Theoretical investigations of TTR derived aggregation-prone peptides’ potential to biochemically attenuate the amyloidogenic propensities of V30 M TTR amyloid fibrils

Journal of the Indian Chemical Society - Tập 100 - Trang 100892 - 2023
G. Chandrasekhar1, R. Rajasekaran1
1Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to be University), Vellore, Tamil Nadu, 632014, India

Tài liệu tham khảo

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