Theoretical investigations of TTR derived aggregation-prone peptides’ potential to biochemically attenuate the amyloidogenic propensities of V30 M TTR amyloid fibrils
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Merlini, 2003, Molecular mechanisms of amyloidosis, N. Engl. J. Med., 349, 583, 10.1056/NEJMra023144
Ruberg, 2012, Transthyretin (TTR) cardiac amyloidosis, Circulation, 126, 1286, 10.1161/CIRCULATIONAHA.111.078915
Ando, 2005, Transthyretin-related familial amyloidotic polyneuropathy, Arch. Neurol., 62, 1057, 10.1001/archneur.62.7.1057
Benson, 2018, Amyloid nomenclature 2018: recommendations by the International Society of Amyloidosis (ISA) nomenclature committee, Amyloid, 25, 215, 10.1080/13506129.2018.1549825
Benson, 2007, The molecular biology and clinical features of amyloid neuropathy, Muscle Nerve, 36, 411, 10.1002/mus.20821
Saraiva, 2001, Transthyretin mutations in hyperthyroxinemia and amyloid diseases, Hum. Mutat., 17, 493, 10.1002/humu.1132
Jacobson, 1992, Transthyretin Pro 55, a variant associated with early-onset, aggressive, diffuse amyloidosis with cardiac and neurologic involvement, Hum. Genet., 89, 10.1007/BF00220559
Ruberg, 2012, Transthyretin (TTR) cardiac amyloidosis, Circulation, 126, 1286, 10.1161/CIRCULATIONAHA.111.078915
Wechalekar, 2016, Systemic amyloidosis, Lancet, 387, 2641, 10.1016/S0140-6736(15)01274-X
Connors, 2003, Tabulation of human transthyretin (TTR) variants, Amyloid, 10, 160, 10.3109/13506120308998998
Saraiva, 1984, Amyloid fibril protein in familial amyloidotic polyneuropathy, Portuguese type. Definition of molecular abnormality in transthyretin (prealbumin), J. Clin. Invest., 74, 104, 10.1172/JCI111390
Buxbaum, 2009, Transthyretin: the servant of many masters, Cell. Mol. Life Sci., 66, 3095, 10.1007/s00018-009-0109-0
Vieira, 2014, Transthyretin: a multifaceted protein, Biomol. Concepts, 5, 45, 10.1515/bmc-2013-0038
Herbert, 1986, Transthyretin: a choroid plexus-specific transport protein in human brain: the 1986 S. Weir Mitchell Award, Neurology, 36, 10.1212/WNL.36.7.900
Murakami, 2010, The transthyretin gene is expressed in Schwann cells of peripheral nerves, Brain Res., 1348, 222, 10.1016/j.brainres.2010.06.017
Gonçalves, 2017, Differential expression of Cathepsin E in transthyretin amyloidosis: from neuropathology to the immune system, J. Neuroinflammation, 14, 115, 10.1186/s12974-017-0891-9
Srinivasan, 2020, TTRMDB: a database for structural and functional analysis on the impact of SNPs over transthyretin (TTR) using bioinformatic tools, Comput. Biol. Chem., 87, 10.1016/j.compbiolchem.2020.107290
Connors, 1998, A simple screening test for variant transthyretins associated with familial transthyretin amyloidosis using isoelectric focusing, Biochim. Biophys. Acta (BBA) - Mol. Basis Dis., 1407, 185, 10.1016/S0925-4439(98)00037-4
Sekijima, 2005, The biological and chemical basis for tissue-selective amyloid disease, Cell, 121, 73, 10.1016/j.cell.2005.01.018
Jesus, 2012, The V30M amyloidogenic mutation decreases the rate of refolding kinetics of the tetrameric protein transthyretin, Spectros. Int. J., 27, 343, 10.1155/2012/502497
Saraiva, 1995, Transthyretin mutations in health and disease, Hum. Mutat., 5, 191, 10.1002/humu.1380050302
McCorquodale, 2019, Clinical electrophysiology of axonal polyneuropathies, Handb. Clin. Neurol., 161, 217, 10.1016/B978-0-444-64142-7.00051-5
Çakar, 2019, Familial amyloid polyneuropathy, Noro. Psikiyatr. Ars., 56, 150
Ando, 2013, Guideline of transthyretin-related hereditary amyloidosis for clinicians, Orphanet J. Rare Dis., 8, 31, 10.1186/1750-1172-8-31
Bonaïti, 2010, TTR familial amyloid polyneuropathy: does a mitochondrial polymorphism entirely explain the parent-of-origin difference in penetrance?, Eur. J. Hum. Genet., 18, 948, 10.1038/ejhg.2010.36
Gertz, 2015, Diagnosis, prognosis, and therapy of transthyretin amyloidosis, J. Am. Coll. Cardiol., 66, 2451, 10.1016/j.jacc.2015.09.075
Adams, 2013, Recent advances in the treatment of familial amyloid polyneuropathy, Ther. Adv. Neurol. Disord, 6, 129, 10.1177/1756285612470192
Maurer, 2018, Tafamidis treatment for patients with transthyretin amyloid cardiomyopathy, N. Engl. J. Med., 379, 1007, 10.1056/NEJMoa1805689
Huber, 2019, A comprehensive safety profile of tafamidis in patients with transthyretin amyloid polyneuropathy, Amyloid, 26, 203, 10.1080/13506129.2019.1643714
Lamb, 2019, Tafamidis: a review in transthyretin amyloidosis with polyneuropathy, Drugs, 79, 863, 10.1007/s40265-019-01129-6
Vidović, 2022, Alpha-synuclein aggregation pathway in Parkinson's disease: current status and novel therapeutic approaches, Cells, 11, 1732, 10.3390/cells11111732
Horsley, 2020, Rationally designed peptide-based inhibitor of Aβ42 fibril formation and toxicity: a potential therapeutic strategy for Alzheimer's disease, Biochem. J., 477, 2039, 10.1042/BCJ20200290
Armiento, 2020, Peptide-based molecular strategies to interfere with protein misfolding, aggregation, and cell degeneration, Angew Chem. Int. Ed. Engl., 59, 3372, 10.1002/anie.201906908
Banerjee, 2016, Superoxide dismutase 1 (SOD1)-Derived peptide inhibits amyloid aggregation of familial amyotrophic lateral sclerosis SOD1 mutants, ACS Chem. Neurosci., 7, 1595, 10.1021/acschemneuro.6b00227
Srinivasan, 2019, Rational design of linear tripeptides against the aggregation of human mutant SOD1 protein causing amyotrophic lateral sclerosis, J. Neurol. Sci., 405, 10.1016/j.jns.2019.116425
Rezaeian, 2017, The inhibitory effects of biomimetically designed peptides on α-synuclein aggregation, Arch. Biochem. Biophys., 634, 96, 10.1016/j.abb.2017.09.015
Srinivasan, 2022, Probing the polyphenolic flavonoid, morin as a highly efficacious inhibitor against amyloid(A4V) mutant SOD1 in fatal amyotrophic lateral sclerosis, Arch. Biochem. Biophys., 727, 10.1016/j.abb.2022.109318
Ramireddy, 2021, Structural localization of pathogenic mutations in the central nucleotide-binding domain (NBD) of nucleotide-binding oligomerization domain-2 (NOD2) protein and their inference in inflammatory disorders, Nucleos Nucleot. Nucleic Acids, 40, 1198, 10.1080/15257770.2021.1986719
Sekar, 2022, Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19, J. Mol. Model., 28, 128, 10.1007/s00894-022-05117-8
kumar Bhardwaj, 2022, Identification and comparison of plant-derived scaffolds as selective CDK5 inhibitors against standard molecules: insights from umbrella sampling simulations, J. Mol. Liq., 348, 10.1016/j.molliq.2021.118015
Kumar, 2022, Identification of acridinedione scaffolds as potential inhibitor of DENV‐2 C protein: an in silico strategy to combat dengue, J. Cell. Biochem., 123, 935, 10.1002/jcb.30237
Jani, 2021, Destabilization potential of beta sheet breaker peptides on Abeta fibril structure: an insight from molecular dynamics simulation study, RSC Adv., 11, 23557, 10.1039/D1RA03609B
Hjalte, 2022, Aggregation behavior of structurally similar therapeutic peptides investigated by 1 H NMR and all-atom molecular dynamics simulations, Mol. Pharm., 19, 904, 10.1021/acs.molpharmaceut.1c00883
Bruce, 2010, Molecular dynamics simulations of Aβ fibril interactions with β-sheet breaker peptides, Peptides, 31, 2100, 10.1016/j.peptides.2010.07.015
Minicozzi, 2014, Computational and experimental studies on β-sheet breakers targeting aβ1–40 fibrils, J. Biol. Chem., 289, 11242, 10.1074/jbc.M113.537472
Schmidt, 2019, Cryo-EM structure of a transthyretin-derived amyloid fibril from a patient with hereditary ATTR amyloidosis, Nat. Commun., 10, 5008, 10.1038/s41467-019-13038-z
Saelices, 2018, Crystal structures of amyloidogenic segments of human transthyretin: amyloid Structures of Transthyretin Segments, Protein Sci., 27, 1295, 10.1002/pro.3420
Saelices, 2018, Crystal structures of amyloidogenic segments of human transthyretin, Protein Sci., 27, 1295, 10.1002/pro.3420
Saelices, 2015, Uncovering the mechanism of aggregation of human transthyretin, J. Biol. Chem., 290, 28932, 10.1074/jbc.M115.659912
Kozakov, 2006, PIPER: an FFT-based protein docking program with pairwise potentials, Proteins, 65, 392, 10.1002/prot.21117
Kozakov, 2017, The ClusPro web server for protein–protein docking, Nat. Protoc., 12, 255, 10.1038/nprot.2016.169
Srinivasan, 2017, Exploring the cause of aggregation and reduced Zn binding affinity by G85R mutation in SOD1 rendering amyotrophic lateral sclerosis: in Silico Study on SOD1 Mutant G85R, Proteins, 85, 1276, 10.1002/prot.25288
Srinivasan, 2017, Probing the inhibitory activity of epigallocatechin-gallate on toxic aggregates of mutant (L84F) SOD1 protein through geometry based sampling and steered molecular dynamics, J. Mol. Graph. Model., 74, 288, 10.1016/j.jmgm.2017.04.019
Van Der Spoel, 2005, GROMACS: fast, flexible, and free, J. Comput. Chem., 26, 1701, 10.1002/jcc.20291
Abraham, 2015, GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers, Software, 1, 19, 10.1016/j.softx.2015.06.001
Carballo-Pacheco, 2017, Comparison of force fields for Alzheimer's A β42: a case study for intrinsically disordered proteins: comparison of Force Fields for Alzheimer's A β42, Protein Sci., 26, 174, 10.1002/pro.3064
Brooks, 2009, CHARMM: the biomolecular simulation program, J. Comput. Chem., 30, 1545, 10.1002/jcc.21287
Man, 2019, Effects of all-atom molecular mechanics force fields on amyloid peptide assembly: the case of aβ16-22 dimer, J. Chem. Theor. Comput., 15, 1440, 10.1021/acs.jctc.8b01107
Berendsen, 1987, The missing term in effective pair potentials, J. Phys. Chem., 91, 6269, 10.1021/j100308a038
Parrinello, 1981, Polymorphic transitions in single crystals: a new molecular dynamics method, J. Appl. Phys., 52, 7182, 10.1063/1.328693
Essmann, 1995, A smooth particle mesh Ewald method, J. Chem. Phys., 103, 8577, 10.1063/1.470117
Pfleger, 2013, Global and local indices for characterizing biomolecular flexibility and rigidity, J. Comput. Chem., 34, 220, 10.1002/jcc.23122
Pfleger, 2013, Constraint network analysis (cna): a Python software package for efficiently linking biomacromolecular structure, flexibility, (Thermo-)Stability, and function, J. Chem. Inf. Model., 53, 1007, 10.1021/ci400044m
Krüger, 2013, CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function, Nucleic Acids Res., 41, W340, 10.1093/nar/gkt292
Parra, 2016, Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics, Nucleic Acids Res., 44, W356, 10.1093/nar/gkw304
Gupta, 2013, Silico approach for predicting toxicity of peptides and proteins, PLoS One, 8, 10.1371/journal.pone.0073957
Chen, 2017, Amyloid beta: structure, biology and structure-based therapeutic development, Acta Pharmacol. Sin., 38, 1205, 10.1038/aps.2017.28
La Manna, 2018, Peptides as therapeutic agents for inflammatory-related diseases, IJMS, 19, 2714, 10.3390/ijms19092714
Srinivasan, 2021, Decoding conformational imprint of convoluted molecular interactions between prenylflavonoids and aggregated amyloid-beta 42 peptide causing Alzheimer's disease, Front. Chem., 9, 10.3389/fchem.2021.753146
Patel, 2014, Steered molecular dynamics simulations for studying protein–ligand interaction in cyclin-dependent kinase 5, J. Chem. Inf. Model., 54, 470, 10.1021/ci4003574
Srinivasan, 2019, Effect of β-cyclodextrin-EGCG complexion against aggregated a-synuclein through density functional theory and discrete molecular dynamics, Chem. Phys. Lett., 717, 38, 10.1016/j.cplett.2018.12.042
Chacón, 2004, Beta-sheet breaker peptide prevents Abeta-induced spatial memory impairments with partial reduction of amyloid deposits, Mol. Psychiatr., 9, 953, 10.1038/sj.mp.4001516
Soto, 1998, Beta-sheet breaker peptides inhibit fibrillogenesis in a rat brain model of amyloidosis: implications for Alzheimer's therapy, Nat. Med., 4, 822, 10.1038/nm0798-822
Liu, 2017, β-Sheet breaker peptide-HPYD for the treatment of Alzheimer's disease: primary studies on behavioral test and transcriptional profiling, Front. Pharmacol., 8, 969, 10.3389/fphar.2017.00969
Viet, 2011, Inhibition of aggregation of amyloid peptides by beta-sheet breaker peptides and their binding affinity, J. Phys. Chem. B, 115, 7433, 10.1021/jp1116728
Close, 2018, Physical basis of amyloid fibril polymorphism, Nat. Commun., 9, 699, 10.1038/s41467-018-03164-5
Fändrich, 2018, Amyloid fibril polymorphism: a challenge for molecular imaging and therapy, J. Intern. Med., 283, 218, 10.1111/joim.12732
Tycko, 2015, Amyloid polymorphism: structural basis and neurobiological relevance, Neuron, 86, 632, 10.1016/j.neuron.2015.03.017
Fenwick, 2014, Correlated motions are a fundamental property of β-sheets, Nat. Commun., 5, 4070, 10.1038/ncomms5070