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Bampali K, Koniuszewski F, Vogel FD, Fabjan J, Andronis C, Lekka E, Virvillis V, Seidel T, Delaunois A, Royer L, Rolf MG, Giuliano C, Traebert M, Roussignol G, Fric-Bordat M, Mazelin-Winum L, Bryant SD, Langer T, Ernst M. GABA A receptor-mediated seizure liabilities: a mixed-methods screening approach. Cell Biol Toxicol 2023; 39:2793-2819. [PMID: 37093397 PMCID: PMC10693519 DOI: 10.1007/s10565-023-09803-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/08/2022] [Accepted: 03/09/2023] [Indexed: 04/25/2023]
Abstract
GABAA receptors, members of the pentameric ligand-gated ion channel superfamily, are widely expressed in the central nervous system and mediate a broad range of pharmaco-toxicological effects including bidirectional changes to seizure threshold. Thus, detection of GABAA receptor-mediated seizure liabilities is a big, partly unmet need in early preclinical drug development. This is in part due to the plethora of allosteric binding sites that are present on different subtypes of GABAA receptors and the critical lack of screening methods that detect interactions with any of these sites. To improve in silico screening methods, we assembled an inventory of allosteric binding sites based on structural data. Pharmacophore models representing several of the binding sites were constructed. These models from the NeuroDeRisk IL Profiler were used for in silico screening of a compiled collection of drugs with known GABAA receptor interactions to generate testable hypotheses. Amoxapine was one of the hits identified and subjected to an array of in vitro assays to examine molecular and cellular effects on neuronal excitability and in vivo locomotor pattern changes in zebrafish larvae. An additional level of analysis for our compound collection is provided by pharmacovigilance alerts using FAERS data. Inspired by the Adverse Outcome Pathway framework, we postulate several candidate pathways leading from specific binding sites to acute seizure induction. The whole workflow can be utilized for any compound collection and should inform about GABAA receptor-mediated seizure risks more comprehensively compared to standard displacement screens, as it rests chiefly on functional data.
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Affiliation(s)
- Konstantina Bampali
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Filip Koniuszewski
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Florian D Vogel
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Jure Fabjan
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | | | | | | | - Thomas Seidel
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Annie Delaunois
- UCB Biopharma SRL, Chemin du Foriest, Braine-L'Alleud, Belgium
| | - Leandro Royer
- UCB Biopharma SRL, Chemin du Foriest, Braine-L'Alleud, Belgium
| | - Michael G Rolf
- R&D Biopharmaceuticals, Astra Zeneca, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Chiara Giuliano
- R&D Biopharmaceuticals, Astra Zeneca, Fleming Building (B623), Babraham Research Park, Babraham, Cambridgeshire, CB22 3AT, UK
| | - Martin Traebert
- Novartis Institutes for Biomedical Research, Fabrikstrasse 2, CH-4056, Basel, Switzerland
| | | | | | | | - Sharon D Bryant
- Inte:Ligand GmbH, Mariahilferstrasse 74B/11, 1070, Vienna, Austria
| | - Thierry Langer
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Margot Ernst
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University Vienna, Spitalgasse 4, 1090, Vienna, Austria.
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2
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Wakefield AE, Kozakov D, Vajda S. Mapping the binding sites of challenging drug targets. Curr Opin Struct Biol 2022; 75:102396. [PMID: 35636004 PMCID: PMC9790766 DOI: 10.1016/j.sbi.2022.102396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/17/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 02/03/2023]
Abstract
An increasing number of medically important proteins are challenging drug targets because their binding sites are too shallow or too polar, are cryptic and thus not detectable without a bound ligand or located in a protein-protein interface. While such proteins may not bind druglike small molecules with sufficiently high affinity, they are frequently druggable using novel therapeutic modalities. The need for such modalities can be determined by experimental or computational fragment based methods. Computational mapping by mixed solvent molecular dynamics simulations or the FTMap server can be used to determine binding hot spots. The strength and location of the hot spots provide very useful information for selecting potentially successful approaches to drug discovery.
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Affiliation(s)
- Amanda E. Wakefield
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215,Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA NY, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215,Department of Chemistry, Boston University, Boston, Massachusetts 02215
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Wah Tan Z, Tee WV, Berezovsky IN. Learning about allosteric drugs and ways to design them. J Mol Biol 2022; 434:167692. [PMID: 35738428 DOI: 10.1016/j.jmb.2022.167692] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 02/27/2022] [Revised: 05/23/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022]
Abstract
While the accelerating quest for precision medicine requires new individually targeting and selective drugs, and the ability to work with so-called undruggable targets, the realm of allosteric drugs meeting this need remains largely uncharted. Generalizing the observations on two major drug targets with widely observed inherent allostery, GPCRs and kinases, we describe and discuss basic allosteric modes of action that are universally applicable in all types of structures and functions. Using examples of Class A GPCRs and CMGC protein kinases, we show how Allosteric Signalling and Probing Fingerprints can be used to identify potential allosteric sites and reveal effector-leads that may serve as a starting point for the development of allosteric drugs targeting these regulatory sites. A set of distinct characteristics of allosteric ligands was established, which highlights the versatility of their design and make them advantageous before their orthosteric counterparts in personalized medicine. We argue that rational design of allosteric drugs should begin with the search for latent sites or design of non-natural binding sites followed by fragment-based design of allosteric ligands and by the mutual adjustment of the site-ligand pair in order to achieve required effects. On the basis of the perturbative nature and reversibility of allosteric communication, we propose a generic protocol for computational design of allosteric effectors, enabling also the allosteric tuning of biologics, in obtaining allosteric control over protein functions.
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Affiliation(s)
- Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore.
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4
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Lu S, Chen Y, Wei J, Zhao M, Ni D, He X, Zhang J. Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators. Acta Pharm Sin B 2021; 11:1355-1361. [PMID: 34094839 PMCID: PMC8148055 DOI: 10.1016/j.apsb.2020.09.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 12/16/2022] Open
Abstract
The recent discovery of activator compounds binding to an allosteric site on the NAD+-dependent protein lysine deacetylase, sirtuin 6 (SIRT6) has attracted interest and presents a pharmaceutical target for aging-related and cancer diseases. However, the mechanism underlying allosteric activation of SIRT6 by the activator MDL-801 remains largely elusive because no major conformational changes are observed upon activator binding. By combining molecular dynamics simulations with biochemical and kinetic analyses of wild-type SIRT6 and its variant M136A, we show that conformational rotation of 2-methyl-4-fluoro-5-bromo substituent on the right phenyl ring (R-ring) of MDL-801, which uncovers previously unseen hydrophobic interactions, contributes to increased activating deacetylation activity of SIRT6. This hypothesis is further supported by the two newly synthesized MDL-801 derivatives through the removal of the 5-Br atom on the R-ring (MDL-801-D1) or the restraint of the rotation of the R-ring (MDL-801-D2). We further propose that the 5-Br atom serves as an allosteric driver that controls the ligand allosteric efficacy. Our study highlights the effect of allosteric enzyme catalytic activity by activator binding and provides a rational approach for enhancing deacetylation activity.
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Key Words
- ADPR, ADP-ribose
- Allosteric driver
- Allosteric mechanisms
- Allosteric sites
- Drug design
- EC50, Effective concentration
- Enzyme catalysis
- FDL, Fluor de Lys
- H3K56, histone 3 lysine 56
- H3K9, histone 3 lysine 9
- HPLC, high-performance liquid chromatography
- MD, molecular dynamics
- MST, microscale thermophoresis
- Myr-H3K9, myristoyl H3K9
- NAM, nicotinamide
- PCA, principal component analysis
- Protein dynamics
- RMSD, root-mean-square deviation
- SIRT6, sirtuin 6
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Liang Z, Zhu Y, Long J, Ye F, Hu G. Both intra and inter-domain interactions define the intrinsic dynamics and allosteric mechanism in DNMT1s. Comput Struct Biotechnol J 2020; 18:749-764. [PMID: 32280430 PMCID: PMC7132064 DOI: 10.1016/j.csbj.2020.03.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 10/23/2019] [Revised: 03/17/2020] [Accepted: 03/17/2020] [Indexed: 01/03/2023] Open
Abstract
Dynamics and allosteric potentials of the RFTS domain are proposed. Hinge sites located at the RFTS-CD interface are key regulators for inter-domain interactions. Network analysis reveals local allosteric networks and inter-domain communication pathways in DNMT1. A potential allosteric site at the TRD interface for DNMT1 is identified.
DNA methyltransferase 1 (DNMT1), a large multidomain enzyme, is believed to be involved in the passive transmission of genomic methylation patterns via methylation maintenance. Yet, the molecular mechanism of interaction networks underlying DNMT1 structures, dynamics, and its biological significance has yet to be fully characterized. In this work, we used an integrated computational strategy that combined coarse-grained and atomistic simulations with coevolution information and network modeling of the residue interactions for the systematic investigation of allosteric dynamics in DNMT1. The elastic network modeling has proposed that the high plasticity of RFTS has strengthened the correlated behaviors of DNMT1 structures through the hinge sites located at the RFTS-CD interface, which mediate the collective motions between domains. The perturbation response scanning (PRS) analysis combined with the enrichment analysis of disease mutations have further highlighted the allosteric potential of the RFTS domain. Furthermore, the long-range paths connect the intra-domain interactions through the TRD interface and catalytic interface, emphasizing some key inter-domain interactions as the bridges in the global allosteric regulation of DNMT1. The observed interplay between conserved intra-domain networks and dynamical plasticity encoded by inter-domain interactions provides insights into the intrinsic dynamics and functional evolution, as well as the design of allosteric modulators of DNMT1 based on the TRD interface.
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Affiliation(s)
- Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Yu Zhu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Jie Long
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
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Abstract
Ras, whose mutants are present in approximately 30% of human tumours, is one of the most important oncogenes. Drugging Ras is thus regarded as the quest for the Holy Grail in cancer therapeutics development. Despite more than three decades of efforts, drug discovery targeting Ras constantly fails, rendering Ras undruggable, due to its smooth surface and picomolar affinity towards guanosine substrates. The most frequently mutated isoform of Ras is K-Ras, accounting for >85% of Ras-driven cancers, and one majority of them is the G12C mutation. Recent advances in structural biology shed light on drugging Ras, and one of the cutting-edge breakthroughs is the design of covalent G12C-specific inhibitors targeting the mutated cysteine. This type of inhibitor can be classified into substrate-competitive orthosteric inhibitors and non-competitive allosteric inhibitors. They display improved selectivity and enhanced potency due to their G12-specific and irreversible covalent binding nature. Thus, they represent a new hope for revolutionizing the conventional characterization of Ras as "undruggable" and pave a promising avenue for further drug discovery. Here, we provide comprehensive structural and medicinal chemical insights into K-Ras covalent inhibitors specific for the G12C mutant. We first present an in-depth analysis of the conformations of the inhibitor binding pockets. Then, all the latest covalent ligands selectively inhibiting K-RasG12C are reviewed. Finally, we examine the current challenges faced by this new class of anti-Ras inhibitors.
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Affiliation(s)
- Duan Ni
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xinyi Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xinheng He
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Hao Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China; Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China; Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.
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7
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Mittal L, Kumari A, Suri C, Bhattacharya S, Asthana S. Insights into structural dynamics of allosteric binding sites in HCV RNA-dependent RNA polymerase. J Biomol Struct Dyn 2019; 38:1612-1625. [PMID: 31057089 DOI: 10.1080/07391102.2019.1614480] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Inhibition of the viral RNA-dependent RNA polymerase (RdRp) to resolve chronic infection is a useful therapeutic strategy against Hepatitis C virus (HCV). Non-nucleoside inhibitors (NNIs) of RdRp are small molecules that bind tightly with allosteric sites on the enzyme, thereby inhibiting polymerase activity. A large number of crystal structures (176) were studied to establish the structure-activity relationship along with the mechanism of inhibition and resistance between HCV RdRp and NNIs at different allosteric sites. The structure and the associated dynamics are the blueprint to understand the function of the protein. We have implemented the ligand-based pharmacophore and molecular dynamic simulations to extract the possible local and global characteristics of RdRp upon NNI binding and the structural-dynamical features possessed by the known actives. Our results suggest that the NNI binding induces significant fluctuations at the atomic level which are critical for enzymatic activity, with minimal global structural alterations. Residue-wise mapping of interactions of NNIs at different sites exhibited some conserved interaction patterns of key amino acids and water molecules. Here, the structural insights are explored to understand the correlation between the dynamics of protein's subdomains and function at the molecular level, useful for genotype-specific rational designing of NNIs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lovika Mittal
- Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Anita Kumari
- Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Charu Suri
- Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Sankar Bhattacharya
- Vaccine and Infectious Disease Research Center (VIDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Shailendra Asthana
- Drug Discovery Research Center (DDRC), Translational Health Science and Technology Institute (THSTI), Faridabad, India
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Abdelkarim H, Hitchinson B, Banerjee A, Gaponenko V. Advances in NMR Methods to Identify Allosteric Sites and Allosteric Ligands. Adv Exp Med Biol 2019; 1163:171-186. [PMID: 31707704 DOI: 10.1007/978-981-13-8719-7_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
NMR allows assessment of protein structure in solution. Unlike conventional X-ray crystallography that provides snapshots of protein conformations, all conformational states are simultaneously accessible to analysis by NMR. This is a significant advantage for discovery and characterization of allosteric effects. These effects are observed when binding at one site of the protein affects another distinct site through conformational transitions. Allosteric regulation of proteins has been observed in multiple physiological processes in health and disease, providing an opportunity for the development of allosteric inhibitors. These compounds do not directly interact with the orthosteric site of the protein but influence its structure and function. In this book chapter, we provide an overview on how NMR methods are utilized to identify allosteric sites and to discover novel inhibitors, highlighting examples from the field. We also describe how NMR has contributed to understanding of allosteric mechanisms and propose that it is likely to play an important role in clarification and further development of key concepts of allostery.
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Affiliation(s)
- Hazem Abdelkarim
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Ben Hitchinson
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Avik Banerjee
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA.
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Capilla AS, Soucek R, Grau L, Romero M, Rubio-Martínez J, Caignard DH, Pujol MD. Substituted tetrahydroisoquinolines: synthesis, characterization, antitumor activity and other biological properties. Eur J Med Chem 2018; 145:51-63. [PMID: 29324343 DOI: 10.1016/j.ejmech.2017.12.098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 09/01/2017] [Revised: 12/29/2017] [Accepted: 12/30/2017] [Indexed: 10/18/2022]
Abstract
This work deals with the molecular design, synthesis and biological activity of a series of tetrahydro[1,4]dioxanisoquinolines and dimethoxyisoquinoline analogues. This study describes the synthesis strategy of these potential antitumor compounds, their multi-step synthesis and their optimization. A series of tetrahydroisoquinolines was synthesized and their cytotoxicity evaluated. Some of these tetrahydroisoquinolines showed promising KRas inhibition, antiangiogenesis activity and antiosteoporosis properties. Molecular modeling studies showed that compound 12 bind in the p1 pocket of the KRas protein making interactions with the hydrophobic residues Leu56, Tyr64, Tyr71 and Thr74 and hydrogen bonds with residues Glu37 and Asp38.
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Affiliation(s)
- A Sergi Capilla
- Laboratori de Química Farmacèutica (Unitat associada al CSIC), Facultat de Farmàcia, Universitat de Barcelona, Spain
| | - Richard Soucek
- Laboratori de Química Farmacèutica (Unitat associada al CSIC), Facultat de Farmàcia, Universitat de Barcelona, Spain
| | - Laura Grau
- Laboratori de Química Farmacèutica (Unitat associada al CSIC), Facultat de Farmàcia, Universitat de Barcelona, Spain
| | - Manel Romero
- Laboratori de Química Farmacèutica (Unitat associada al CSIC), Facultat de Farmàcia, Universitat de Barcelona, Spain
| | - Jaime Rubio-Martínez
- Department of Physical Chemistry, Faculty of Chemistry, University of Barcelona and the Institut de Recerca en Química Teòrica i Computacional (IQTCUB), Barcelona, Spain
| | - Daniel H Caignard
- Les laboratoires Servier, 1 rue Carle Hébert-92415, Courbevoie Cedex, 92200 Neuilly-sur Seine, France
| | - Maria Dolors Pujol
- Laboratori de Química Farmacèutica (Unitat associada al CSIC), Facultat de Farmàcia, Universitat de Barcelona, Spain.
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Marreiros R, Müller-Schiffmann A, Bader V, Selvarajah S, Dey D, Lingappa VR, Korth C. Viral capsid assembly as a model for protein aggregation diseases: Active processes catalyzed by cellular assembly machines comprising novel drug targets. Virus Res 2014; 207:155-64. [PMID: 25451064 DOI: 10.1016/j.virusres.2014.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 06/30/2014] [Revised: 09/09/2014] [Accepted: 10/01/2014] [Indexed: 11/18/2022]
Abstract
Viruses can be conceptualized as self-replicating multiprotein assemblies, containing coding nucleic acids. Viruses have evolved to exploit host cellular components including enzymes to ensure their replicative life cycle. New findings indicate that also viral capsid proteins recruit host factors to accelerate their assembly. These assembly machines are RNA-containing multiprotein complexes whose composition is governed by allosteric sites. In the event of viral infection, the assembly machines are recruited to support the virus over the host and are modified to achieve that goal. Stress granules and processing bodies may represent collections of such assembly machines, readily visible by microscopy but biochemically labile and difficult to isolate by fractionation. We hypothesize that the assembly of protein multimers such as encountered in neurodegenerative or other protein conformational diseases, is also catalyzed by assembly machines. In the case of viral infection, the assembly machines have been modified by the virus to meet the virus' need for rapid capsid assembly rather than host homeostasis. In the case of the neurodegenerative diseases, it is the monomers and/or low n oligomers of the so-called aggregated proteins that are substrates of assembly machines. Examples for substrates are amyloid β peptide (Aβ) and tau in Alzheimer's disease, α-synuclein in Parkinson's disease, prions in the prion diseases, Disrupted-in-schizophrenia 1 (DISC1) in subsets of chronic mental illnesses, and others. A likely continuum between virus capsid assembly and cell-to-cell transmissibility of aggregated proteins is remarkable. Protein aggregation diseases may represent dysfunction and dysregulation of these assembly machines analogous to the aberrations induced by viral infection in which cellular homeostasis is pathologically reprogrammed. In this view, as for viral infection, reset of assembly machines to normal homeostasis should be the goal of protein aggregation therapeutics. A key basis for the commonality between viral and neurodegenerative disease aggregation is a broader definition of assembly as more than just simple aggregation, particularly suited for the crowded cytoplasm. The assembly machines are collections of proteins that catalytically accelerate an assembly reaction that would occur spontaneously but too slowly to be relevant in vivo. Being an enzyme complex with a functional allosteric site, appropriated for a non-physiological purpose (e.g. viral infection or conformational disease), these assembly machines present a superior pharmacological target because inhibition of their active site will amplify an effect on their substrate reaction. Here, we present this hypothesis based on recent proof-of-principle studies against Aβ assembly relevant in Alzheimer's disease.
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Affiliation(s)
- Rita Marreiros
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Andreas Müller-Schiffmann
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Verian Bader
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | | | | | | | - Carsten Korth
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany.
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