1
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Santos TB, de Moraes LGC, Pacheco PAF, dos Santos DG, Ribeiro RMDAC, Moreira CDS, da Rocha DR. Naphthoquinones as a Promising Class of Compounds for Facing the Challenge of Parkinson's Disease. Pharmaceuticals (Basel) 2023; 16:1577. [PMID: 38004442 PMCID: PMC10674926 DOI: 10.3390/ph16111577] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Parkinson's disease (PD) is a degenerative disease that affects approximately 6.1 million people and is primarily caused by the loss of dopaminergic neurons. Naphthoquinones have several biological activities explored in the literature, including neuroprotective effects. Therefore, this review shows an overview of naphthoquinones with neuroprotective effects, such as shikonin, plumbagin and vitamin K, that prevented oxidative stress, in addition to multiple mechanisms. Synthetic naphthoquinones with inhibitory activity on the P2X7 receptor were also found, leading to a neuroprotective effect on Neuro-2a cells. It was found that naphthazarin can act as inhibitors of the MAO-B enzyme. Vitamin K and synthetic naphthoquinones hybrids with tryptophan or dopamine showed inhibition of the aggregation of α-synuclein. Synthetic derivatives of juglone and naphthazarin were able to protect Neuro-2a cells against neurodegenerative effects of neurotoxins. In addition, routes for producing synthetic derivatives were also discussed. With the data presented, 1,4-naphthoquinones can be considered as a promising class in the treatment of PD and this review aims to assist the scientific community in the application of these compounds. The derivatives presented can also support further research that explores their structures as synthetic platforms, in addition to helping to understand the interaction of naphthoquinones with biological targets related to PD.
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Affiliation(s)
- Thaís Barreto Santos
- Instituto de Química, Universidade Federal Fluminense, Outeiro de São João Batista s/n°, Niterói CEP 24.020-141, RJ, Brazil; (T.B.S.); (L.G.C.d.M.); (P.A.F.P.); (D.G.d.S.); (R.M.d.A.C.R.); (C.d.S.M.)
| | - Leonardo Gomes Cavalieri de Moraes
- Instituto de Química, Universidade Federal Fluminense, Outeiro de São João Batista s/n°, Niterói CEP 24.020-141, RJ, Brazil; (T.B.S.); (L.G.C.d.M.); (P.A.F.P.); (D.G.d.S.); (R.M.d.A.C.R.); (C.d.S.M.)
| | - Paulo Anastácio Furtado Pacheco
- Instituto de Química, Universidade Federal Fluminense, Outeiro de São João Batista s/n°, Niterói CEP 24.020-141, RJ, Brazil; (T.B.S.); (L.G.C.d.M.); (P.A.F.P.); (D.G.d.S.); (R.M.d.A.C.R.); (C.d.S.M.)
| | - Douglas Galdino dos Santos
- Instituto de Química, Universidade Federal Fluminense, Outeiro de São João Batista s/n°, Niterói CEP 24.020-141, RJ, Brazil; (T.B.S.); (L.G.C.d.M.); (P.A.F.P.); (D.G.d.S.); (R.M.d.A.C.R.); (C.d.S.M.)
| | - Rafaella Machado de Assis Cabral Ribeiro
- Instituto de Química, Universidade Federal Fluminense, Outeiro de São João Batista s/n°, Niterói CEP 24.020-141, RJ, Brazil; (T.B.S.); (L.G.C.d.M.); (P.A.F.P.); (D.G.d.S.); (R.M.d.A.C.R.); (C.d.S.M.)
| | - Caroline dos Santos Moreira
- Instituto de Química, Universidade Federal Fluminense, Outeiro de São João Batista s/n°, Niterói CEP 24.020-141, RJ, Brazil; (T.B.S.); (L.G.C.d.M.); (P.A.F.P.); (D.G.d.S.); (R.M.d.A.C.R.); (C.d.S.M.)
- Instituto Federal do Rio de Janeiro, Campus Paracambi, Rua Sebastião Lacerda s/n°, Fábrica, Paracambi CEP 26.600-000, RJ, Brazil
| | - David Rodrigues da Rocha
- Instituto de Química, Universidade Federal Fluminense, Outeiro de São João Batista s/n°, Niterói CEP 24.020-141, RJ, Brazil; (T.B.S.); (L.G.C.d.M.); (P.A.F.P.); (D.G.d.S.); (R.M.d.A.C.R.); (C.d.S.M.)
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2
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Campora M, Canale C, Gatta E, Tasso B, Laurini E, Relini A, Pricl S, Catto M, Tonelli M. Multitarget Biological Profiling of New Naphthoquinone and Anthraquinone-Based Derivatives for the Treatment of Alzheimer's Disease. ACS Chem Neurosci 2021; 12:447-461. [PMID: 33428389 PMCID: PMC7880572 DOI: 10.1021/acschemneuro.0c00624] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
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Two
series of naphthoquinone and anthraquinone derivatives decorated
with an aromatic/heteroaromatic chain have been synthesized and evaluated
as potential promiscuous agents capable of targeting different factors
playing a key role in Alzheimer’s disease (AD) pathogenesis.
On the basis of the in vitro biological profiling,
most of them exhibited a significant ability to inhibit amyloid aggregation,
PHF6 tau sequence aggregation, acetylcholinesterase (AChE), and monoamine
oxidase (MAO) B. In particular, naphthoquinone 2 resulted
as one of the best performing multitarget-directed ligand (MTDL) experiencing
a high potency profile in inhibiting β-amyloid (Aβ40) aggregation (IC50 = 3.2 μM), PHF6 tau
fragment (91% at 10 μM), AChE enzyme (IC50 = 9.2
μM) jointly with a remarkable inhibitory activity against MAO
B (IC50 = 7.7 nM). Molecular modeling studies explained
the structure–activity relationship (SAR) around the binding
modes of representative compound 2 in complex with hMAO
B and hAChE enzymes, revealing inhibitor/protein key contacts and
the likely molecular rationale for enzyme selectivity. Compound 2 was also demonstrated to be a strong inhibitor of Aβ42 aggregation, with potency comparable to quercetin. Accordingly,
atomic force microscopy (AFM) revealed that the most promising naphthoquinones 2 and 5 and anthraquinones 11 and 12 were able to impair Aβ42 fibrillation,
deconstructing the morphologies of its fibrillar aggregates. Moreover,
the same compounds exerted a moderate neuroprotective effect against
Aβ42 toxicity in primary cultures of cerebellar granule
cells. Therefore, our findings demonstrate that these molecules may
represent valuable chemotypes toward the development of promising
candidates for AD therapy.
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Affiliation(s)
- Marta Campora
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Claudio Canale
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Elena Gatta
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Bruno Tasso
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Annalisa Relini
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
| | - Marco Catto
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Michele Tonelli
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
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3
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Campora M, Francesconi V, Schenone S, Tasso B, Tonelli M. Journey on Naphthoquinone and Anthraquinone Derivatives: New Insights in Alzheimer's Disease. Pharmaceuticals (Basel) 2021; 14:ph14010033. [PMID: 33466332 PMCID: PMC7824805 DOI: 10.3390/ph14010033] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/27/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disease that is characterized by memory loss, cognitive impairment, and functional decline leading to dementia and death. AD imposes neuronal death by the intricate interplay of different neurochemical factors, which continue to inspire the medicinal chemist as molecular targets for the development of new agents for the treatment of AD with diverse mechanisms of action, but also depict a more complex AD scenario. Within the wide variety of reported molecules, this review summarizes and offers a global overview of recent advancements on naphthoquinone (NQ) and anthraquinone (AQ) derivatives whose more relevant chemical features and structure-activity relationship studies will be discussed with a view to providing the perspective for the design of viable drugs for the treatment of AD. In particular, cholinesterases (ChEs), β-amyloid (Aβ) and tau proteins have been identified as key targets of these classes of compounds, where the NQ or AQ scaffold may contribute to the biological effect against AD as main unit or significant substructure. The multitarget directed ligand (MTDL) strategy will be described, as a chance for these molecules to exhibit significant potential on the road to therapeutics for AD.
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2-Propargylamino-naphthoquinone derivatives as multipotent agents for the treatment of Alzheimer's disease. Eur J Med Chem 2020; 211:113112. [PMID: 33360800 DOI: 10.1016/j.ejmech.2020.113112] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 01/21/2023]
Abstract
Alzheimer's disease is a progressive brain disorder with characteristic symptoms and several pathological hallmarks. The concept of "one drug, one target" has not generated any new drugs since 2004. The new era of drug development in the field of AD builds upon rationally designed multi-target directed ligands that can better address the complexity of AD. Herewith, we designed ten novel derivatives of 2-propargylamino-naphthoquinone. The biological evaluation of these compounds includes inhibition of monoamine oxidase A/B, inhibition of amyloid-beta aggregation, radical-scavenging, and metal-chelating properties. Some of the compounds possess low cytotoxicity profile with an anti-inflammatory ability in the lipopolysaccharide-stimulated cellular model. All these features warrant their further testing in the field of AD.
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5
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Mezeiova E, Soukup O, Korabecny J. Huprines — an insight into the synthesis and biological properties. RUSSIAN CHEMICAL REVIEWS 2020. [DOI: 10.1070/rcr4938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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6
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Viswanathan GK, Paul A, Gazit E, Segal D. Naphthoquinone Tryptophan Hybrids: A Promising Small Molecule Scaffold for Mitigating Aggregation of Amyloidogenic Proteins and Peptides. Front Cell Dev Biol 2019; 7:242. [PMID: 31750300 PMCID: PMC6843079 DOI: 10.3389/fcell.2019.00242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 10/02/2019] [Indexed: 12/22/2022] Open
Abstract
A current challenge faced by researchers is the lack of disease-modifying therapeutics for amyloid formation that is associated with several human diseases. Although the monomeric proteins or peptides involved in various amyloidogenic diseases do not have amino acid sequence homology, there appears to be a structural correlation among the amyloid assemblies, which are responsible for distinct pathological conditions. Here, we review our work on Naphthoquinone Tryptophan (NQTrp) hybrids, a small molecule scaffold that can generically modulate neuronal and non-neuronal amyloid aggregation both in vitro and in vivo. NQTrp reduces the net amyloid load by inhibiting the process of amyloid formation and disassembling the pre-formed fibrils, both in a dose-dependent manner. As a plausible mechanism of action, NQTrp effectively forms hydrogen bonding and hydrophobic interactions, such as π-π stacking, with the vital residues responsible for the initial nucleation of protein/peptide aggregation. This review highlights the effectiveness of the NQTrp hybrid scaffold for developing novel small molecule modulators of amyloid aggregation.
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Affiliation(s)
- Guru KrishnaKumar Viswanathan
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ashim Paul
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel.,Interdisciplinary Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
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7
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Salveson PJ, Haerianardakani S, Thuy-Boun A, Yoo S, Kreutzer AG, Demeler B, Nowick JS. Repurposing Triphenylmethane Dyes to Bind to Trimers Derived from Aβ. J Am Chem Soc 2018; 140:11745-11754. [PMID: 30125493 DOI: 10.1021/jacs.8b06568] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Soluble oligomers of the β-amyloid peptide, Aβ, are associated with the progression of Alzheimer's disease. Although many small molecules bind to these assemblies, the details of how these molecules interact with Aβ oligomers remain unknown. This paper reports that crystal violet, and other C3 symmetric triphenylmethane dyes, bind to C3 symmetric trimers derived from Aβ17-36. Binding changes the color of the dyes from purple to blue, and causes them to fluoresce red when irradiated with green light. Job plot and analytical ultracentrifugation experiments reveal that two trimers complex with one dye molecule. Studies with several triphenylmethane dyes reveal that three N, N-dialkylamino substituents are required for complexation. Several mutant trimers, in which Phe19, Phe20, and Ile31 were mutated to cyclohexylalanine, valine, and cyclohexylglycine, were prepared to probe the triphenylmethane dye binding site. Size exclusion chromatography, SDS-PAGE, and X-ray crystallographic studies demonstrate that these mutations do not impact the structure or assembly of the triangular trimer. Fluorescence spectroscopy and analytical ultracentrifugation experiments reveal that the dye packs against an aromatic surface formed by the Phe20 side chains and is clasped by the Ile31 side chains. Docking and molecular modeling provide a working model of the complex in which the triphenylmethane dye is sandwiched between two triangular trimers. Collectively, these findings demonstrate that the X-ray crystallographic structures of triangular trimers derived from Aβ can be used to guide the discovery of ligands that bind to soluble oligomers derived from Aβ.
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Affiliation(s)
- Patrick J Salveson
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Sepehr Haerianardakani
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Alexander Thuy-Boun
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Stan Yoo
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Adam G Kreutzer
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Borries Demeler
- Department of Biochemistry , University of Texas Health Science Center , San Antonio , Texas 78229-3900 , United States
| | - James S Nowick
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
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8
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Creasey RCG, Louzao I, Arnon ZA, Marco P, Adler-Abramovich L, Roberts CJ, Gazit E, Tendler SJB. Disruption of diphenylalanine assembly by a Boc-modified variant. SOFT MATTER 2016; 12:9451-9457. [PMID: 27841428 DOI: 10.1039/c6sm01770c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Peptide-based biomaterials are key to the future of diagnostics and therapy, promoting applications such as tissue scaffolds and drug delivery vehicles. To realise the full potential of the peptide systems, control and optimisation of material properties are essential. Here we investigated the co-assembly of the minimal amyloid motif peptide, diphenylalanine (FF), and its tert-butoxycarbonyl (Boc)-modified derivative. Using Atomic Force Microscopy, we demonstrated that the co-assembled fibers are less rigid and show a curvier morphology. We propose that the Boc-modification of FF disrupts the hydrogen bond packing of adjacent N-termini, as supported by Fourier transform infrared and fluorescence spectroscopic data. Such rationally modified co-assemblies offer chemical functionality for after-assembly modification and controllable surface properties for tissue engineering scaffolds, along with tunable morphological vs. mechanical properties.
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Affiliation(s)
| | - Iria Louzao
- School of Pharmacy, University of Nottingham, NG7 2RD Nottingham, UK
| | - Zohar A Arnon
- Department for Molecular Microbiology and Biotechnology, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Pini Marco
- Department for Molecular Microbiology and Biotechnology, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Clive J Roberts
- School of Pharmacy, University of Nottingham, NG7 2RD Nottingham, UK
| | - Ehud Gazit
- Department for Molecular Microbiology and Biotechnology, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Saul J B Tendler
- School of Pharmacy, University of Nottingham, NG7 2RD Nottingham, UK
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9
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Mishra NK, Krishna Deepak RNV, Sankararamakrishnan R, Verma S. Controlling in Vitro Insulin Amyloidosis with Stable Peptide Conjugates: A Combined Experimental and Computational Study. J Phys Chem B 2015; 119:15395-406. [DOI: 10.1021/acs.jpcb.5b08215] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Narendra Kumar Mishra
- Department of Chemistry, DST Thematic
Unit of Excellence on Soft
Nanofabrication and ‡Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 Uttar Pradesh, India
| | - R. N. V. Krishna Deepak
- Department of Chemistry, DST Thematic
Unit of Excellence on Soft
Nanofabrication and ‡Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 Uttar Pradesh, India
| | - Ramasubbu Sankararamakrishnan
- Department of Chemistry, DST Thematic
Unit of Excellence on Soft
Nanofabrication and ‡Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 Uttar Pradesh, India
| | - Sandeep Verma
- Department of Chemistry, DST Thematic
Unit of Excellence on Soft
Nanofabrication and ‡Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 Uttar Pradesh, India
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10
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Berthoumieu O, Nguyen PH, Castillo-Frias MPD, Ferre S, Tarus B, Nasica-Labouze J, Noël S, Saurel O, Rampon C, Doig AJ, Derreumaux P, Faller P. Combined experimental and simulation studies suggest a revised mode of action of the anti-Alzheimer disease drug NQ-Trp. Chemistry 2015; 21:12657-66. [PMID: 26179053 DOI: 10.1002/chem.201500888] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Indexed: 11/09/2022]
Abstract
Inhibition of the aggregation of the monomeric peptide β-amyloid (Aβ) into oligomers is a widely studied therapeutic approach in Alzheimer's disease (AD). Many small molecules have been reported to work in this way, including 1,4-naphthoquinon-2-yl-L-tryptophan (NQ-Trp). NQ-Trp has been reported to inhibit aggregation, to rescue cells from Aβ toxicity, and showed complete phenotypic recovery in an in vivo AD model. In this work we investigated its molecular mechanism by using a combined approach of experimental and theoretical studies, and obtained converging results. NQ-Trp is a relatively weak inhibitor and the fluorescence data obtained by employing the fluorophore widely used to monitor aggregation into fibrils can be misinterpreted due to the inner filter effect. Simulations and NMR experiments showed that NQ-Trp has no specific "binding site"-type interaction with mono- and dimeric Aβ, which could explain its low inhibitory efficiency. This suggests that the reported anti-AD activity of NQ-Trp-type molecules in in vivo models has to involve another mechanism. This study has revealed the potential pitfalls in the development of aggregation inhibitors for amyloidogenic peptides, which are of general interest for all the molecules studied in the context of inhibiting the formation of toxic aggregates.
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Affiliation(s)
- Olivia Berthoumieu
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4 (France) and Université de Toulouse, UPS, INPT, 31077 Toulouse Cedex 4 (France)
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)
| | - Maria P Del Castillo-Frias
- Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK)
| | - Sabrina Ferre
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4 (France) and Université de Toulouse, UPS, INPT, 31077 Toulouse Cedex 4 (France)
| | - Bogdan Tarus
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)
| | - Jessica Nasica-Labouze
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)
| | - Sabrina Noël
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4 (France) and Université de Toulouse, UPS, INPT, 31077 Toulouse Cedex 4 (France)
| | - Olivier Saurel
- IPBS Institute of Pharmacology and Structural Biology, Université de Toulouse, UPS, 205 route de Narbonne, 31077 Toulouse (France).,IPBS, UMR 5089, CNRS, 205 route de Narbonne, BP 64182, 31077 Toulouse (France)
| | - Claire Rampon
- Université de Toulouse, UPS, CNRS, Centre de Recherches sur la Cognition, Animale, 118 route de Narbonne, 31062 Toulouse Cedex 4 (France)
| | - Andrew J Doig
- Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN (UK).
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France). .,Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris (France).
| | - Peter Faller
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4 (France) and Université de Toulouse, UPS, INPT, 31077 Toulouse Cedex 4 (France).
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11
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Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015; 115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 473] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Sébastien Coté
- ∥Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3T5, Canada
| | - Alfonso De Simone
- ⊥Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrew J Doig
- #Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Faller
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Alessandro Laio
- ○The International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Mai Suan Li
- ◆Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.,¶Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Simone Melchionna
- ⬠Instituto Processi Chimico-Fisici, CNR-IPCF, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | | | - Yuguang Mu
- ▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anant Paravastu
- ⊕National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuela Pasquali
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | - Birgit Strodel
- △Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bogdan Tarus
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - John H Viles
- ▼School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Tong Zhang
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,□Institut Universitaire de France, 75005 Paris, France
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Rajasekhar K, Chakrabarti M, Govindaraju T. Function and toxicity of amyloid beta and recent therapeutic interventions targeting amyloid beta in Alzheimer's disease. Chem Commun (Camb) 2015; 51:13434-50. [DOI: 10.1039/c5cc05264e] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Our Feature Article details the physiological role of amyloid beta (Aβ), elaborates its toxic effects and outlines therapeutic molecules designed in the last two years targeting different aspects of Aβ for preventing AD.
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Affiliation(s)
- K. Rajasekhar
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Malabika Chakrabarti
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - T. Govindaraju
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
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13
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Domínguez JL, Fernández-Nieto F, Castro M, Catto M, Paleo MR, Porto S, Sardina FJ, Brea JM, Carotti A, Villaverde MC, Sussman F. Computer-aided structure-based design of multitarget leads for Alzheimer's disease. J Chem Inf Model 2014; 55:135-48. [PMID: 25483751 DOI: 10.1021/ci500555g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease is a neurodegenerative pathology with unmet clinical needs. A highly desirable approach to this syndrome would be to find a single lead that could bind to some or all of the selected biomolecules that participate in the amyloid cascade, the most accepted route for Alzheimer disease genesis. In order to circumvent the challenge posed by the sizable differences in the binding sites of the molecular targets, we propose a computer-assisted protocol based on a pharmacophore and a set of required interactions with the targets that allows for the automated screening of candidates. We used a combination of docking and molecular dynamics protocols in order to discard nonbinders, optimize the best candidates, and provide a rationale for their potential as inhibitors. To provide a proof of concept, we proceeded to screen the literature and databases, a task that allowed us to identify a set of carbazole-containing compounds that initially showed affinity only for the cholinergic targets in our experimental assays. Two cycles of design based on our protocol led to a new set of analogues that were synthesized and assayed. The assay results revealed that the designed inhibitors had improved affinities for BACE-1 by more than 3 orders of magnitude and also displayed amyloid aggregation inhibition and affinity for AChE and BuChE, a result that led us to a group of multitarget amyloid cascade inhibitors that also could have a positive effect at the cholinergic level.
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Affiliation(s)
- José L Domínguez
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela , 15782 Santiago de Compostela, Spain
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Tarus B, Nguyen PH, Berthoumieu O, Faller P, Doig AJ, Derreumaux P. Molecular structure of the NQTrp inhibitor with the Alzheimer Aβ1-28 monomer. Eur J Med Chem 2014; 91:43-50. [PMID: 25011560 DOI: 10.1016/j.ejmech.2014.07.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/19/2014] [Accepted: 07/01/2014] [Indexed: 01/28/2023]
Abstract
The self-assembly of the amyloid-β (Aβ) peptide of various amino acid lengths into senile plaques is one hallmark of Alzheimer's disease pathology. In the past decade, many small molecules, including NQTrp, have been identified to reduce aggregation and toxicity. However, due to the heterogeneity of the conformational ensemble of Aβ with drugs, we lack detailed structures of the transient complexes. Following our previous simulation of the monomer of Aβ1-28, here we characterize the equilibrium ensemble of the Aβ1-28 monomer with NQTrp by means of extensive atomistic replica exchange molecular dynamics simulations using a force field known to fold diverse proteins correctly. While the secondary structure content and the intrinsic disorder of the whole peptides are very similar and the lifetimes of the salt-bridges remain constant, the population of β-hairpin is reduced by a factor of 1.5 and the population of α-helix in the region 17-24 is increased by a factor of two upon NQTrp binding. These two factors, which impact the free energy barrier for nucleation, provide a first explanation for the reported reduced Aβ1-40/1-42 aggregation kinetics in the presence of NQTrp. Backbone and side-chain interactions of Aβ with NQTrp may also inhibit Aβ-Aβ contacts. The fraction of free Aβ1-28 monomer is, however, on the order of 20-25% at 17.5 mM, and this shows that the affinity of NQTrp is low and hence its inhibitory activity is not very strong. This inhibitor can be improved to reduce the formation of dimer, a critical step in aggregation and toxicity.
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Affiliation(s)
- Bogdan Tarus
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 Route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France; Université de Toulouse, UPS, INPT, F-31077 Toulouse Cedex 4, France
| | - Peter Faller
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 Route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France; Université de Toulouse, UPS, INPT, F-31077 Toulouse Cedex 4, France
| | - Andrew J Doig
- Manchester Institute of Biotechnology, Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France; Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris, France.
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Zhang T, Xu W, Mu Y, Derreumaux P. Atomic and dynamic insights into the beneficial effect of the 1,4-naphthoquinon-2-yl-L-tryptophan inhibitor on Alzheimer's Aβ1-42 dimer in terms of aggregation and toxicity. ACS Chem Neurosci 2014; 5:148-59. [PMID: 24246047 DOI: 10.1021/cn400197x] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Aggregation of the amyloid β protein (Aβ) peptide with 40 or 42 residues is one key feature in Alzheimer's disease (AD). The 1,4-naphthoquinon-2-yl-L-tryptophan (NQTrp) molecule was reported to alter Aβ self-assembly and reduce toxicity. Though nuclear magnetic resonance experiments and various simulations provided atomic information about the interaction of NQTrp with Aβ peptides spanning the regions of residues 12-28 and 17-42, none of these studies were conducted on the full-length Aβ1-42 peptide. To this end, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1-42 dimer with two NQTrp molecules in explicit solvent, by using a force field known to fold diverse proteins correctly. The interactions between NQTrp and Aβ1-42, which change the Aβ interface by reducing most of the intermolecular contacts, are found to be very dynamic and multiple, leading to many transient binding sites. The most favorable binding residues are Arg5, Asp7, Tyr10, His13, Lys16, Lys18, Phe19/Phe20, and Leu34/Met35, providing therefore a completely different picture from in vitro and in silico experiments with NQTrp with shorter Aβ fragments. Importantly, the 10 hot residues that we identified explain the beneficial effect of NQTrp in reducing both the level of Aβ1-42 aggregation and toxicity. Our results also indicate that there is room to design more efficient drugs targeting Aβ1-42 dimer against AD.
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Affiliation(s)
- Tong Zhang
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Weixin Xu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- State Key Laboratory of Precision Spectroscopy, Department
of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
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Nguyen P, Derreumaux P. Understanding amyloid fibril nucleation and aβ oligomer/drug interactions from computer simulations. Acc Chem Res 2014; 47:603-11. [PMID: 24368046 DOI: 10.1021/ar4002075] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Evolution has fine-tuned proteins to accomplish a variety of tasks. Yet, with aging, some proteins assemble into harmful amyloid aggregates associated with neurodegenerative diseases, such as Alzheimer's disease (AD), which presents a complex and costly challenge to our society. Thus, far, drug after drug has failed to slow the progression of AD, characterized by the self-assembly of the 39-43 amino acid β-amyloid (Aβ) protein into extracellular senile plaques that form a cross-β structure. While there is experimental evidence that the Aβ small oligomers are the primary toxic species, standard tools of biology have failed to provide structures of these transient, inhomogeneous assemblies. Despite extensive experimental studies, researchers have not successfully characterized the nucleus ensemble, the starting point for rapid fibril formation. Similarly scientists do not have atomic data to show how the compounds that reduce both fibril formation and toxicity in cells bind to Aβ42 oligomers. In this context, computer simulations are important tools for gaining insights into the self-assembly of amyloid peptides and the molecular mechanism of inhibitors. This Account reviews what analytical models and simulations at different time and length scales tell us about the dynamics, kinetics, and thermodynamics of amyloid fibril formation and, notably, the nucleation process. Though coarse-grained and mesoscopic protein models approximate atomistic details by averaging out unimportant degrees of freedom, they provide generic features of amyloid formation and insights into mechanistic details of the self-assembly process. The thermodynamics and kinetics vary from linear peptides adopting straight β-strands in fibrils to longer peptides adopting in parallel U shaped conformations in fibrils. In addition, these properties change with the balance between electrostatic and hydrophobic interactions and the intrinsic disorder of the system. However, simulations suggest that the critical nucleus size might be on the order of 20 chains under physiological conditions. The transition state might be characterized by a simultaneous change from mixed antiparallel/parallel β-strands with random side-chain packing to the final antiparallel or parallel states with the steric zipper packing of the side chains. Second, we review our current computer-based knowledge of the 3D structures of inhibitors with Aβ42 monomer and oligomers, a prerequisite for developing new drugs against AD. Recent extensive all-atom simulations of Aβ42 dimers with known inhibitors such as the green tea compound epigallocatechin-3-gallate and 1,4-naphthoquinon-2-yl-l-tryptophan provide a spectrum of initial Aβ42/inhibitor structures useful for screening and drug design. We conclude by discussing future directions that may offer opportunities to fully understand nucleation and further AD drug development.
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Affiliation(s)
- Phuong Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris, France
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