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Angera IJ, Wright MM, Del Valle JR. Beyond N-Alkylation: Synthesis, Structure, and Function of N-Amino Peptides. Acc Chem Res 2024; 57:1287-1297. [PMID: 38626119 DOI: 10.1021/acs.accounts.4c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
The growing list of physiologically important protein-protein interactions (PPIs) has amplified the need for compounds to target topologically complex biomolecular surfaces. In contrast to small molecules, peptide and protein mimics can exhibit three-dimensional shape complementarity across a large area and thus have the potential to significantly expand the "druggable" proteome. Strategies to stabilize canonical protein secondary structures without sacrificing side-chain content are particularly useful in the design of peptide-based chemical probes and therapeutics.Substitution of the backbone amide in peptides represents a subtle chemical modification with profound effects on conformation and stability. Studies focused on N-alkylation have already led to broad-ranging applications in peptidomimetic design. Inspired by nonribosomal peptide natural products harboring amide N-oxidations, we envisioned that main-chain hydrazide and hydroxamate bonds would impose distinct conformational preferences and offer unique opportunities for backbone diversification. This Account describes our exploration of peptide N-amination as a strategy for stabilizing canonical protein folds and for the structure-based design of soluble amyloid mimics.We developed a general synthetic protocol to access N-amino peptides (NAPs) on solid support. In an effort to stabilize β-strand conformation, we designed stitched peptidomimetics featuring covalent tethering of the backbone N-amino substituent to the preceding residue side chain. Using a combination of NMR, X-ray crystallography, and molecular dynamics simulations, we discovered that backbone N-amination alone could significantly stabilize β-hairpin conformation in multiple models of folding. Our studies revealed that the amide NH2 substituent in NAPs participates in cooperative noncovalent interactions that promote β-sheet secondary structure. In contrast to Cα-substituted α-hydrazino acids, we found that N-aminoglycine and its N'-alkylated derivatives instead stabilize polyproline II (PPII) conformation. The reactivity of hydrazides also allows for late-stage peptide macrocyclization, affording novel covalent surrogates of side-chain-backbone H-bonds.The pronounced β-sheet propensity of Cα-substituted α-hydrazino acids prompted us to target amyloidogenic proteins using NAP-based β-strand mimics. Backbone N-amination was found to render aggregation-prone lead sequences soluble and resistant to proteolysis. Inhibitors of Aβ and tau identified through N-amino scanning blocked protein aggregation and the formation of mature fibrils in vitro. We further identified NAP-based single-strand and cross-β tau mimics capable of inhibiting the prion-like cellular seeding activity of recombinant and patient-derived tau fibrils.Our studies establish backbone N-amination as a valuable addition to the peptido- and proteomimetic tool kit. α-Hydrazino acids show particular promise as minimalist β-strand mimics that retain side-chain information. Late-stage derivatization of hydrazides also provides facile entry into libraries of backbone-edited peptides. We anticipate that NAPs will thus find applications in the development of optimally constrained folds and modulators of PPIs.
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Affiliation(s)
- Isaac J Angera
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Madison M Wright
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Juan R Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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2
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Liu H, Cui Y, Zhao X, Wei L, Wang X, Shen N, Odom T, Li X, Lawless W, Karunarathne K, Muschol M, Guida W, Cao C, Ye L, Cai J. Helical sulfonyl-γ-AApeptides modulating Aβ oligomerization and cytotoxicity by recognizing Aβ helix. Proc Natl Acad Sci U S A 2024; 121:e2311733121. [PMID: 38285951 PMCID: PMC10861862 DOI: 10.1073/pnas.2311733121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/10/2023] [Indexed: 01/31/2024] Open
Abstract
In contrast to prevalent strategies which make use of β-sheet mimetics to block Aβ fibrillar growth, in this study, we designed a series of sulfonyl-γ-AApeptide helices that targeted the crucial α-helix domain of Aβ13-26 and stabilized Aβ conformation to avoid forming the neurotoxic Aβ oligomeric β-sheets. Biophysical assays such as amyloid kinetics and TEM demonstrated that the Aβ oligomerization and fibrillation could be greatly prevented and even reversed in the presence of sulfonyl-γ-AApeptides in a sequence-specific and dose-dependent manner. The studies based on circular dichroism, Two-dimensional nuclear magnetic resonance spectroscopy (2D-NMR) spectra unambiguously suggested that the sulfonyl-γ-AApeptide Ab-6 could bind to the central region of Aβ42 and induce α-helix conformation in Aβ. Additionally, Electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) was employed to rule out a colloidal mechanism of inhibitor and clearly supported the capability of Ab-6 for inhibiting the formation of Aβ aggregated forms. Furthermore, Ab-6 could rescue neuroblastoma cells by eradicating Aβ-mediated cytotoxicity even in the presence of pre-formed Aβ aggregates. The confocal microscopy demonstrated that Ab-6 could still specifically bind Aβ42 and colocalize into mitochondria in the cellular environment, suggesting the rescue of cell viability might be due to the protection of mitochondrial function otherwise impaired by Aβ42 aggregation. Taken together, our studies indicated that sulfonyl-γ-AApeptides as helical peptidomimetics could direct Aβ into the off-pathway helical secondary structure, thereby preventing the formation of Aβ oligomerization, fibrillation and rescuing Aβ induced cell cytotoxicity.
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Affiliation(s)
- Heng Liu
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Yunpeng Cui
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Xue Zhao
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Lulu Wei
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Xudong Wang
- Department of Molecular Biosciences, University of South Florida, Tampa, FL33620
| | - Ning Shen
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Timothy Odom
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Xuming Li
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - William Lawless
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | | | - Martin Muschol
- Department of Physics, University of South Florida, Tampa, FL33620
| | - Wayne Guida
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Chuanhai Cao
- Taneja College of Pharmacy, University of South Florida, Tampa, FL33612
| | - Libin Ye
- Department of Molecular Biosciences, University of South Florida, Tampa, FL33620
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL33620
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3
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La Manna S, Di Natale C, Panzetta V, Leone M, Mercurio FA, Cipollone I, Monti M, Netti PA, Ferraro G, Terán A, Sánchez-Peláez AE, Herrero S, Merlino A, Marasco D. A Diruthenium Metallodrug as a Potent Inhibitor of Amyloid-β Aggregation: Synergism of Mechanisms of Action. Inorg Chem 2024; 63:564-575. [PMID: 38117944 PMCID: PMC10777406 DOI: 10.1021/acs.inorgchem.3c03441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023]
Abstract
The physical and chemical properties of paddlewheel diruthenium compounds are highly dependent on the nature of the ligands surrounding the bimetallic core. Herein, we compare the ability of two diruthenium compounds, [Ru2Cl(D-p-FPhF)(O2CCH3)3]·H2O (1) (D-p-FPhF- = N,N'-bis(4-fluorophenyl)formamidinate) and K3[Ru2(O2CO)4]·3H2O (2), to act as inhibitors of amyloid aggregation of the Aβ1-42 peptide and its peculiar fragments, Aβ1-16 and Aβ21-40. A wide range of biophysical techniques has been used to determine the inhibition capacity against aggregation and the possible mechanism of action of these compounds (Thioflavin T fluorescence and autofluorescence assays, UV-vis absorption spectroscopy, circular dichroism, nuclear magnetic resonance, mass spectrometry, and electron scanning microscopy). Data show that the most effective inhibitory effect is shown for compound 1. This compound inhibits fiber formation and completely abolishes the cytotoxicity of Aβ1-42. The antiaggregatory capacity of this complex can be explained by a binding mechanism of the dimetallic units to the peptide chain along with π-π interactions between the formamidinate ligand and the aromatic side chains. The results suggest the potential use of paddlewheel diruthenium complexes as neurodrugs and confirm the importance of the steric and charge effects on the properties of diruthenium compounds.
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Affiliation(s)
- Sara La Manna
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Concetta Di Natale
- Department
of Chemical, Materials, and Industrial Production Engineering (DICMaPI), University of Naples Federico II, 80125 Naples, Italy
| | - Valeria Panzetta
- Department
of Chemical, Materials, and Industrial Production Engineering (DICMaPI), University of Naples Federico II, 80125 Naples, Italy
- Interdisciplinary
Research Centre on Biomaterials (CRIB), University of Naples Federico II, Istituto Italiano di Tecnologia, 80125 Naples, Italy
| | - Marilisa Leone
- Institute
of Biostructures and Bioimaging - CNR, 80145 Naples, Italy
| | | | - Irene Cipollone
- Department
of Chemical Sciences, University of Naples
“Federico II”, 80126 Naples, Italy
- CEINGE
Biotecnologie
Avanzate “Franco Salvatore” S.c.a r.l., 80131 Naples, Italy
| | - Maria Monti
- Department
of Chemical Sciences, University of Naples
“Federico II”, 80126 Naples, Italy
- CEINGE
Biotecnologie
Avanzate “Franco Salvatore” S.c.a r.l., 80131 Naples, Italy
| | - Paolo A. Netti
- Department
of Chemical, Materials, and Industrial Production Engineering (DICMaPI), University of Naples Federico II, 80125 Naples, Italy
- Interdisciplinary
Research Centre on Biomaterials (CRIB), University of Naples Federico II, Istituto Italiano di Tecnologia, 80125 Naples, Italy
| | - Giarita Ferraro
- Department
of Chemical Sciences, University of Naples
“Federico II”, 80126 Naples, Italy
| | - Aarón Terán
- MatMoPol
Research Group, Department of Inorganic Chemistry, Faculty of Chemical
Science, Complutense University of Madrid, Avenida Complutense s/n, 28040 Madrid, Spain
| | - Ana E. Sánchez-Peláez
- MatMoPol
Research Group, Department of Inorganic Chemistry, Faculty of Chemical
Science, Complutense University of Madrid, Avenida Complutense s/n, 28040 Madrid, Spain
| | - Santiago Herrero
- MatMoPol
Research Group, Department of Inorganic Chemistry, Faculty of Chemical
Science, Complutense University of Madrid, Avenida Complutense s/n, 28040 Madrid, Spain
| | - Antonello Merlino
- Department
of Chemical Sciences, University of Naples
“Federico II”, 80126 Naples, Italy
| | - Daniela Marasco
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
- Institute
of Biostructures and Bioimaging - CNR, 80145 Naples, Italy
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4
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Sato W, Watanabe-Takahashi M, Murata T, Utsunomiya-Tate N, Motoyama J, Anzai M, Ishihara S, Nishioka N, Uchiyama H, Togashi J, Nishihara S, Kawasaki K, Saito T, Saido TC, Funamoto S, Nishikawa K. A tailored tetravalent peptide displays dual functions to inhibit amyloid β production and aggregation. Commun Biol 2023; 6:383. [PMID: 37031306 PMCID: PMC10082830 DOI: 10.1038/s42003-023-04771-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
Inhibition of amyloid-β peptide (Aβ) accumulation in the brain is a promising approach for treatment of Alzheimer's disease (AD). Aβ is produced by β-secretase and γ-secretase in endosomes via sequential proteolysis of amyloid precursor protein (APP). Aβ and APP have a common feature to readily cluster to form multimers. Here, using multivalent peptide library screens, we identified a tetravalent peptide, LME-tet, which binds APP and Aβ via multivalent interactions. In cells, LME-tet-bound APP in the plasma membrane is transported to endosomes, blocking Aβ production through specific inhibition of β-cleavage, but not γ-cleavage. LME-tet further suppresses Aβ aggregation by blocking formation of the β-sheet conformation. Inhibitory effects are not observed with a monomeric peptide, emphasizing the significance of multivalent interactions for mediating these activities. Critically, LME-tet efficiently reduces Aβ levels in the brain of AD model mice, suggesting it may hold promise for treatment of AD.
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Affiliation(s)
- Waka Sato
- Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Miho Watanabe-Takahashi
- Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Takuya Murata
- Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | | | - Jun Motoyama
- Laboratory of Developmental Neurobiology, Graduate School of Brain Science, Doshisha University, Kyoto, Japan
| | - Masataka Anzai
- Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Seiko Ishihara
- Department of Neuropathology, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Nanako Nishioka
- Department of Neuropathology, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Hina Uchiyama
- Department of Neuropathology, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Juri Togashi
- Department of Neuropathology, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Saeka Nishihara
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kyoto, Japan
| | - Kiyoshi Kawasaki
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kyoto, Japan
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Graduate School of Medical Sciences, Nagoya City University, Aichi, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, Riken Center For Brain Science, Saitama, Japan
| | - Satoru Funamoto
- Department of Neuropathology, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan.
| | - Kiyotaka Nishikawa
- Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan.
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Dolenc J, Haywood EJ, Zhu T, Smith LJ. Backbone N-Amination Promotes the Folding of β-Hairpin Peptides via a Network of Hydrogen Bonds. J Chem Inf Model 2022; 62:6704-6714. [PMID: 35816656 PMCID: PMC9795546 DOI: 10.1021/acs.jcim.2c00516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Molecular dynamics (MD) simulations have been used to characterize the effects of backbone N-amination of residues in a model β-hairpin peptide. This modification is of considerable interest as N-aminated peptides have been shown to inhibit amyloid-type aggregation. Six derivatives of the β-hairpin peptide, which contain one, two, or four N-aminated residues, have been studied. For each peptide 100 ns MD simulations starting from the folded β-hairpin structure were performed. The effects of the N-amination prove to be very sequence dependent. N-Amination of a residue involved in interstrand hydrogen bonding (Val3) leads to unfolding of the β-hairpin, whereas N-amination of a residue toward the C-terminus (Leu11) gives fraying at the termini of the peptide. In the other derivatives the peptide remains folded, with increasing levels of N-amination reducing the right-handed twist of the β-hairpin and favoring population of a type II' rather than a type I' β-turn. MD simulations (100 ns) have also been run for each peptide starting from an unfolded extended chain. Here, the peptide with four N-aminated residues shows the most folding into the β-hairpin (34%). Analysis of the simulations shows that N-amination favors the population of β (φ, ψ) conformations by the preceding residue due to, at least in part, a network of weak NH2(i)-CO(i) and NH2(i)-CO(i-2) hydrogen bonds. It also leads to a reduction of misfolding because of changes in the hydrogen-bonding potential. Both of these features help funnel the peptide to the folded β-hairpin structure. The conformational insights provided through this work give a firm foundation for the design of N-aminated peptide inhibitors for modulating protein-protein interactions and aggregation.
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Affiliation(s)
- Jožica Dolenc
- Chemistry
- Biology
- Pharmacy Information Center, ETH Zurich, Zurich CH-8093, Switzerland
| | - Esme J. Haywood
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Tingting Zhu
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Lorna J. Smith
- Inorganic
Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom, (L.J.S.)
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6
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Peptides for disrupting and degrading amyloids. Curr Opin Chem Biol 2021; 64:124-130. [PMID: 34274561 DOI: 10.1016/j.cbpa.2021.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/13/2021] [Accepted: 05/18/2021] [Indexed: 01/23/2023]
Abstract
Amyloid proteins can aggregate into insoluble fibrils and form amyloid deposits in the human brain, which is the hallmark of many neurodegenerative diseases. Promising strategies toward pathological amyloid proteins and deposition include investigating inhibitors that can disrupt amyloid aggregation or induce misfolding protein degradation. In this review, recent progress of peptide-based inhibitors, including amyloid sequence-derived inhibitors, designed peptides, and peptide mimics, is highlighted. Based on the increased understanding of peptide design and precise amyloid structures, these peptides exhibit advanced inhibitory activities against fibrous aggregation as well as enhanced druggability.
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Rathman BM, Rowe JL, Del Valle JR. Synthesis and conformation of backbone N-aminated peptides. Methods Enzymol 2021; 656:271-294. [PMID: 34325790 DOI: 10.1016/bs.mie.2021.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The chemical modification of peptides is a promising approach for the design of protein-protein interaction inhibitors and peptide-based drug candidates. Among several peptidomimetic strategies, substitution of the amide backbone maintains side-chain functionality that may be important for engagement of biological targets. Backbone amide substitution has been largely limited to N-alkylation, which can promote cis amide geometry and disrupt important H-bonding interactions. In contrast, N-amination of peptides induces distinct backbone geometries and maintains H-bond donor capacity. In this chapter we discuss the conformational characteristics of designed N-amino peptides and present a detailed protocol for their synthesis on solid support. The described methods allow for backbone N-amino scanning of biologically active parent sequences.
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