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Satalkar V, Degaga GD, Li W, Pang YT, McShan AC, Gumbart JC, Mitchell JC, Torres MP. Generative β-hairpin design using a residue-based physicochemical property landscape. Biophys J 2024:S0006-3495(24)00070-5. [PMID: 38297834 DOI: 10.1016/j.bpj.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/20/2023] [Accepted: 01/25/2024] [Indexed: 02/02/2024] Open
Abstract
De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe. In this study, we created and tested a custom peptide generative adversarial network intended to design peptide sequences that can fold into the β-hairpin secondary structure. This deep neural network model is designed to establish a preliminary foundation of the generative approach based on physicochemical and conformational properties of 20 canonical amino acids, for example, hydrophobicity and residue volume, using extant structure-specific sequence data from the PDB. The beta generative adversarial network model robustly distinguishes secondary structures of β hairpin from α helix and intrinsically disordered peptides with an accuracy of up to 96% and generates artificial β-hairpin peptide sequences with minimum sequence identities around 31% and 50% when compared against the current NCBI PDB and nonredundant databases, respectively. These results highlight the potential of generative models specifically anchored by physicochemical and conformational property features of amino acids to expand the sequence-to-structure landscape of proteins beyond evolutionary limits.
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Affiliation(s)
- Vardhan Satalkar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Gemechis D Degaga
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Wei Li
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Matthew P Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia.
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2
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La Manna S, Leone M, Iacobucci I, Annuziata A, Di Natale C, Lagreca E, Malfitano AM, Ruffo F, Merlino A, Monti M, Marasco D. Glucosyl Platinum(II) Complexes Inhibit Aggregation of the C-Terminal Region of the Aβ Peptide. Inorg Chem 2022; 61:3540-3552. [PMID: 35171608 PMCID: PMC9951207 DOI: 10.1021/acs.inorgchem.1c03540] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Neurodegenerative diseases are often caused by uncontrolled amyloid aggregation. Hence, many drug discovery processes are oriented to evaluate new compounds that are able to modulate self-recognition mechanisms. Herein, two related glycoconjugate pentacoordinate Pt(II) complexes were analyzed in their capacity to affect the self-aggregation processes of two amyloidogenic fragments, Aβ21-40 and Aβ25-35, of the C-terminal region of the β-amyloid (Aβ) peptide, the major component of Alzheimer's disease (AD) neuronal plaques. The most water-soluble complex, 1Ptdep, is able to bind both fragments and to deeply influence the morphology of peptide aggregates. Thioflavin T (ThT) binding assays, electrospray ionization mass spectrometry (ESI-MS), and ultraviolet-visible (UV-vis) absorption spectroscopy indicated that 1Ptdep shows different kinetics and mechanisms of inhibition toward the two sequences and demonstrated that the peptide aggregation inhibition is associated with a direct coordinative bond of the compound metal center to the peptides. These data support the in vitro ability of pentacoordinate Pt(II) complexes to inhibit the formation of amyloid aggregates and pave the way for the application of this class of compounds as potential neurotherapeutics.
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Affiliation(s)
- Sara La Manna
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy
| | - Marilisa Leone
- Institute
of Biostructures and Bioimaging - CNR, 80134 Naples, Italy
| | - Ilaria Iacobucci
- Department
of Chemical Sciences, University of Naples
“Federico II”, 80126 Naples, Italy,CEINGE
Biotecnologie Avanzate S.c.a r.l., “University
of Naples Federico II”, 80131 Naples, Italy
| | - Alfonso Annuziata
- Department
of Chemical Sciences, University of Naples
“Federico II”, 80126 Naples, Italy
| | - Concetta Di Natale
- Interdisciplinary
Research Centre on Biomaterials (CRIB), Department of Ingegneria Chimica
del Materiali e della Produzione Industriale (DICMAPI), University “Federico II”, 80125 Naples, Italy
| | - Elena Lagreca
- Interdisciplinary
Research Centre on Biomaterials (CRIB), Department of Ingegneria Chimica
del Materiali e della Produzione Industriale (DICMAPI), University “Federico II”, 80125 Naples, Italy
| | - Anna Maria Malfitano
- Department
of Translational Medical Science, University
of Naples “Federico II”, 80131 Naples, Italy
| | - Francesco Ruffo
- Department
of Chemical Sciences, University of Naples
“Federico II”, 80126 Naples, Italy
| | - Antonello Merlino
- Department
of Chemical Sciences, University of Naples
“Federico II”, 80126 Naples, Italy
| | - Maria Monti
- Department
of Chemical Sciences, University of Naples
“Federico II”, 80126 Naples, Italy,CEINGE
Biotecnologie Avanzate S.c.a r.l., “University
of Naples Federico II”, 80131 Naples, Italy,. Tel: +39-081-674474; +39-081-3737919
| | - Daniela Marasco
- Department
of Pharmacy, University of Naples “Federico
II”, 80131 Naples, Italy,Institute
of Biostructures and Bioimaging - CNR, 80134 Naples, Italy,. Tel: +39-081-2532043
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3
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La Manna S, De Benedictis I, Marasco D. Proteomimetics of Natural Regulators of JAK-STAT Pathway: Novel Therapeutic Perspectives. Front Mol Biosci 2022; 8:792546. [PMID: 35047557 PMCID: PMC8762217 DOI: 10.3389/fmolb.2021.792546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/29/2021] [Indexed: 12/16/2022] Open
Abstract
The JAK-STAT pathway is a crucial cellular signaling cascade, including an intricate network of Protein-protein interactions (PPIs) responsible for its regulation. It mediates the activities of several cytokines, interferons, and growth factors and transduces extracellular signals into transcriptional programs to regulate cell growth and differentiation. It is essential for the development and function of both innate and adaptive immunities, and its aberrant deregulation was highlighted in neuroinflammatory diseases and in crucial mechanisms for tumor cell recognition and tumor-induced immune escape. For its involvement in a multitude of biological processes, it can be considered a valuable target for the development of drugs even if a specific focus on possible side effects associated with its inhibition is required. Herein, we review the possibilities to target JAK-STAT by focusing on its natural inhibitors as the suppressor of cytokine signaling (SOCS) proteins. This protein family is a crucial checkpoint inhibitor in immune homeostasis and a valuable target in immunotherapeutic approaches to cancer and immune deficiency disorders.
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Affiliation(s)
| | | | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
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La Manna S, Florio D, Di Natale C, Scognamiglio PL, Sibillano T, Netti PA, Giannini C, Marasco D. Type F mutation of nucleophosmin 1 Acute Myeloid Leukemia: A tale of disorder and aggregation. Int J Biol Macromol 2021; 188:207-214. [PMID: 34364939 DOI: 10.1016/j.ijbiomac.2021.08.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 01/15/2023]
Abstract
Protein aggregation is suggested as a reversible, wide-spread physiological process used by cells to regulate their growth and adapt to different stress conditions. Nucleophosmin 1(NPM1) protein is an abundant multifunctional nucleolar chaperone and its gene is the most frequently mutated in Acute Myeloid Leukemia (AML) patients. So far, the role of NPM1 mutations in leukemogenesis has remained largely elusive considering that they have the double effect of unfolding the C-terminal domain (CTD) and delocalizing the protein in the cytosol (NPM1c+). This mislocalization heavily impacts on cell cycle regulation. Our recent investigations unequivocally demonstrated an amyloid aggregation propensity introduced by AML mutations. Herein, employing complementary biophysical assays, we have characterized a N-terminal extended version of type F AML mutation of CTD and proved that it is able to form assemblies with amyloid character and fibrillar morphology. The present study represents an additional phase of knowledge to deepen the roles exerted by different types of cytoplasmatic NPM1c+ forms to develop in the future potential therapeutics for their selective targeting.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, University of Naples "Federico II", 80134 Naples, Italy
| | - Daniele Florio
- Department of Pharmacy, University of Naples "Federico II", 80134 Naples, Italy
| | - Concetta Di Natale
- Interdisciplinary Research Centre on Biomaterials (CRIB), Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", Italy
| | - Pasqualina Liana Scognamiglio
- Interdisciplinary Research Centre on Biomaterials (CRIB), Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", Italy
| | - Teresa Sibillano
- Institute of Crystallography (IC), National Research Council, 70125 Bari, Italy
| | - Paolo A Netti
- Interdisciplinary Research Centre on Biomaterials (CRIB), Department of Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University of Naples "Federico II", Italy
| | - Cinzia Giannini
- Institute of Crystallography (IC), National Research Council, 70125 Bari, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", 80134 Naples, Italy.
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5
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Profeta M, Di Natale C, Lagreca E, Mollo V, Netti PA, Vecchione R. Cell Membrane-Coated Oil in Water Nano-Emulsions as Biomimetic Nanocarriers for Lipophilic Compounds Conveyance. Pharmaceutics 2021; 13:1069. [PMID: 34371760 PMCID: PMC8309122 DOI: 10.3390/pharmaceutics13071069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/04/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Recently, we developed ultra-stable oil in water nano-emulsions (O/W NEs), able to carry both internal and external cargos (Somes), such as lipophilic compounds and hydrophilic coatings, respectively, that we call here NEsoSomes. O/W NEs are an excellent bioengineering tool for drug and molecules delivery, due to their ability to dissolve a large number of hydrophobic compounds and protect them from hydrolysis and degradation under biological conditions. At present, no report is available on the combination of cell membrane coatings with such nanocarriers, probably due to their typical instability feature. Since then, we have reported, for the first time, a new cell membrane (CM)-coated nanomaterial composed of membranes extracted from glioblastoma cancer cells (U87-MG) deposited on NEsoSomes, through a liquid-liquid interface method, to produce highly controllable membrane caked nano-capsules, namely CM-NEsoSomes. CM-NEsoSomes were physically characterized by dynamic light scattering (DLS) over time and their correct morphology was analyzed by confocal and transmission electron microscopy (TEM) microscopy. Moreover, CM-NEsoSomes biocompatibility was tested on the healthy model cell line, performing cell cytotoxicity and uptake assay, showing nanocarriers uptake by cells with no induced cytotoxicity.
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Affiliation(s)
- Martina Profeta
- Center for Advanced Biomaterials for Health Care (CABHC), Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Napoli, Italy; (M.P.); (C.D.N.); (E.L.); (V.M.); (P.A.N.)
| | - Concetta Di Natale
- Center for Advanced Biomaterials for Health Care (CABHC), Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Napoli, Italy; (M.P.); (C.D.N.); (E.L.); (V.M.); (P.A.N.)
- Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, P.le Tecchio 80, 80125 Naples, Italy
| | - Elena Lagreca
- Center for Advanced Biomaterials for Health Care (CABHC), Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Napoli, Italy; (M.P.); (C.D.N.); (E.L.); (V.M.); (P.A.N.)
- Department of Chemical Materials and Industrial Production (DICMAPI), University of Naples Federico II, P.le Tecchio 80, 80125 Naples, Italy
| | - Valentina Mollo
- Center for Advanced Biomaterials for Health Care (CABHC), Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Napoli, Italy; (M.P.); (C.D.N.); (E.L.); (V.M.); (P.A.N.)
| | - Paolo Antonio Netti
- Center for Advanced Biomaterials for Health Care (CABHC), Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Napoli, Italy; (M.P.); (C.D.N.); (E.L.); (V.M.); (P.A.N.)
- Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, P.le Tecchio 80, 80125 Naples, Italy
- Department of Chemical Materials and Industrial Production (DICMAPI), University of Naples Federico II, P.le Tecchio 80, 80125 Naples, Italy
| | - Raffaele Vecchione
- Center for Advanced Biomaterials for Health Care (CABHC), Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Napoli, Italy; (M.P.); (C.D.N.); (E.L.); (V.M.); (P.A.N.)
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6
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Delfi M, Sartorius R, Ashrafizadeh M, Sharifi E, Zhang Y, De Berardinis P, Zarrabi A, Varma RS, Tay FR, Smith BR, Makvandi P. Self-assembled peptide and protein nanostructures for anti-cancer therapy: Targeted delivery, stimuli-responsive devices and immunotherapy. NANO TODAY 2021; 38:101119. [PMID: 34267794 PMCID: PMC8276870 DOI: 10.1016/j.nantod.2021.101119] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Self-assembled peptides and proteins possess tremendous potential as targeted drug delivery systems and key applications of these well-defined nanostructures reside in anti-cancer therapy. Peptides and proteins can self-assemble into nanostructures of diverse sizes and shapes in response to changing environmental conditions such as pH, temperature, ionic strength, as well as host and guest molecular interactions; their countless benefits include good biocompatibility and high loading capacity for hydrophobic and hydrophilic drugs. These self-assembled nanomaterials can be adorned with functional moieties to specifically target tumor cells. Stimuli-responsive features can also be incorporated with respect to the tumor microenvironment. This review sheds light on the growing interest in self-assembled peptides and proteins and their burgeoning applications in cancer treatment and immunotherapy.
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Affiliation(s)
- Masoud Delfi
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia, Naples 80126, Italy
| | - Rossella Sartorius
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Naples 80131, Italy
| | - Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956, Istanbul, Turkey
| | - Esmaeel Sharifi
- Department of Tissue Engineering and Biomaterials, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, 6517838736, Hamadan, Iran
- Institute for Polymers, Composites and Biomaterials, National Research Council, IPCB-CNR, Naples 80125, Italy
| | - Yapei Zhang
- Department of Biomedical Engineering, Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
| | | | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956, Istanbul, Turkey
| | - Rajender S. Varma
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Franklin R Tay
- The Graduate School, Augusta University, Augusta, GA 30912, USA
| | - Bryan Ronain Smith
- Department of Biomedical Engineering, Institute for Quantitative Health Science & Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Radiology and the Molecular Imaging Program, Stanford University, Stanford, CA, 94305, USA
| | - Pooyan Makvandi
- Istituto Italiano di Tecnologia, Centre for Micro-BioRobotics, Viale Rinaldo Piaggio 34, 56025 Pontedera, Pisa, Italy
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7
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Manna SL, Florio D, Iacobucci I, Napolitano F, Benedictis ID, Malfitano AM, Monti M, Ravera M, Gabano E, Marasco D. A Comparative Study of the Effects of Platinum (II) Complexes on β-Amyloid Aggregation: Potential Neurodrug Applications. Int J Mol Sci 2021; 22:ijms22063015. [PMID: 33809522 PMCID: PMC7998721 DOI: 10.3390/ijms22063015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 01/21/2023] Open
Abstract
Herein the effects of three platinum complexes, namely (SP-4-2)-(2,2'-bipyridine)dichloridoplatinum(II), Pt-bpy, (SP-4-2)-dichlorido(1,10-phenanthroline) platinum(II), Pt-phen, and (SP-4-2)-chlorido(2,2':6',2''-terpyridine)platinum(II) chloride, Pt-terpy, on the aggregation of an amyloid model system derived from the C-terminal domain of Aβ peptide (Aβ21-40) were investigated. Thioflavin T (ThT) binding assays revealed the ability of Pt(II) compounds to repress amyloid aggregation in a dose-dependent way, whereas the ability of Aβ21-40 peptide to interfere with ligand field of metal complexes was analyzed through UV-Vis absorption spectroscopy and electrospray ionization mass spectrometry. Spectroscopic data provided micromolar EC50 values and allowed to assess that the observed inhibition of amyloid aggregation is due to the formation of adducts between Aβ21-40 peptide and complexes upon the release of labile ligands as chloride and that they can explore different modes of coordination toward Aβ21-40 with respect to the entire Aβ1-40 polypeptide. In addition, conformational studies through circular dichroism (CD) spectroscopy suggested that Pt-terpy induces soluble β-structures of monomeric Aβ21-40, thus limiting self-recognition. Noticeably, Pt-terpy demonstrated the ability to reduce the cytotoxicity of amyloid peptide in human SH-SY5Y neuroblastoma cells. Presented data corroborate the hypothesis to enlarge the application field of already known metal-based agents to neurodegenerative diseases, as potential neurodrugs.
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Affiliation(s)
- Sara La Manna
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy; (S.L.M.); (D.F.); (I.D.B.)
| | - Daniele Florio
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy; (S.L.M.); (D.F.); (I.D.B.)
| | - Ilaria Iacobucci
- Department of Chemical Sciences, CEINGE Biotecnologie Avanzate S.c.a r.l., “University of Naples Federico II”, 80131 Naples, Italy; (I.I.); (M.M.)
| | - Fabiana Napolitano
- Department of Translational Medical Science, University of Naples “Federico II”, 80131 Naples, Italy; (F.N.); (A.M.M.)
| | - Ilaria De Benedictis
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy; (S.L.M.); (D.F.); (I.D.B.)
| | - Anna Maria Malfitano
- Department of Translational Medical Science, University of Naples “Federico II”, 80131 Naples, Italy; (F.N.); (A.M.M.)
| | - Maria Monti
- Department of Chemical Sciences, CEINGE Biotecnologie Avanzate S.c.a r.l., “University of Naples Federico II”, 80131 Naples, Italy; (I.I.); (M.M.)
| | - Mauro Ravera
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale “A. Avogadro”, 15121 Alessandria, Italy; (M.R.); (E.G.)
| | - Elisabetta Gabano
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale “A. Avogadro”, 15121 Alessandria, Italy; (M.R.); (E.G.)
| | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, 80131 Naples, Italy; (S.L.M.); (D.F.); (I.D.B.)
- Correspondence: ; Tel.: +39-081-2534512; Fax: +39-081-2534574
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DuPai CD, Davies BW, Wilke CO. A systematic analysis of the beta hairpin motif in the Protein Data Bank. Protein Sci 2021; 30:613-623. [PMID: 33389765 DOI: 10.1002/pro.4020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 12/31/2022]
Abstract
The beta hairpin motif is a ubiquitous protein structural motif that can be found in molecules across the tree of life. This motif, which is also popular in synthetically designed proteins and peptides, is known for its stability and adaptability to broad functions. Here, we systematically probe all 49,000 unique beta hairpin substructures contained within the Protein Data Bank (PDB) to uncover key characteristics correlated with stable beta hairpin structure, including amino acid biases and enriched interstrand contacts. We find that position specific amino acid preferences, while seen throughout the beta hairpin structure, are most evident within the turn region, where they depend on subtle turn dynamics associated with turn length and secondary structure. We also establish a set of broad design principles, such as the inclusion of aspartic acid residues at a specific position and the careful consideration of desired secondary structure when selecting residues for the turn region, that can be applied to the generation of libraries encoding proteins or peptides containing beta hairpin structures.
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Affiliation(s)
- Cory D DuPai
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.,Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Bryan W Davies
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology, John Ring LaMontagne Center for Infectious Diseases, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - Claus O Wilke
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
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9
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Plant isoquinoline alkaloids as potential neurodrugs: A comparative study of the effects of benzo[c]phenanthridine and berberine-based compounds on β-amyloid aggregation. Chem Biol Interact 2020; 334:109300. [PMID: 33098838 PMCID: PMC7577920 DOI: 10.1016/j.cbi.2020.109300] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/17/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
Herein we present a comparative study of the effects of isoquinoline alkaloids belonging to benzo[c]phenanthridine and berberine families on β-amyloid aggregation. Results obtained using a Thioflavine T (ThT) fluorescence assay and circular dichroism (CD) spectroscopy suggested that the benzo[c]phenanthridine nucleus, present in both sanguinarine and chelerythrine molecules, was directly involved in an inhibitory effect of Aβ1-42 aggregation. Conversely, coralyne, that contains the isomeric berberine nucleus, significantly increased propensity for Aβ1-42 to aggregate. Surface Plasmon Resonance (SPR) experiments provided quantitative estimation of these interactions: coralyne bound to Aβ1-42 with an affinity (KD = 11.6 μM) higher than benzo[c]phenanthridines. Molecular docking studies confirmed that all three compounds are able to recognize Aβ1-42 in different aggregation forms suggesting their effective capacity to modulate the Aβ1-42 self-recognition mechanism. Molecular dynamics simulations indicated that coralyne increased the β-content of Aβ1-42, in early stages of aggregation, consistent with fluorescence-based promotion of the Aβ1-42 self-recognition mechanism by this alkaloid. At the same time, sanguinarine induced Aβ1-42 helical conformation corroborating its ability to delay aggregation as experimentally proved in vitro. The investigated compounds were shown to interfere with aggregation of Aβ1-42 demonstrating their potential as starting leads for the development of therapeutic strategies in neurodegenerative diseases.
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