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Zhou S, Zou H, Wang Y, Lo GV, Yuan S. Atomic Mechanisms of Transthyretin Tetramer Dissociation Studied by Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:6667-6678. [PMID: 35993568 DOI: 10.1021/acs.jcim.2c00447] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The dissociation of the transthyretin (TTR) tetramer into a monomer is closely related to various TTR amyloidoses in humans. While the tetramer dissociation has been reported to be the rate-limiting step for TTR aggregation, few details are known about the mechanism. Here, molecular dynamics (MD) simulations were performed by combining conventional MD and biased metadynamics to investigate the mechanism for the wild-type (WT) and mutant (T119M) structures. Both were found to have a great deal in common. Conventional MD simulations reveal that interfacial hydrophobic interactions contribute significantly to stabilize the tetramer. Interfacial residues including L17, V20, L110, and V121 with close contacts form a hydrophobic channel. Metadynamics simulations indicate that the mouth opening of the hydrophobic channel is the first and the most difficult step for dissociation. Interactions of V20 between opposing dimers lock four monomers into the tetramer, and disruption of the interactions is found to be involved in the final step. During the dissociation, an increasing extent of solvation was observed by calculating the radial distribution functions of water around interfacial hydrophobic residues, suggesting that water plays a role in driving the tetramer dissociation. Moreover, compared to T119, residue M119 has a longer side chain that extends into the hydrophobic channel, making solvation more difficult, consistent with a higher energy barrier for dissociation of the T119M tetramer. This result provides a good explanation for the protective role of the T119M mutation. Overall, this study can provide atomic-level insights to better understand the pathogenesis of TTR amyloidosis and guide rational drug design in the future.
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Affiliation(s)
- Shuangyan Zhou
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Huizhen Zou
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yu Wang
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Glenn V Lo
- Department of Chemistry and Physical Sciences, Nicholls State University, P.O. Box 2022, Thibodaux, Louisiana 70310, United States
| | - Shuai Yuan
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
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2
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The discovery and development of transthyretin amyloidogenesis inhibitors: what are the lessons? Future Med Chem 2021; 13:2083-2105. [PMID: 34633220 DOI: 10.4155/fmc-2021-0248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Transthyretin (TTR) is associated with several human amyloid diseases. Various kinetic stabilizers have been developed to inhibit the dissociation of TTR tetramer and the formation of amyloid fibrils. Most of them are bisaryl derivatives, natural flavonoids, crown ethers and carborans. In this review article, we focus on TTR tetramer stabilizers, genetic therapeutic approaches and fibril remodelers. The binding modes of typical bisaryl derivatives, natural flavonoids, crown ethers and carborans are discussed. Based on knowledge of the binding of thyroxine to TTR tetramer, many stabilizers have been screened to dock into the thyroxine binding sites, leading to TTR tetramer stabilization. Particularly, those stabilizers with unique binding profiles have shown great potential in developing the therapeutic management of TTR amyloidogenesis.
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3
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Ciccone L, Tonali N, Nencetti S, Orlandini E. Natural compounds as inhibitors of transthyretin amyloidosis and neuroprotective agents: analysis of structural data for future drug design. J Enzyme Inhib Med Chem 2020; 35:1145-1162. [PMID: 32419519 PMCID: PMC7301710 DOI: 10.1080/14756366.2020.1760262] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
Natural compounds, such as plant and fruit extracts have shown neuroprotective effect against neurodegenerative diseases. It has been reported that several natural compounds binding to transthyretin (TTR) can be useful in amyloidosis prevention. TTR is a transporter protein that under physiological condition carries thyroxine (T4) and retinol in plasma and in cerebrospinal fluid (CSF); it also has a neuroprotective role against Alzheimer's disease (AD). However, TTR also is an amyloidogenic protein responsible for familial amyloid polyneuropathy (FAP) and familial amyloid cardiomyopathy (FAC). The TTR amyloidogenic potential is speeded up by several point mutations. One therapeutic strategy against TTR amyloidosis is the stabilisation of the native tetramer by natural compounds and small molecules. In this review, we examine the natural products that, starting from 2012 to present, have been studied as a stabiliser of TTR tetramer. In particular, we discussed the chemical and structural features which will be helpful for future drug design of new TTR stabilisers.
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Affiliation(s)
- Lidia Ciccone
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Nicoló Tonali
- CNRS, Université Paris-Saclay, Châtenay-Malabry, France
| | - Susanna Nencetti
- Department of Pharmacy, University of Pisa, Pisa, Italy
- Interdepartmental Research Centre “Nutraceuticals and Food for Health (NUTRAFOOD), University of Pisa, Pisa, Italy
| | - Elisabetta Orlandini
- Department of Earth Sciences, University of Pisa, Pisa, Italy
- Research Center “E. Piaggio”, University of Pisa, Pisa, Italy
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4
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Bruder M, Polo G, Trivella DBB. Natural allosteric modulators and their biological targets: molecular signatures and mechanisms. Nat Prod Rep 2020; 37:488-514. [PMID: 32048675 DOI: 10.1039/c9np00064j] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2008 to 2018Over the last decade more than two hundred single natural products were confirmed as natural allosteric modulators (alloNPs) of proteins. The compounds are presented and discussed with the support of a chemical space, constructed using a principal component analysis (PCA) of molecular descriptors from chemical compounds of distinct databases. This analysis showed that alloNPs are dispersed throughout the majority of the chemical space defined by natural products in general. Moreover, a cluster of alloNPs was shown to occupy a region almost devoid of allosteric modulators retrieved from a dataset composed mainly of synthetic compounds, further highlighting the importance to explore the entire natural chemical space for probing allosteric mechanisms. The protein targets which alloNPs bind to comprised 81 different proteins, which were classified into 5 major groups, with enzymes, in particular hydrolases, being the main representative group. The review also brings a critical interpretation on the mechanisms by which alloNPs display their molecular action on proteins. In the latter analysis, alloNPs were classified according to their final effect on the target protein, resulting in 3 major categories: (i) local alteration of the orthosteric site; (ii) global alteration in protein dynamics that change function; and (iii) oligomer stabilisation or protein complex destabilisation via protein-protein interaction in sites distant from the orthosteric site. G-protein coupled receptors (GPCRs), which use a combination of the three types of allosteric regulation found, were also probed by natural products. In summary, the natural allosteric modulators reviewed herein emphasise their importance for exploring alternative chemotherapeutic strategies, potentially pushing the boundaries of the druggable space of pharmacologically relevant drug targets.
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Affiliation(s)
- Marjorie Bruder
- Brazilian Biosciences National Laboratory (LNBio), National Centre for Research in Energy and Materials (CNPEM), 13083-970 Campinas, SP, Brazil.
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5
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Zapadka KL, Becher FJ, Gomes Dos Santos AL, Jackson SE. Factors affecting the physical stability (aggregation) of peptide therapeutics. Interface Focus 2017; 7:20170030. [PMID: 29147559 DOI: 10.1098/rsfs.2017.0030] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The number of biological therapeutic agents in the clinic and development pipeline has increased dramatically over the last decade and the number will undoubtedly continue to increase in the coming years. Despite this fact, there are considerable challenges in the development, production and formulation of such biologics particularly with respect to their physical stabilities. There are many cases where self-association to form either amorphous aggregates or highly structured fibrillar species limits their use. Here, we review the numerous factors that influence the physical stability of peptides including both intrinsic and external factors, wherever possible illustrating these with examples that are of therapeutic interest. The effects of sequence, concentration, pH, net charge, excipients, chemical degradation and modification, surfaces and interfaces, and impurities are all discussed. In addition, the effects of physical parameters such as pressure, temperature, agitation and lyophilization are described. We provide an overview of the structures of aggregates formed, as well as our current knowledge of the mechanisms for their formation.
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Affiliation(s)
| | - Frederik J Becher
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | | | - Sophie E Jackson
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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6
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Saldaño TE, Zanotti G, Parisi G, Fernandez-Alberti S. Evaluating the effect of mutations and ligand binding on transthyretin homotetramer dynamics. PLoS One 2017; 12:e0181019. [PMID: 28704493 PMCID: PMC5509292 DOI: 10.1371/journal.pone.0181019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/23/2017] [Indexed: 01/08/2023] Open
Abstract
Native transthyretin (TTR) homotetramer dissociation is the first step of the fibrils formation process in amyloid disease. A large number of specific point mutations that destabilize TTR quaternary structure have shown pro-amyloidogenic effects. Besides, several compounds have been proposed as drugs in the therapy of TTR amyloidosis due to their TTR tetramer binding affinities, and therefore, contribution to its integrity. In the present paper we have explored key positions sustaining TTR tetramer dynamical stability. We have identified positions whose mutations alter the most the TTR tetramer equilibrium dynamics based on normal mode analysis and their response to local perturbations. We have found that these positions are mostly localized at β-strands E and F and EF-loop. The monomer-monomer interface is pointed out as one of the most vulnerable regions to mutations that lead to significant changes in the TTR-tetramer equilibrium dynamics and, therefore, induces TTR amyloidosis. Besides, we have found that mutations on residues localized at the dimer-dimer interface and/or at the T4 hormone binding site destabilize the tetramer more than the average. Finally, we were able to compare several compounds according to their effect on vibrations associated to the ligand binding. Our ligand comparison is discussed and analyzed in terms of parameters and measurements associated to TTR-ligand binding affinities and the stabilization of its native state.
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Affiliation(s)
| | - Giuseppe Zanotti
- Department of Biomedical Science, University of Padua, Padova, Italy
| | - Gustavo Parisi
- Universidad Nacional de Quilmes/CONICET, Bernal, Argentina
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7
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Vimal A, Kumar A. The morpheein model of allosterism: a remedial step for targeting virulent l -asparaginase. Drug Discov Today 2017; 22:814-822. [DOI: 10.1016/j.drudis.2016.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/02/2016] [Accepted: 10/03/2016] [Indexed: 11/15/2022]
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8
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Lim KH, Dasari AKR, Hung I, Gan Z, Kelly JW, Wright PE, Wemmer DE. Solid-State NMR Studies Reveal Native-like β-Sheet Structures in Transthyretin Amyloid. Biochemistry 2016; 55:5272-8. [PMID: 27589034 DOI: 10.1021/acs.biochem.6b00649] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range (13)C-(13)C correlation MAS spectra obtained with selectively (13)CO- and (13)Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid.
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Affiliation(s)
- Kwang Hun Lim
- Department of Chemistry, East Carolina University , Greenville, North Carolina 27858, United States
| | - Anvesh K R Dasari
- Department of Chemistry, East Carolina University , Greenville, North Carolina 27858, United States
| | - Ivan Hung
- Center of Interdisciplinary Magnetic Resonance (CIMAR), National High Magnetic Field Laboratory (NHMFL) , 1800 East, Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Zhehong Gan
- Center of Interdisciplinary Magnetic Resonance (CIMAR), National High Magnetic Field Laboratory (NHMFL) , 1800 East, Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | | | | | - David E Wemmer
- Department of Chemistry, University of California , Berkeley, California 94720, United States
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9
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Baranczak A, Connelly S, Liu Y, Choi S, Grimster NP, Powers ET, Wilson IA, Kelly JW. Fluorogenic small molecules requiring reaction with a specific protein to create a fluorescent conjugate for biological imaging--what we know and what we need to learn. Biopolymers 2016; 101:484-95. [PMID: 24105107 DOI: 10.1002/bip.22407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/03/2013] [Indexed: 01/03/2023]
Abstract
We seek fluorogenic small molecules that generate a fluorescent conjugate signal if and only if they react with a given protein-of-interest (i.e., small molecules for which noncovalent binding to the protein-of-interest is insufficient to generate fluorescence). Consequently, it is the new chemical entity afforded by the generally irreversible reaction between the small molecule and the protein-of-interest that enables the energy of an electron occupying the lowest unoccupied molecular orbital (LUMO) of the chromophore to be given off as a photon instead of being dissipated by nonradiative mechanisms in complex biological environments. This category of fluorogenic small molecules is created by starting with environmentally sensitive fluorophores that are modified by an essential functional group that efficiently quenches the fluorescence until a chemoselective reaction between that functional group and the protein-of-interest occurs, yielding the fluorescent conjugate. Fluorogenic small molecules are envisioned to be useful for a wide variety of applications, including live cell imaging without the requirement for washing steps and pulse-chase kinetic analyses of protein synthesis, trafficking, degradation, etc.
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Affiliation(s)
- Aleksandra Baranczak
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, 92037
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10
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Ciccone L, Nencetti S, Rossello A, Stura EA, Orlandini E. Synthesis and structural analysis of halogen substituted fibril formation inhibitors of Human Transthyretin (TTR). J Enzyme Inhib Med Chem 2016; 31:40-51. [PMID: 27067161 DOI: 10.3109/14756366.2016.1167048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Transthyretin (TTR), a β-sheet-rich tetrameric protein, in equilibrium with an unstable amyloidogenic monomeric form is responsible for extracellular deposition of amyloid fibrils, is associated with the onset of neurodegenerative diseases, such as senile systemic amyloidosis, familial amyloid polyneuropathy and familial amyloid cardiomyopathy. One of the therapeutic strategies is to use small molecules to stabilize the TTR tetramer and thus curb amyloid fibril formation. Here, we report the synthesis, the in vitro evaluation of several halogen substituted 9-fluorenyl- and di-benzophenon-based ligands and their three-dimensional crystallographic analysis in complex with TTR. The synthesized compounds bind TTR and stabilize the tetramer with different potency. Of these compounds, 2c is the best inhibitor. The dual binding mode prevalent in the absence of substitutions on the fluorenyl ring, is disfavored by (2,7-dichloro-fluoren-9-ylideneaminooxy)-acetic acid (1b), (2,7-dibromo-fluoren-9-ylideneaminooxy)-acetic acid (1c) and (E/Z)-((3,4-dichloro-phenyl)-methyleneaminooxy)-acetic acid (2c), all with halogen substitutions.
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Affiliation(s)
- Lidia Ciccone
- a Dipartimento di Farmacia , Università di Pisa , Pisa , Italy and.,b CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Gif-sur-Yvette , France
| | - Susanna Nencetti
- a Dipartimento di Farmacia , Università di Pisa , Pisa , Italy and
| | - Armando Rossello
- a Dipartimento di Farmacia , Università di Pisa , Pisa , Italy and
| | - Enrico Adriano Stura
- b CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Gif-sur-Yvette , France
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11
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Polsinelli I, Nencetti S, Shepard W, Ciccone L, Orlandini E, Stura EA. A new crystal form of human transthyretin obtained with a curcumin derived ligand. J Struct Biol 2016; 194:8-17. [PMID: 26796656 DOI: 10.1016/j.jsb.2016.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/14/2016] [Accepted: 01/16/2016] [Indexed: 12/18/2022]
Abstract
Transthyretin (TTR), a 54kDa homotetrameric protein that transports thyroxine (T4), has been associated with clinical cases of TTR amyloidosis for its tendency to aggregate to form fibrils. Many ligands with a potential to inhibit fibril formation have been studied by X-ray crystallography in complex with TTR. Unfortunately, the ligand is often found in ambiguous electron density that is difficult to interpret. The ligand validation statistics suggest over-interpretation, even for the most active compounds like diflunisal. The primary technical reason is its position on a crystallographic 2-fold axis in the most common crystal form. Further investigations with the use of polyethylene glycol (PEG) to crystallize TTR complexes have resulted in a new trigonal polymorph with two tetramers in the asymmetric unit. The ligand used to obtain this new polymorph, 4-hydroxychalcone, is related to curcumin. Here we evaluate this crystal form to understand the contribution it may bring to the study of TTR ligands complexes, which are often asymmetric.
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Affiliation(s)
- Ivan Polsinelli
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France; Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Susanna Nencetti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - William Shepard
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Lidia Ciccone
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | - Enrico A Stura
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France; CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Gif-sur-Yvette F-91191, France.
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12
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Callies O, Hernández Daranas A. Application of isothermal titration calorimetry as a tool to study natural product interactions. Nat Prod Rep 2016; 33:881-904. [DOI: 10.1039/c5np00094g] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of molecular interactions of natural products by isothermal titration calorimetry (ITC) is a potent tool to get new insights of the underpinning driving forces.
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Affiliation(s)
- O. Callies
- Institute of Bioorganic Chemistry “Antonio González”
- Center for Biomedical Research of the Canary Islands
- University of La Laguna
- 38206 La Laguna
- Spain
| | - A. Hernández Daranas
- Institute of Bioorganic Chemistry “Antonio González”
- Center for Biomedical Research of the Canary Islands
- University of La Laguna
- 38206 La Laguna
- Spain
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13
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Florio P, Folli C, Cianci M, Del Rio D, Zanotti G, Berni R. Transthyretin Binding Heterogeneity and Anti-amyloidogenic Activity of Natural Polyphenols and Their Metabolites. J Biol Chem 2015; 290:29769-80. [PMID: 26468275 DOI: 10.1074/jbc.m115.690172] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Indexed: 12/11/2022] Open
Abstract
Transthyretin (TTR) is an amyloidogenic protein, the amyloidogenic potential of which is enhanced by a number of specific point mutations. The ability to inhibit TTR fibrillogenesis is known for several classes of compounds, including natural polyphenols, which protect the native state of TTR by specifically interacting with its thyroxine binding sites. Comparative analyses of the interaction and of the ability to protect the TTR native state for polyphenols, both stilbenoids and flavonoids, and some of their main metabolites have been carried out. A main finding of this investigation was the highly preferential binding of resveratrol and thyroxine, both characterized by negative binding cooperativity, to distinct sites in TTR, consistent with the data of x-ray analysis of TTR in complex with both ligands. Although revealing the ability of the two thyroxine binding sites of TTR to discriminate between different ligands, this feature has allowed us to evaluate the interactions of polyphenols with both resveratrol and thyroxine preferential binding sites, by using resveratrol and radiolabeled T4 as probes. Among flavonoids, genistein and apigenin were able to effectively displace resveratrol from its preferential binding site, whereas genistein also showed the ability to interact, albeit weakly, with the preferential thyroxine binding site. Several glucuronidated polyphenol metabolites did not exhibit significant competition for resveratrol and thyroxine preferential binding sites and lacked the ability to stabilize TTR. However, resveratrol-3-O-sulfate was able to significantly protect the protein native state. A rationale for the in vitro properties found for polyphenol metabolites was provided by x-ray analysis of their complexes with TTR.
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Affiliation(s)
- Paola Florio
- From the Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Claudia Folli
- the Department of Food Science, University of Parma, 43124 Parma, Italy
| | - Michele Cianci
- the European Molecular Biology Laboratory, 22607 Hamburg, Germany, and
| | - Daniele Del Rio
- the Department of Food Science, University of Parma, 43124 Parma, Italy
| | - Giuseppe Zanotti
- the Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Rodolfo Berni
- From the Department of Life Sciences, University of Parma, 43124 Parma, Italy,
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14
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Discovery of γ-Mangostin as an Amyloidogenesis Inhibitor. Sci Rep 2015; 5:13570. [PMID: 26310724 PMCID: PMC4550876 DOI: 10.1038/srep13570] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/30/2015] [Indexed: 11/30/2022] Open
Abstract
Transthyretin (TTR) is a homotetrameric protein involved in human hereditary amyloidoses. The discovery and development of small molecules that inhibit the amyloid fibril formation of TTR is one of the therapeutic strategies for these diseases. Herein, we discovered that γ-mangostin (γ-M) is an effective inhibitor against the amyloid fibril formation of V30M amyloidogenic TTR. In-vitro binding assays revealed that γ-M was the most potent of the selected xanthone derivatives, and it bound to the thyroxine (T4)-binding sites and stabilized the TTR tetramer. X-ray crystallographic analysis revealed the diagonal binding mode of γ-M and the two binding sites of chloride ions at the T4-binding site. One of the chloride ions was replaced with a water molecule in the α-mangostin complex, which is a methylated derivative of γ-M. The stronger inhibitory potency of γ-M could be explained by the additional hydrogen bonds with the chloride ion. The present study establishes γ-M as a novel inhibitor of TTR fibrillization.
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15
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Ciccone L, Nencetti S, Rossello A, Tepshi L, Stura EA, Orlandini E. X-ray crystal structure and activity of fluorenyl-based compounds as transthyretin fibrillogenesis inhibitors. J Enzyme Inhib Med Chem 2015; 31:824-33. [PMID: 26235916 DOI: 10.3109/14756366.2015.1070265] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Transthyretin (TTR) is a 54 kDa homotetrameric protein that transports thyroxine (T4) and retinol (vitamin A), through its association with retinol binding protein (RBP). Under unknown conditions, it aggregates to form fibrils associated with TTR amyloidosis. Ligands able to inhibit fibril formation have been studied by X-ray crystallography. The use of polyethylene glycol (PEG) instead of ammonium sulphate or citrate has been evaluated as an alternative to obtain new TTR complexes with (R)-3-(9-fluoren-9-ylideneaminooxy)-2-methyl-N-(methylsulfonyl) propionamide (48R(1)) and 2-(9H-fluoren-9-ylideneaminooxy) acetic acid (ES8(2)). The previously described fluorenyl based inhibitors (S)-3-((9H-fluoren-9-ylideneamino)oxy)-2-methylpropanoic acid (6BD) and 3-((9H-fluoren-9-ylideneamino)oxy)propanoic acid (7BD) have been re-evaluated with the changed crystallization method. The new TTR complexes with compounds of the same family show that the 9-fluorenyl motif can occupy alternative hydrophobic binding sites. This augments the potential use of this scaffold to yield a large variety of differently substituted mono-aryl compounds able to inhibit TTR fibril formation.
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Affiliation(s)
- Lidia Ciccone
- a CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Gif-sur-Yvette , France and.,b Dipartimento di Farmacia , Università di Pisa , Pisa , Italy
| | | | | | - Livia Tepshi
- a CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Gif-sur-Yvette , France and.,b Dipartimento di Farmacia , Università di Pisa , Pisa , Italy
| | - Enrico A Stura
- a CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Gif-sur-Yvette , France and
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Cianci M, Folli C, Zonta F, Florio P, Berni R, Zanotti G. Structural evidence for asymmetric ligand binding to transthyretin. ACTA ACUST UNITED AC 2015; 71:1582-92. [DOI: 10.1107/s1399004715010585] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 06/01/2015] [Indexed: 12/22/2022]
Abstract
Human transthyretin (TTR) represents a notable example of an amyloidogenic protein, and several compounds that are able to stabilize its native state have been proposed as effective drugs in the therapy of TTR amyloidosis. The two thyroxine (T4) binding sites present in the TTR tetramer display negative binding cooperativity. Here, structures of TTR in complex with three natural polyphenols (pterostilbene, quercetin and apigenin) have been determined, in which this asymmetry manifests itself as the presence of a main binding site with clear ligand occupancy and related electron density and a second minor site with a much lower ligand occupancy. The results of an analysis of the structural differences between the two binding sites are consistent with such a binding asymmetry. The different ability of TTR ligands to saturate the two T4 binding sites of the tetrameric protein can be ascribed to the different affinity of ligands for the weaker binding site. In comparison, the high-affinity ligand tafamidis, co-crystallized under the same experimental conditions, was able to fully saturate the two T4 binding sites. This asymmetry is characterized by the presence of small but significant differences in the conformation of the cavity of the two binding sites. Molecular-dynamics simulations suggest the presence of even larger differences in solution. Competition binding assays carried out in solution revealed the presence of a preferential binding site in TTR for the polyphenols pterostilbene and quercetin that was different from the preferential binding site for T4. The TTR binding asymmetry could possibly be exploited for the therapy of TTR amyloidosis by using a cocktail of two drugs, each of which exhibits preferential binding for a distinct binding site, thus favouring saturation of the tetrameric protein and consequently its stabilization.
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Das JK, Mall SS, Bej A, Mukherjee S. Conformational flexibility tunes the propensity of transthyretin to form fibrils through non-native intermediate states. Angew Chem Int Ed Engl 2014; 53:12781-4. [PMID: 25251500 DOI: 10.1002/anie.201407323] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/29/2014] [Indexed: 12/17/2022]
Abstract
The formation of partially unfolded intermediates through conformational excursions out of the native state is the starting point of many diseases involving protein aggregation. Therapeutic strategies often aim to stabilize the native structure and prevent the formation of intermediates that are also cytotoxic in vivo. However, their transient nature and low population makes it difficult to characterize these intermediates. We have probed the backbone dynamics of transthyretin (TTR) over an extended timescale by using NMR spectroscopy and MD simulations. The location and extent of these motions indicates that the backbone flexibility of TTR is a cause of dissociation and destabilization, both of which are responsible for fibril formation. Importantly, approximately 10 % of wild-type TTR exists in an intermediate state, which increased to up to 28 % for pathogenic TTR mutants, for which the formation of the intermediate state is shown to be energetically more favorable compared to the wild type. This result suggests an important role for the intermediates in TTR amyloidosis.
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Affiliation(s)
- Jitendra K Das
- Structural Biology and Bioinformatics division CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, West Bengal, 700032 (India) https://sites.google.com/site/mukherjeelab/
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Das JK, Mall SS, Bej A, Mukherjee S. Conformational Flexibility Tunes the Propensity of Transthyretin to Form Fibrils Through Non-Native Intermediate States. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Transthyretin complexes with curcumin and bromo-estradiol: evaluation of solubilizing multicomponent mixtures. N Biotechnol 2014; 32:54-64. [PMID: 25224922 DOI: 10.1016/j.nbt.2014.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/05/2014] [Accepted: 09/07/2014] [Indexed: 12/15/2022]
Abstract
Crystallographic structure determination of protein-ligand complexes of transthyretin (TTR) has been hindered by the low affinity of many compounds that bind to the central cavity of the tetramer. Because crystallization trials are carried out at protein and ligand concentration that approach the millimolar range, low affinity is less of a problem than the poor solubility of many compounds that have been shown to inhibit amyloid fibril formation. To achieve complete occupancy in co-crystallization experiments, the minimal requirement is one ligand for each of the two sites within the TTR tetramer. Here we present a new strategy for the co-crystallization of TTR using high molecular weight polyethylene glycol instead of high ionic strength precipitants, with ligands solubilized in multicomponent mixtures of compounds. This strategy is applied to the crystallization of TTR complexes with curcumin and 16α-bromo-estradiol. Here we report the crystal structures with these compounds and with the ferulic acid that results from curcumin degradation.
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Li R, He P, Cui J, Staufenbiel M, Harada N, Shen Y. Brain endogenous estrogen levels determine responses to estrogen replacement therapy via regulation of BACE1 and NEP in female Alzheimer's transgenic mice. Mol Neurobiol 2012. [PMID: 23180279 DOI: 10.1007/s12035-012-8377-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Estrogens have been found to improve memory and reduce risk of dementia, although conflicting results such as failure of estrogen replacement therapy for treatment of Alzheimer's disease (AD) also has been reported. Only recently, our published human brain studies showed a depletion of brain estrogen in women with AD, while other studies have demonstrated cognitive impairment believed to be caused by inhibition of endogenous estrogen synthesis in females. To investigate whether the shortage of brain estrogen alters the sensitivity of response to estrogen replacement therapy, we have used genetic and surgical animal models to examine the response of estrogen treatment in AD neuropathology. Our studies have shown that early treatment with 17β-estradiol (E2) or genistein could reduce brain amyloid levels by increasing Aβ clearance in both APP23 mice with genetic deficiency of aromatase (APP/Ar(+/-)), in which the brains contain nondetectable levels of estrogen, and in APP23 mice with an ovariectomy (APP/OVX), in which the brains still contain certain levels of estrogen. However, only APP/Ar(+/-) mice showed a great reduction in brain amyloid plaque formation after E2 or genistein treatment along with downregulation of β-secretase (BACE1) mRNA and protein expression. Our results suggest that early and long-term usage of E2 and/or genistein may prevent AD pathologies in a dependent manner on endogenous brain estrogen levels in aged females.
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Affiliation(s)
- Rena Li
- Center for Hormone Advanced Science and Education, Roskamp Institute, 2040 Whitfield Ave., Sarasota, FL 34243, USA.
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Ribeiro CA, Saraiva MJ, Cardoso I. Stability of the transthyretin molecule as a key factor in the interaction with a-beta peptide--relevance in Alzheimer's disease. PLoS One 2012; 7:e45368. [PMID: 23028965 PMCID: PMC3444465 DOI: 10.1371/journal.pone.0045368] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 08/21/2012] [Indexed: 11/19/2022] Open
Abstract
Transthyretin (TTR) protects against A-Beta toxicity by binding the peptide thus inhibiting its aggregation. Previous work showed different TTR mutations interact differently with A-Beta, with increasing affinities correlating with decreasing amyloidogenecity of the TTR mutant; this did not impact on the levels of inhibition of A-Beta aggregation, as assessed by transmission electron microscopy. Our work aimed at probing differences in binding to A-Beta by WT, T119M and L55P TTR using quantitative assays, and at identifying factors affecting this interaction. We addressed the impact of such factors in TTR ability to degrade A-Beta. Using a dot blot approach with the anti-oligomeric antibody A11, we showed that A-Beta formed oligomers transiently, indicating aggregation and fibril formation, whereas in the presence of WT and T119M TTR the oligomers persisted longer, indicative that these variants avoided further aggregation into fibrils. In contrast, L55PTTR was not able to inhibit oligomerization or to prevent evolution to aggregates and fibrils. Furthermore, apoptosis assessment showed WT and T119M TTR were able to protect against A-Beta toxicity. Because the amyloidogenic potential of TTR is inversely correlated with its stability, the use of drugs able to stabilize TTR tetrameric fold could result in increased TTR/A-Beta binding. Here we showed that iododiflunisal, 3-dinitrophenol, resveratrol, [2-(3,5-dichlorophenyl)amino] (DCPA) and [4-(3,5-difluorophenyl)] (DFPB) were able to increase TTR binding to A-Beta; however only DCPA and DFPB improved TTR proteolytic activity. Thyroxine, a TTR ligand, did not influence TTR/A-Beta interaction and A-Beta degradation by TTR, whereas RBP, another TTR ligand, not only obstructed the interaction but also inhibited TTR proteolytic activity. Our results showed differences between WT and T119M TTR, and L55PTTR mutant regarding their interaction with A-Beta and prompt the stability of TTR as a key factor in this interaction, which may be relevant in AD pathogenesis and for the design of therapeutic TTR-based therapies.
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Affiliation(s)
- Carlos A. Ribeiro
- Molecular Neurobiology Unit, IBMC- Instituto de Biologia Molecular e Celular, Porto, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, Porto Portugal
| | - Maria João Saraiva
- Molecular Neurobiology Unit, IBMC- Instituto de Biologia Molecular e Celular, Porto, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, Porto Portugal
| | - Isabel Cardoso
- Molecular Neurobiology Unit, IBMC- Instituto de Biologia Molecular e Celular, Porto, Portugal
- Escola Superior de Tecnologia da Saúde do Porto, Instituto Politécnico do Porto, Vila Nova de Gaia, Portugal
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Johnson SM, Connelly S, Fearns C, Powers ET, Kelly JW. The transthyretin amyloidoses: from delineating the molecular mechanism of aggregation linked to pathology to a regulatory-agency-approved drug. J Mol Biol 2012; 421:185-203. [PMID: 22244854 PMCID: PMC3350832 DOI: 10.1016/j.jmb.2011.12.060] [Citation(s) in RCA: 231] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 12/22/2011] [Accepted: 12/29/2011] [Indexed: 12/31/2022]
Abstract
Transthyretin (TTR) is one of the many proteins that are known to misfold and aggregate (i.e., undergo amyloidogenesis) in vivo. The process of TTR amyloidogenesis causes nervous system and/or heart pathology. While several of these maladies are associated with mutations that destabilize the native TTR quaternary and/or tertiary structure, wild-type TTR amyloidogenesis also leads to the degeneration of postmitotic tissue. Over the past 20 years, much has been learned about the factors that influence the propensity of TTR to aggregate. This biophysical information led to the development of a therapeutic strategy, termed "kinetic stabilization," to prevent TTR amyloidogenesis. This strategy afforded the drug tafamidis which was recently approved by the European Medicines Agency for the treatment of TTR familial amyloid polyneuropathy, the most common familial TTR amyloid disease. Tafamidis is the first and currently the only medication approved to treat TTR familial amyloid polyneuropathy. Here we review the biophysical basis for the kinetic stabilization strategy and the structure-based drug design effort that led to this first-in-class pharmacologic agent.
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Affiliation(s)
- Steven M. Johnson
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
| | - Stephen Connelly
- Department of Molecular Biology, La Jolla, California 92037, USA
| | - Colleen Fearns
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Evan T. Powers
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
| | - Jeffery W. Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
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Trivella DBB, dos Reis CV, Lima LMTR, Foguel D, Polikarpov I. Flavonoid interactions with human transthyretin: combined structural and thermodynamic analysis. J Struct Biol 2012; 180:143-53. [PMID: 22842046 DOI: 10.1016/j.jsb.2012.07.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 07/10/2012] [Accepted: 07/16/2012] [Indexed: 11/29/2022]
Abstract
Transthyretin (TTR) is a carrier protein involved in human amyloidosis. The development of small molecules that may act as TTR amyloid inhibitors is a promising strategy to treat these pathologies. Here we selected and characterized the interaction of flavonoids with the wild type and the V30M amyloidogenic mutant TTR. TTR acid aggregation was evaluated in vitro in the presence of the different flavonoids. The best TTR aggregation inhibitors were studied by Isothermal Titration Calorimetry (ITC) in order to reveal their thermodynamic signature of binding to TTRwt. Crystal structures of TTRwt in complex with the top binders were also obtained, enabling us to in depth inspect TTR interactions with these flavonoids. The results indicate that changing the number and position of hydroxyl groups attached to the flavonoid core strongly influence flavonoid recognition by TTR, either by changing ligand affinity or its mechanism of interaction with the two sites of TTR. We also compared the results obtained for TTRwt with the V30M mutant structure in the apo form, allowing us to pinpoint structural features that may facilitate or hamper ligand binding to the V30M mutant. Our data show that the TTRwt binding site is labile and, in particular, the central region of the cavity is sensible for the small differences in the ligands tested and can be influenced by the Met30 amyloidogenic mutation, therefore playing important roles in flavonoid binding affinity, mechanism and mutant protein ligand binding specificities.
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Affiliation(s)
- Daniela B B Trivella
- Instituto de Física de São Carlos, Universidade de São Paulo, 13560-970 São Carlos, SP, Brazil.
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Ghai R, Falconer RJ, Collins BM. Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. J Mol Recognit 2012; 25:32-52. [PMID: 22213449 DOI: 10.1002/jmr.1167] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.
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Affiliation(s)
- Rajesh Ghai
- Institute for Molecular Bioscience (IMB), University of Queensland, St. Lucia, Queensland, 4072, Australia
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Oliveira SM, Cardoso I, Saraiva MJ. Transthyretin: roles in the nervous system beyond thyroxine and retinol transport. Expert Rev Endocrinol Metab 2012; 7:181-189. [PMID: 30764010 DOI: 10.1586/eem.12.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transthyretin (TTR) is a plasma- and cerebrospinal fluid-circulating protein. Besides the primordially attributed systemic role as a transporter molecule of thyroxine (T4) and retinol (through the binding to retinol-binding protein [RBP]), TTR has been recognized as a protein with important functions in several aspects of the nervous system physiology. TTR has been shown to play an important role in behavior, cognition, amidated neuropeptide processing and nerve regeneration. Furthermore, it has been proposed that TTR is neuroprotective in Alzheimer's disease and cerebral ischemia. Mutations in TTR are a well-known cause of familial amyloidotic polyneuropathy, an autosomal dominant neurodegenerative disorder characterized by systemic deposition of TTR amyloid fibrils, particularly in the peripheral nervous system. The purpose of this review is to highlight the roles of TTR in the nervous system, beyond its systemic role as a transporter molecule of T4 and RBP-retinol.
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Affiliation(s)
- Sandra Marisa Oliveira
- a Molecular Neurobiology, IBMC- Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180, Porto, Portugal
| | - Isabel Cardoso
- a Molecular Neurobiology, IBMC- Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180, Porto, Portugal
- b Escola Superior de Tecnologia da Saúde do Porto, Instituto Politécnico do Porto, Portugal
| | - Maria João Saraiva
- a Molecular Neurobiology, IBMC- Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180, Porto, Portugal
- c ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal.
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Alhamadsheh MM, Connelly S, Cho A, Reixach N, Powers ET, Pan DW, Wilson IA, Kelly JW, Graef IA. Potent kinetic stabilizers that prevent transthyretin-mediated cardiomyocyte proteotoxicity. Sci Transl Med 2012; 3:97ra81. [PMID: 21865539 DOI: 10.1126/scitranslmed.3002473] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A valine-to-isoleucine mutation at position 122 of the serum protein transthyretin (TTR), found in 3 to 4% of African Americans, alters its stability, leading to amyloidogenesis and cardiomyopathy. In addition, 10 to 15% of individuals older than 65 years develop senile systemic amyloidosis and cardiac TTR deposits because of wild-type TTR amyloidogenesis. Although several drugs are in development, no approved therapies for TTR amyloid cardiomyopathy are yet available, so the identification of additional compounds that prevent amyloid-mediated cardiotoxicity is needed. To this aim, we developed a fluorescence polarization-based high-throughput screen and used it to identify several new chemical scaffolds that target TTR. These compounds were potent kinetic stabilizers of TTR and prevented TTR tetramer dissociation, partial unfolding, and aggregation of both wild type and the most common cardiomyopathy-associated TTR mutant, V122I-TTR. High-resolution co-crystal structures and characterization of the binding energetics revealed how these diverse structures bound to tetrameric TTR. These compounds effectively inhibited the proteotoxicity of V122I-TTR toward human cardiomyocytes. Several of these ligands stabilized TTR in human serum more effectively than diflunisal, which is a well-studied inhibitor of TTR aggregation, and may be promising leads for the treatment or prevention of TTR-mediated cardiomyopathy.
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Affiliation(s)
- Mamoun M Alhamadsheh
- Department of Pathology, Stanford University Medical School, Stanford, CA 94305, USA
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28
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Roach CA, Simpson JV, JiJi RD. Evolution of quantitative methods in protein secondary structure determination via deep-ultraviolet resonance Raman spectroscopy. Analyst 2012; 137:555-62. [DOI: 10.1039/c1an15755h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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29
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Sziegat F, Wirmer-Bartoschek J, Schwalbe H. Characteristics of Human Lysozyme and Its Disease-Related Mutants in their Unfolded States. Angew Chem Int Ed Engl 2011; 50:5514-8. [DOI: 10.1002/anie.201008040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 04/06/2011] [Indexed: 11/10/2022]
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30
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Sziegat F, Wirmer-Bartoschek J, Schwalbe H. Characteristics of Human Lysozyme and Its Disease-Related Mutants in their Unfolded States. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Ostroumova OS, Efimova SS, Schagina LV. 5- and 4'-Hydroxylated flavonoids affect voltage gating of single alpha-hemolysin pore. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2051-8. [PMID: 21527242 DOI: 10.1016/j.bbamem.2011.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/27/2011] [Accepted: 04/11/2011] [Indexed: 10/18/2022]
Abstract
Molecular mechanisms of the influence of flavonoids on the voltage gating of a single alpha-hemolysin channel in planar lipid membranes are studied. It is shown that the addition of flavonoids hydroxylated in position 5 of the A-ring and in position 4' of the B-ring into bilayer bathing solution shifts the voltage dependence of channel switching from high- to low-conductance states to voltages nearer zero. It is concluded that the effect is likely to be attributed to a specific interaction of at least three flavonoid molecules with the voltage sensor of an alpha-hemolysin pore. Possible flavonoid binding sites and identification of amino acid residues included into the voltage sensor domain of the alpha-hemolysin channel are discussed.
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Affiliation(s)
- Olga S Ostroumova
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia.
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Choi S, Kelly JW. A competition assay to identify amyloidogenesis inhibitors by monitoring the fluorescence emitted by the covalent attachment of a stilbene derivative to transthyretin. Bioorg Med Chem 2010; 19:1505-14. [PMID: 21273081 DOI: 10.1016/j.bmc.2010.12.050] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 12/21/2022]
Abstract
Herein we demonstrate that competition between candidate kinetic stabilizer binding to transthyretin (TTR) and stilbene binding to and reaction with the same thyroxine sites within TTR can be utilized to discover potent and highly selective non-covalent TTR amyloidogenesis inhibitors. We report two stilbenes, S1 and S2, for use in distinct competition assays. Each bind selectively to TTR and then chemoselectively react to form an amide bond with the Lys-15 residue of TTR, creating a fluorescent conjugate. We used 28 TTR kinetic stabilizers exhibiting a known spectrum of plasma TTR binding selectivities and TTR amyloid fibril inhibition efficacies to validate the 'TTR fluorescence conjugate competition assay'. The kinetic stabilizers competed with S1 for binding to recombinant TTR in buffer and with S2 for binding to endogenous levels of TTR in human blood serum. In both assay scenarios, we demonstrate that the lower the TTR-stilbene conjugate fluorescence after a 3 h competition, the greater the binding selectivity and potency of the candidate TTR kinetic stabilizer. These assays, particularly the assay utilizing S2 in human serum, replace two assays previously utilized to gather the same information. While not the focus of this manuscript, it is clear that the 'TTR fluorescence conjugate competition assay' could be adapted for high throughput screening applications.
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Affiliation(s)
- Sungwook Choi
- Department of New Drug Discovery and Development, Chungnam National University, Daejon 305-764, Republic of Korea
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Lignin-derived oak phenolics: a theoretical examination of additional potential health benefits of red wine. J Mol Model 2010; 17:1841-5. [DOI: 10.1007/s00894-010-0893-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 10/31/2010] [Indexed: 10/18/2022]
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Trivella DBB, Sairre MI, Foguel D, Lima LMTR, Polikarpov I. The binding of synthetic triiodo l-thyronine analogs to human transthyretin: molecular basis of cooperative and non-cooperative ligand recognition. J Struct Biol 2010; 173:323-32. [PMID: 20937391 DOI: 10.1016/j.jsb.2010.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2010] [Revised: 10/03/2010] [Accepted: 10/05/2010] [Indexed: 11/25/2022]
Abstract
Transthyretin (TTR) is a tetrameric β-sheet-rich transporter protein directly involved in human amyloid diseases. Several classes of small molecules can bind to TTR delaying its amyloid fibril formation, thus being promising drug candidates to treat TTR amyloidoses. In the present study, we characterized the interactions of the synthetic triiodo L-thyronine analogs and thyroid hormone nuclear receptor TRβ-selective agonists GC-1 and GC-24 with the wild type and V30M variant of human transthyretin (TTR). To achieve this aim, we conducted in vitro TTR acid-mediated aggregation and isothermal titration calorimetry experiments and determined the TTR:GC-1 and TTR:GC-24 crystal structures. Our data indicate that both GC-1 and GC-24 bind to TTR in a non-cooperative manner and are good inhibitors of TTR aggregation, with dissociation constants for both hormone binding sites (HBS) in the low micromolar range. Analysis of the crystal structures of TTRwt:GC-1(24) complexes and their comparison with the TTRwt X-ray structure bound to its natural ligand thyroxine (T4) suggests, at the molecular level, the basis for the cooperative process displayed by T4 and the non-cooperative process provoked by both GC-1 and GC-24 during binding to TTR.
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Affiliation(s)
- Daniela B B Trivella
- Instituto de Física de São Carlos-Universidade de São Paulo, São Carlos, SP, Brazil
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