmias. Since the cardiac cellular effects of lubeluzole have not been described thus far, an explanation for the lubeluzole-induced QT interval prolongation is lacking. METHODS We tested the affinity of lubeluzole, its enantiomer, and the racemate for hERG channel using the patch-clamp technique. We synthesized and tested two simplified model compounds corresponding to two moieties included in the lubeluzole structure. The obtained experimental results were rationalized by docking simulation on the recently reported cryo-electron microscopy (cryo-EM) structure of hERG. Group efficiency analysis was performed in order to individuate the fragment most contributing to binding. RESULTS We found that lubeluzole and its R enantiomer are highly potent inhibitors of human ether-ago-go-related gene (hERG) channel with an IC50 value of 12.9 ± 0.7 nM and 11.3 ± 0.8 nM, respectively. In the presence of lubeluzole, steady-state activation and inactivation of hERG channel were shifted to more negative potentials and inactivation kinetics was accelerated. Mutations of aromatic residues (Y652A and F656A) in the channel inner cavity significantly reduced the inhibitory effect of lubeluzole. Molecular docking simulations performed on the near atomic resolution cryo-electron microscopy structures of hERG supported the role of Y652 and F656 as the main contributors to high affinity binding. Group efficiency analysis indicated that both 1,3-benzothiazol-2-amine and 3-aryloxy-2-propanolamine moieties contribute to drug binding with the former giving higher contribution. CONCLUSIONS This study suggests the possibility to modulate lubeluzole hERG blockade by introducing suitable substituents onto one or both constituting portions of the parent compound in order to either reduce potency (i. e. torsadogenic potential) or potentiate affinity (useful for class III antiarrhythmic and anticancer agent development).
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Affiliation(s)
- Roberta Gualdani
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Sesto Fiorentino, Italy
- Université catholique de Louvain, Institute of Neuroscience, Laboratory of Cell Physiology, Brussels, Belgium
| | | | | | - Marino Convertino
- University of North Carolina at Chapel Hill - Department of Biochemistry and Biophysics, Chapel Hill, North Carolina, USA
| | - Philippe Gailly
- Université catholique de Louvain, Institute of Neuroscience, Laboratory of Cell Physiology, Brussels, Belgium
| | | | - Giovanni Lentini
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "A. Moro, Bari, Italy
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Williams B, Convertino M, Das J, Dokholyan NV. Molecular Mechanisms of the R61T Mutation in Apolipoprotein E4: A Dynamic Rescue. Biophys J 2017; 113:2192-2198. [PMID: 28916386 PMCID: PMC5700245 DOI: 10.1016/j.bpj.2017.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/02/2017] [Accepted: 08/17/2017] [Indexed: 10/18/2022] Open
Abstract
The apolipoprotein E4 (ApoE4) gene is the strongest genetic risk factor for Alzheimer's disease (AD). With respect to the other common isoforms of this protein (ApoE2 and ApoE3), ApoE4 is characterized by lower stability that underlies the formation of a stable interaction between the protein's N- and C-terminal domains. AD-related cellular dysfunctions have been linked to this ApoE4 misfolded state. In this regard, it has been reported that the mutation R61T is able to rescue the deleterious cellular effects of ApoE4 by preventing the formation of the misfolded intermediate state. However, a clear description of the structural features at the basis of the R61T-ApoE4 mutant's protective effect is still missing. Recently, using extensive molecular dynamics simulations, we have identified a structural model of an ApoE4 misfolded intermediate state. Building on our previous work, here we explore the dynamical changes induced by the R61T mutation in the ApoE4 native and misfolded states. Notably, we do not observe any local changes in the domains in the R61T-ApoE4 system, rather a general loss of correlated movements in the entire protein structure. More specifically, we detect increased dynamics in the hinge region, which is essential for ApoE4 domain-domain interaction. Consistent with previously reported data on altered phospholipid and receptor binding, we hypothesize that mutations destabilizing the ApoE4 intermediate state change hinge region dynamics, which propagates to distal functional regions of the protein and modifies ApoE4's functional properties. This unique behavior of the ApoE4 hinge region provides, to our knowledge, a novel understanding of ApoE4's role in AD.
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Affiliation(s)
- Benfeard Williams
- Biochemistry and Biophysics Department, University of North Carolina, Chapel Hill, North Carolina
| | - Marino Convertino
- Biochemistry and Biophysics Department, University of North Carolina, Chapel Hill, North Carolina
| | - Jhuma Das
- Biochemistry and Biophysics Department, University of North Carolina, Chapel Hill, North Carolina
| | - Nikolay V Dokholyan
- Biochemistry and Biophysics Department, University of North Carolina, Chapel Hill, North Carolina.
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Peón A, Robles A, Blanco B, Convertino M, Thompson P, Hawkins AR, Caflisch A, González-Bello C. Reducing the Flexibility of Type II Dehydroquinase for Inhibition: A Fragment-Based Approach and Molecular Dynamics Study. ChemMedChem 2017; 12:1512-1524. [DOI: 10.1002/cmdc.201700396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/01/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Antonio Peón
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Adrián Robles
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Beatriz Blanco
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Marino Convertino
- Department of Biochemistry; University of Zurich; 8057 Zurich Switzerland
- Current address: Department of Biochemistry and Biophysics; University of North Carolina, School of Medicine; Chapel Hill NC 27599 USA
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne; Catherine Cookson Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne; Catherine Cookson Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Amedeo Caflisch
- Department of Biochemistry; University of Zurich; 8057 Zurich Switzerland
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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Convertino M, Das J, Dokholyan NV. Pharmacological Chaperones: Design and Development of New Therapeutic Strategies for the Treatment of Conformational Diseases. ACS Chem Biol 2016; 11:1471-89. [PMID: 27097127 DOI: 10.1021/acschembio.6b00195] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Errors in protein folding may result in premature clearance of structurally aberrant proteins, or in the accumulation of toxic misfolded species or protein aggregates. These pathological events lead to a large range of conditions known as conformational diseases. Several research groups have presented possible therapeutic solutions for their treatment by developing novel compounds, known as pharmacological chaperones. These cell-permeable molecules selectively provide a molecular scaffold around which misfolded proteins can recover their native folding and, thus, their biological activities. Here, we review therapeutic strategies, clinical potentials, and cost-benefit impacts of several classes of pharmacological chaperones for the treatment of a series of conformational diseases.
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Affiliation(s)
- Marino Convertino
- Department of Biochemistry
and Biophysics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Jhuma Das
- Department of Biochemistry
and Biophysics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Nikolay V. Dokholyan
- Department of Biochemistry
and Biophysics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
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12
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Politi R, Convertino M, Popov K, Dokholyan NV, Tropsha A. Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise. J Chem Inf Model 2016; 56:1032-41. [DOI: 10.1021/acs.jcim.5b00751] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Regina Politi
- Laboratory for Molecular Modeling,
Division of Chemical Biology and
Medicinal Chemistry, UNC Eshelman School of Pharmacy,
and ‡Department of Biochemistry
and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Marino Convertino
- Laboratory for Molecular Modeling,
Division of Chemical Biology and
Medicinal Chemistry, UNC Eshelman School of Pharmacy,
and ‡Department of Biochemistry
and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Konstantin Popov
- Laboratory for Molecular Modeling,
Division of Chemical Biology and
Medicinal Chemistry, UNC Eshelman School of Pharmacy,
and ‡Department of Biochemistry
and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nikolay V. Dokholyan
- Laboratory for Molecular Modeling,
Division of Chemical Biology and
Medicinal Chemistry, UNC Eshelman School of Pharmacy,
and ‡Department of Biochemistry
and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alexander Tropsha
- Laboratory for Molecular Modeling,
Division of Chemical Biology and
Medicinal Chemistry, UNC Eshelman School of Pharmacy,
and ‡Department of Biochemistry
and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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13
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Abstract
Understanding and controlling biological phenomena via structure-based drug screening efforts often critically rely on accurate description of protein-ligand interactions. However, most of the currently available computational techniques are affected by severe deficiencies in both protein and ligand conformational sampling as well as in the scoring of the obtained docking solutions. To overcome these limitations, we have recently developed MedusaDock, a novel docking methodology, which simultaneously models ligand and receptor flexibility. Coupled with MedusaScore, a physical force field-based scoring function that accounts for the protein-ligand interaction energy, MedusaDock, has reported the highest success rate in the CSAR 2011 exercise. Here, we present a standard computational protocol to evaluate the binding properties of the two enantiomers of the non-selective β-blocker propanolol in the β2 adrenergic receptor's binding site. We describe details of our protocol, which have been successfully applied to several other targets.
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Affiliation(s)
- Marino Convertino
- Department of Biochemistry and Biophysics, University of North Carolina, 120 Mason Farm Road, 27599, Chapel Hill, NC, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina, 120 Mason Farm Road, 27599, Chapel Hill, NC, USA.
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14
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Palermo G, Favia AD, Convertino M, De Vivo M. The Molecular Basis for Dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) Inhibition. ChemMedChem 2015; 11:1252-8. [PMID: 26593700 PMCID: PMC5063142 DOI: 10.1002/cmdc.201500507] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Indexed: 12/20/2022]
Abstract
The design of multitarget‐directed ligands is a promising strategy for discovering innovative drugs. Here, we report a mechanistic study that clarifies key aspects of the dual inhibition of the fatty acid amide hydrolase (FAAH) and the cyclooxygenase (COX) enzymes by a new multitarget‐directed ligand named ARN2508 (2‐[3‐fluoro‐4‐[3‐(hexylcarbamoyloxy)phenyl]phenyl]propanoic acid). This potent dual inhibitor combines, in a single scaffold, the pharmacophoric elements often needed to block FAAH and COX, that is, a carbamate moiety and the 2‐arylpropionic acid functionality, respectively. Molecular modeling and molecular dynamics simulations suggest that ARN2508 uses a noncovalent mechanism of inhibition to block COXs, while inhibiting FAAH via the acetylation of the catalytic Ser241, in line with previous experimental evidence for covalent FAAH inhibition. This study proposes the molecular basis for the dual FAAH/COX inhibition by this novel hybrid scaffold, stimulating further experimental studies and offering new insights for the rational design of novel anti‐inflammatory agents that simultaneously act on FAAH and COX.
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Affiliation(s)
- Giulia Palermo
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Angelo D Favia
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marino Convertino
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy. .,Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428, Jülich, Germany.
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15
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Convertino M, Samoshkin A, Viet CT, Gauthier J, Li Fraine SP, Sharif-Naeini R, Schmidt BL, Maixner W, Diatchenko L, Dokholyan NV. Differential Regulation of 6- and 7-Transmembrane Helix Variants of μ-Opioid Receptor in Response to Morphine Stimulation. PLoS One 2015; 10:e0142826. [PMID: 26554831 PMCID: PMC4640872 DOI: 10.1371/journal.pone.0142826] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/27/2015] [Indexed: 11/18/2022] Open
Abstract
The pharmacological effect of opioids originates, at the cellular level, by their interaction with the μ-opioid receptor (mOR) resulting in the regulation of voltage-gated Ca2+ channels and inwardly rectifying K+ channels that ultimately modulate the synaptic transmission. Recently, an alternative six trans-membrane helix isoform of mOR, (6TM-mOR) has been identified, but its function and signaling are still largely unknown. Here, we present the structural and functional mechanisms of 6TM-mOR signaling activity upon binding to morphine. Our data suggest that despite the similarity of binding modes of the alternative 6TM-mOR and the dominant seven trans-membrane helix variant (7TM-mOR), the interaction with morphine generates different dynamic responses in the two receptors, thus, promoting the activation of different mOR-specific signaling pathways. We characterize a series of 6TM-mOR-specific cellular responses, and observed that they are significantly different from those for 7TM-mOR. Morphine stimulation of 6TM-mOR does not promote a cellular cAMP response, while it increases the intracellular Ca2+ concentration and reduces the cellular K+ conductance. Our findings indicate that 6TM-mOR has a unique contribution to the cellular opioid responses. Therefore, it should be considered as a relevant target for the development of novel pharmacological tools and medical protocols involving the use of opioids.
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Affiliation(s)
- Marino Convertino
- Biochemistry and Biophysics Department, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, United States of America, 27599
| | - Alexander Samoshkin
- Alan Edwards Centre for Research on Pain, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1
| | - Chi T Viet
- Bluestone Center for Clinic Research, New York University, New York, NY, United States of America, 10010
| | - Josee Gauthier
- Center for Pain Research and Innovation, University of North Carolina, 385 S. Columbia Street, Chapel Hill, NC, United States of America, 27599
| | - Steven P Li Fraine
- Department of Physiology and Cell Information Systems, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada, H3G 0B1
| | - Reza Sharif-Naeini
- Department of Physiology and Cell Information Systems, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada, H3G 0B1
| | - Brian L Schmidt
- Bluestone Center for Clinic Research, New York University, New York, NY, United States of America, 10010
| | - William Maixner
- Center for Pain Research and Innovation, University of North Carolina, 385 S. Columbia Street, Chapel Hill, NC, United States of America, 27599
| | - Luda Diatchenko
- Alan Edwards Centre for Research on Pain, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1
| | - Nikolay V Dokholyan
- Biochemistry and Biophysics Department, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, United States of America, 27599.,Center for Pain Research and Innovation, University of North Carolina, 385 S. Columbia Street, Chapel Hill, NC, United States of America, 27599
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16
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Martin LJ, Piltonen MH, Gauthier J, Convertino M, Acland EL, Dokholyan NV, Mogil JS, Diatchenko L, Maixner W. Differences in the Antinociceptive Effects and Binding Properties of Propranolol and Bupranolol Enantiomers. J Pain 2015; 16:1321-1333. [PMID: 26456674 DOI: 10.1016/j.jpain.2015.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/07/2015] [Accepted: 09/21/2015] [Indexed: 12/17/2022]
Abstract
UNLABELLED Recent efforts have suggested that the β-adrenergic receptor (β-AR) system may be a novel and viable therapeutic target for pain reduction; however, most of the work to date has focused on the β(2)-adrenergic receptor (AR). Here, we compared the antinociceptive effects of enantiomeric configurations of propranolol and bupranolol, two structurally similar nonselective β-blocking drugs, against mouse models of inflammatory and chronic pain. In addition, we calculated in silico docking and measured the binding properties of propranolol and bupranolol for all 3 β-ARs. Of the agents examined, S-bupranolol is superior in terms of its antinociceptive effect and exhibited fewer side effects than propranolol or its associated enantiomers. In contrast to propranolol, S-bupranolol exhibited negligible β-AR intrinsic agonist activity and displayed a full competitive antagonist profile at β(1)/β(2)/β(3)-ARs, producing a unique blockade of β(3)-ARs. We have shown that S-bupranolol is an effective antinociceptive agent in mice without negative side effects. The distinctive profile of S-bupranolol is most likely mediated by its negligible β-AR intrinsic agonist activity and unique blockade of β(3)-AR. These findings suggest that S-bupranolol instead of propranolol may represent a new and effective treatment for a variety of painful conditions. PERSPECTIVE The S enantiomer of bupranolol, a β-receptor antagonist, shows greater antinociceptive efficacy and a superior preclinical safety profile and it should be considered as a unique β-adrenergic receptor compound to advance future clinical pain studies.
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Affiliation(s)
- Loren J Martin
- Department of Psychology, McGill University, Montreal, Quebec, Canada; Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada; Department of Psychology, University of Toronto Mississauga, Mississauga, Ontario, Canada.
| | - Marjo H Piltonen
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada; Department of Anesthesiology, McGill University, Montreal, Quebec, Canada
| | - Josee Gauthier
- Center for Pain Research and Innovation, University of North Carolina, Chapel Hill, North Carolina
| | - Marino Convertino
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
| | - Erinn L Acland
- Department of Psychology, McGill University, Montreal, Quebec, Canada; Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada; Department of Psychology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
| | - Jeffrey S Mogil
- Department of Psychology, McGill University, Montreal, Quebec, Canada; Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
| | - Luda Diatchenko
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada; Department of Anesthesiology, McGill University, Montreal, Quebec, Canada; Center for Pain Research and Innovation, University of North Carolina, Chapel Hill, North Carolina
| | - William Maixner
- Center for Pain Research and Innovation, University of North Carolina, Chapel Hill, North Carolina
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17
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Convertino M, Samoshkin A, Gauthier J, Gold MS, Maixner W, Dokholyan NV, Diatchenko L. μ-Opioid receptor 6-transmembrane isoform: A potential therapeutic target for new effective opioids. Prog Neuropsychopharmacol Biol Psychiatry 2015; 62:61-7. [PMID: 25485963 PMCID: PMC4646084 DOI: 10.1016/j.pnpbp.2014.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 11/04/2014] [Accepted: 11/20/2014] [Indexed: 01/19/2023]
Abstract
The μ-opioid receptor (MOR) is the primary target for opioid analgesics. MOR induces analgesia through the inhibition of second messenger pathways and the modulation of ion channels activity. Nevertheless, cellular excitation has also been demonstrated, and proposed to mediate reduction of therapeutic efficacy and opioid-induced hyperalgesia upon prolonged exposure to opioids. In this mini-perspective, we review the recently identified, functional MOR isoform subclass, which consists of six transmembrane helices (6 TM) and may play an important role in MOR signaling. There is evidence that 6 TM MOR signals through very different cellular pathways and may mediate excitatory cellular effects rather than the classic inhibitory effects produced by the stimulation of the major (7 TM) isoform. Therefore, the development of 6 TM and 7 TM MOR selective compounds represents a new and exciting opportunity to better understand the mechanisms of action and the pharmacodynamic properties of a new class of opioids.
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Affiliation(s)
- Marino Convertino
- Biochemistry and Biophysics Department, University of North Carolina, 120 Mason Farm Rd., CB #7260 Genetic Medicine, Chapel Hill, NC, USA, 27599
| | - Alexander Samoshkin
- The Alan Edwards Centre for Research on Pain, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1
| | - Josee Gauthier
- Center for Pain Research and Innovation, University of North Carolina, 385 S. Columbia St., CB #7455, KOHSB, Chapel Hill, NC, USA, 27599
| | - Michael S. Gold
- Department of Anesthesiology, University of Pittsburgh School of Medicine, 200 Lothrop St., Pittsburgh, PA, USA 15213
| | - William Maixner
- Center for Pain Research and Innovation, University of North Carolina, 385 S. Columbia St., CB #7455, KOHSB, Chapel Hill, NC 27599, USA.
| | - Nikolay V. Dokholyan
- Biochemistry and Biophysics Department, University of North Carolina, 120 Mason Farm Rd., CB #7260 Genetic Medicine, Chapel Hill, NC, USA, 27599.,CORRESPONDING AUTHORS: Dr. Luda Diatchenko, The Alan Edwards Centre for Research on Pain, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1, Phone: +1 514 398-2878, . Dr. William Maixner, Center for Pain Research and Innovation, University of North Carolina, 385 S. Columbia St., CB #7455, KOHSB, Chapel Hill, NC, USA, 27599, Phone: +1 919 537-3289, . Dr. Nikolay V. Dokholyan, Biochemistry and Biophysics Department, University of North Carolina, 120 Mason Farm Rd., CB #7260 Genetic Medicine, Chapel Hill, NC, USA, 27599, Phone: +1 919 843-2513.
| | - Luda Diatchenko
- The Alan Edwards Centre for Research on Pain, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1, Canada.
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18
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Palermo G, Minniti E, Greco ML, Riccardi L, Simoni E, Convertino M, Marchetti C, Rosini M, Sissi C, Minarini A, De Vivo M. An optimized polyamine moiety boosts the potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512. Chem Commun (Camb) 2015; 51:14310-3. [PMID: 26234198 DOI: 10.1039/c5cc05065k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combined computational-experimental analyses explain and quantify the spermine-vectorized F14512's boosted potency as a topoII poison. We found that an optimized polyamine moiety boosts drug binding to the topoII/DNA cleavage complex, rather than to the DNA alone. These results provide new structural bases and key reference data for designing new human topoII poisons.
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Affiliation(s)
- Giulia Palermo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.
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Park J, Seager TP, Rao PSC, Convertino M, Linkov I. Integrating risk and resilience approaches to catastrophe management in engineering systems. Risk Anal 2013; 33:356-367. [PMID: 22967095 DOI: 10.1111/j.1539-6924.2012.01885.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Recent natural and man-made catastrophes, such as the Fukushima nuclear power plant, flooding caused by Hurricane Katrina, the Deepwater Horizon oil spill, the Haiti earthquake, and the mortgage derivatives crisis, have renewed interest in the concept of resilience, especially as it relates to complex systems vulnerable to multiple or cascading failures. Although the meaning of resilience is contested in different contexts, in general resilience is understood to mean the capacity to adapt to changing conditions without catastrophic loss of form or function. In the context of engineering systems, this has sometimes been interpreted as the probability that system conditions might exceed an irrevocable tipping point. However, we argue that this approach improperly conflates resilience and risk perspectives by expressing resilience exclusively in risk terms. In contrast, we describe resilience as an emergent property of what an engineering system does, rather than a static property the system has. Therefore, resilience cannot be measured at the systems scale solely from examination of component parts. Instead, resilience is better understood as the outcome of a recursive process that includes: sensing, anticipation, learning, and adaptation. In this approach, resilience analysis can be understood as differentiable from, but complementary to, risk analysis, with important implications for the adaptive management of complex, coupled engineering systems. Management of the 2011 flooding in the Mississippi River Basin is discussed as an example of the successes and challenges of resilience-based management of complex natural systems that have been extensively altered by engineered structures.
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Affiliation(s)
- J Park
- School of Civil Engineering, Purdue University, West Lafayette, IN, USA
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20
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Attanasio F, Convertino M, Magno A, Caflisch A, Corazza A, Haridas H, Esposito G, Cataldo S, Pignataro B, Milardi D, Rizzarelli E. Carnosine inhibits Aβ(42) aggregation by perturbing the H-bond network in and around the central hydrophobic cluster. Chembiochem 2013; 14:583-92. [PMID: 23440928 DOI: 10.1002/cbic.201200704] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Indexed: 02/06/2023]
Abstract
Aggregation of the amyloid-β peptide (Aβ) into fibrillar structures is a hallmark of Alzheimer's disease. Thus, preventing self-assembly of the Aβ peptide is an attractive therapeutic strategy. Here, we used experimental techniques and atomistic simulations to investigate the influence of carnosine, a dipeptide naturally occurring in the brain, on Aβ aggregation. Scanning force microscopy, circular dichroism and thioflavin T fluorescence experiments showed that carnosine does not modify the conformational features of Aβ42 but nonetheless inhibits amyloid growth. Molecular dynamics (MD) simulations indicated that carnosine interacts transiently with monomeric Aβ42 by salt bridges with charged side chains, and van der Waals contacts with residues in and around the central hydrophobic cluster ((17)LVFFA(21)). NMR experiments on the nonaggregative fragment Aβ12-28 did not evidence specific intermolecular interactions between the peptide and carnosine, in agreement with MD simulations. However, a close inspection of the spectra revealed that carnosine interferes with the local propensity of the peptide to form backbone hydrogen bonds close to the central hydrophobic cluster (residues E22, S26 and N27). Finally, MD simulations of aggregation-prone Aβ heptapeptide segments show that carnosine reduces the propensity to form intermolecular backbone hydrogen bonds in the region 18-24. Taken together, the experimental and simulation results (cumulative MD sampling of 0.2 ms) suggest that, despite the inability of carnosine to form stable contacts with Aβ, it might block the pathway toward toxic aggregates by perturbing the hydrogen bond network near residues with key roles in fibrillogenesis.
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Affiliation(s)
- Francesco Attanasio
- Istituto di Biostrutture e Bioimmagini-UOS CT, Consiglio Nazionale delle Ricerche, V.le A. Doria 6, 95125 Catania, Italy
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21
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Scherzer-Attali R, Convertino M, Pellarin R, Gazit E, Segal D, Caflisch A. Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation. J Phys Chem B 2013; 117:1780-9. [PMID: 23259849 DOI: 10.1021/jp309066p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aggregation of amyloid beta (Aβ) is the hallmark of Alzheimer's disease (AD). Small molecules inhibiting Aβ can be valuable therapeutics for AD. We have previously reported that 1,4-naphthoquinon-2-yl-l-tryptophan (NQTrp), reduces aggregation and oligomerization of Aβ in vitro and in vivo. In silico analysis further showed that certain functional groups of NQTrp, not in the aromatic rings, are also involved in binding and inhibiting Aβ. To better understand the exact mode of action and identify the groups crucial for NQTrp inhibitory activity, we conducted structure-activity analysis. Four derivatives of NQTrp were studied in silico: a D-isomer, two single-methylated and one double-methylated derivative. In silico results showed that the NQTrp groups involved in hydrogen bonds are the anilinic NH (i.e., the NH linker between the quinone and tryptophan moieties), the quinonic carbonyls, and the carboxylic acid. These predictions were supported by in vitro results. Our results should aid in designing improved small-molecule inhibitors of Aβ aggregation for treating AD.
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Affiliation(s)
- Roni Scherzer-Attali
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
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22
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Nicolotti O, Convertino M, Leonetti F, Catto M, Cellamare S, Carotti A. Estimation of the Binding Free Energy by Linear Interaction Energy Models. Mini Rev Med Chem 2012; 12:551-61. [DOI: 10.2174/138955712800493843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 06/20/2011] [Accepted: 06/21/2011] [Indexed: 11/22/2022]
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23
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Convertino M. Neutral metacommunity clustering and SAR: River basin vs. 2-D landscape biodiversity patterns [Ecol. Model. 222 (June (11)) (2011) 1863–1879]. Ecol Modell 2012. [DOI: 10.1016/j.ecolmodel.2011.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Abstract
In recent years, an increasing number of small molecules and short peptides have been identified that interfere with aggregation and/or oligomerization of the Alzheimer β-amyloid peptide (Aβ). Many of them possess aromatic moieties, suggesting a dominant role for those in interacting with Aβ along various stages of the aggregation process. In this study, we attempt to elucidate whether interactions of such aromatic inhibitors with monomeric Aβ(12-28) point to a common mechanism of action by performing atomistic molecular dynamics simulations at equilibrium. Our results suggest that, independently of the presence of inhibitors, monomeric Aβ(12-28) populates a partially collapsed ensemble that is largely devoid of canonical secondary structure at 300 K and neutral pH. The small molecules have different affinities for Aβ(12-28) that can be partially rationalized by the balance of aromatic and charged moieties constituting the molecules. There are no predominant binding modes, although aggregation inhibitors preferentially interact with the N-terminal portion of the fragment (residues 13-20). Analysis of the free energy landscape of Aβ(12-28) reveals differences highlighted by altered populations of a looplike conformer in the presence of inhibitors. We conclude that intrinsic disorder of Aβ persists at the level of binding small molecules and that inhibitors can significantly alter properties of monomeric Aβ via multiple routes of differing specificity.
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Affiliation(s)
- Marino Convertino
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Vitalis
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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25
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Convertino M, Kiker G, Muñoz-Carpena R, Chu-Agor M, Fischer R, Linkov I. Scale- and resolution-invariance of suitable geographic range for shorebird metapopulations. Ecological Complexity 2011. [DOI: 10.1016/j.ecocom.2011.07.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Frydman-Marom A, Convertino M, Pellarin R, Lampel A, Shaltiel-Karyo R, Segal D, Caflisch A, Shalev DE, Gazit E. Structural basis for inhibiting β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue. ACS Chem Biol 2011; 6:1265-76. [PMID: 21892833 DOI: 10.1021/cb200103h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The distribution of endomorphins (EM) 1 and 2 in the human brain inversely correlates with cerebral neurodegeneration in Alzheimer's disease (AD), implying a protective role. These endogenous opioid peptides incorporate aromatic residues and a β-breaker motif, as seen in several optimized inhibitors of Aβ aggregation. The activity of native endomorphins was studied, as well as the rationally designed analogue Aib-1, which includes a remarkably efficient β-breaker, α-aminoisobutyric acid (Aib). In vitro and GFP fusion protein assays showed that Aib-1 interacted with Aβ and markedly inhibited the formation of toxic oligomer and fibril growth. Moreover, Aib-1 prevented the toxicity of Aβ toward neuronal PC12 cells and markedly rectified reduced longevity of an AD fly model. Atomistic simulations and NMR-derived solution structures revealed that Aib-1 significantly reduced the propensity of Aβ to aggregate due to multimode interactions including aromatic, hydrophobic, and polar contacts. We suggest that hindering the self-assembly process by interfering with the aromatic core of amyloidogenic peptides may pave the way toward developing therapeutic agents to treat amyloid-associated diseases.
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Affiliation(s)
- Anat Frydman-Marom
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Marino Convertino
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Riccardo Pellarin
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Ayala Lampel
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Ronit Shaltiel-Karyo
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Daniel Segal
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Deborah E. Shalev
- Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
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Scherzer-Attali R, Pellarin R, Convertino M, Frydman-Marom A, Egoz-Matia N, Peled S, Levy-Sakin M, Shalev DE, Caflisch A, Gazit E, Segal D. Complete phenotypic recovery of an Alzheimer's disease model by a quinone-tryptophan hybrid aggregation inhibitor. PLoS One 2010; 5:e11101. [PMID: 20559435 PMCID: PMC2885425 DOI: 10.1371/journal.pone.0011101] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 05/20/2010] [Indexed: 11/29/2022] Open
Abstract
The rational design of amyloid oligomer inhibitors is yet an unmet drug development need. Previous studies have identified the role of tryptophan in amyloid recognition, association and inhibition. Furthermore, tryptophan was ranked as the residue with highest amyloidogenic propensity. Other studies have demonstrated that quinones, specifically anthraquinones, can serve as aggregation inhibitors probably due to the dipole interaction of the quinonic ring with aromatic recognition sites within the amyloidogenic proteins. Here, using in vitro, in vivo and in silico tools we describe the synthesis and functional characterization of a rationally designed inhibitor of the Alzheimer's disease-associated β-amyloid. This compound, 1,4-naphthoquinon-2-yl-L-tryptophan (NQTrp), combines the recognition capacities of both quinone and tryptophan moieties and completely inhibited Aβ oligomerization and fibrillization, as well as the cytotoxic effect of Aβ oligomers towards cultured neuronal cell line. Furthermore, when fed to transgenic Alzheimer's disease Drosophila model it prolonged their life span and completely abolished their defective locomotion. Analysis of the brains of these flies showed a significant reduction in oligomeric species of Aβ while immuno-staining of the 3rd instar larval brains showed a significant reduction in Aβ accumulation. Computational studies, as well as NMR and CD spectroscopy provide mechanistic insight into the activity of the compound which is most likely mediated by clamping of the aromatic recognition interface in the central segment of Aβ. Our results demonstrate that interfering with the aromatic core of amyloidogenic peptides is a promising approach for inhibiting various pathogenic species associated with amyloidogenic diseases. The compound NQTrp can serve as a lead for developing a new class of disease modifying drugs for Alzheimer's disease.
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Affiliation(s)
- Roni Scherzer-Attali
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Riccardo Pellarin
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Marino Convertino
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Anat Frydman-Marom
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Nirit Egoz-Matia
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Sivan Peled
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Levy-Sakin
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Deborah E. Shalev
- Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail: (EG); (DS)
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail: (EG); (DS)
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Nicolotti O, Giangreco I, Miscioscia TF, Convertino M, Leonetti F, Pisani L, Carotti A. Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model. J Comput Aided Mol Des 2010; 24:117-29. [DOI: 10.1007/s10822-010-9320-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 01/28/2010] [Indexed: 10/19/2022]
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Convertino M, Pellarin R, Catto M, Carotti A, Caflisch A. 9,10-Anthraquinone hinders beta-aggregation: how does a small molecule interfere with Abeta-peptide amyloid fibrillation? Protein Sci 2009; 18:792-800. [PMID: 19309732 DOI: 10.1002/pro.87] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Amyloid aggregation is linked to a number of neurodegenerative syndromes, the most prevalent one being Alzheimer's disease. In this pathology, the beta-amyloid peptides (Abeta) aggregate into oligomers, protofibrils, and fibrils and eventually into plaques, which constitute the characteristic hallmark of Alzheimer's disease. Several low-molecular-weight compounds able to impair the Abeta aggregation process have been recently discovered; yet, a detailed description of their interactions with oligomers and fibrils is hitherto missing. Here, molecular dynamics simulations are used to investigate the influence of two relatively similar tricyclic, planar compounds, that is, 9, 10-anthraquinone (AQ) and anthracene (AC), on the early phase of the aggregation of the Abeta heptapeptide segment H(14)QKLVFF(20), the hydrophobic stretch that promotes the Abeta self-assembly. The simulations show that AQ interferes with beta-sheet formation more than AC. In particular, AQ intercalates into the beta-sheet because polar interactions between the compound and the peptide backbone destabilize the interstrand hydrogen bonds, thereby favoring disorder. The thioflavin T-binding assay indicates that AQ, but not AC, sensibly reduces the amount of aggregated Abeta(1-40) peptide. Taken together, the in silico and in vitro results provide evidence that structural perturbations by AQ can remarkably affect ordered oligomerization. Moreover, the simulations shed light at the atomic level on the interactions between AQ and Abeta oligomers, providing useful insights for the design of small-molecule inhibitors of aggregation with therapeutic potential in Alzheimer's disease.
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Affiliation(s)
- Marino Convertino
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
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