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Tomasello B, Bellia F, Naletova I, Magrì A, Tabbì G, Attanasio F, Tomasello MF, Cairns WRL, Fortino M, Pietropaolo A, Greco V, La Mendola D, Sciuto S, Arena G, Rizzarelli E. BDNF- and VEGF-Responsive Stimulus to an NGF Mimic Cyclic Peptide with Copper Ionophore Capability and Ctr1/CCS-Driven Signaling. ACS Chem Neurosci 2024; 15:1755-1769. [PMID: 38602894 DOI: 10.1021/acschemneuro.3c00716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024] Open
Abstract
Neurotrophins are a family of growth factors that play a key role in the development and regulation of the functioning of the central nervous system. Their use as drugs is made difficult by their poor stability, cellular permeability, and side effects. Continuing our effort to use peptides that mimic the neurotrophic growth factor (NGF), the family model protein, and specifically the N-terminus of the protein, here we report on the spectroscopic characterization and resistance to hydrolysis of the 14-membered cyclic peptide reproducing the N-terminus sequence (SSSHPIFHRGEFSV (c-NGF(1-14)). Far-UV CD spectra and a computational study show that this peptide has a rigid conformation and left-handed chirality typical of polyproline II that favors its interaction with the D5 domain of the NGF receptor TrkA. c-NGF(1-14) is able to bind Cu2+ with good affinity; the resulting complexes have been characterized by potentiometric and spectroscopic measurements. Experiments on PC12 cells show that c-NGF(1-14) acts as an ionophore, influencing the degree and the localization of both the membrane transporter (Ctr1) and the copper intracellular transporter (CCS). c-NGF(1-14) induces PC12 differentiation, mimics the protein in TrkA phosphorylation, and activates the kinase cascade, inducing Erk1/2 phosphorylation. c-NGF(1-14) biological activities are enhanced when the peptide interacts with Cu2+ even with the submicromolar quantities present in the culture media as demonstrated by ICP-OES measurements. Finally, c-NGF(1-14) and Cu2+ concur to activate the cAMP response element-binding protein CREB that, in turn, induces the brain-derived neurotrophic factor (BDNF) and the vascular endothelial growth factor (VEGF) release.
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Affiliation(s)
- Barbara Tomasello
- Department of Drug and Health Sciences, University of Catania, V.le Andrea Doria 6, Catania 95125, Italy
| | - Francesco Bellia
- Institute of Crystallography, CNR, P. Gaifami 18, Catania 95126, Italy
| | - Irina Naletova
- Institute of Crystallography, CNR, P. Gaifami 18, Catania 95126, Italy
| | - Antonio Magrì
- Institute of Crystallography, CNR, P. Gaifami 18, Catania 95126, Italy
| | - Giovanni Tabbì
- Institute of Crystallography, CNR, P. Gaifami 18, Catania 95126, Italy
| | | | | | - Warren R L Cairns
- Istituto di Scienze Polari (ISP), c/o Campus Scientifico, Università Ca' Foscari Venezia Via Torino, Venezia Mestre 155-30170, Italy
| | - Mariagrazia Fortino
- Dipartimento di Scienze della Salute, Università di Catanzaro, Viale Europa, Catanzaro 88100, Italy
| | - Adriana Pietropaolo
- Dipartimento di Scienze della Salute, Università di Catanzaro, Viale Europa, Catanzaro 88100, Italy
| | - Valentina Greco
- Department of Chemical Sciences, University of Catania, A. Doria 6, Catania 95125, Italy
| | - Diego La Mendola
- Department of Pharmaceutical Sciences, University of Pisa, Bonanno Pisano 12, Pisa 56126, Italy
| | - Sebastiano Sciuto
- Department of Chemical Sciences, University of Catania, A. Doria 6, Catania 95125, Italy
| | - Giuseppe Arena
- Department of Chemical Sciences, University of Catania, A. Doria 6, Catania 95125, Italy
| | - Enrico Rizzarelli
- Institute of Crystallography, CNR, P. Gaifami 18, Catania 95126, Italy
- Department of Chemical Sciences, University of Catania, A. Doria 6, Catania 95125, Italy
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2
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Kijewska M, Wołczański G, Kosson P, Wieczorek R, Lisowski M, Stefanowicz P. Stapling of leu-enkephalin analogs with bifunctional reagents for prolonged analgesic activity. Chem Commun (Camb) 2024; 60:3023-3026. [PMID: 38356394 DOI: 10.1039/d3cc06345c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The design and synthesis of leu-enkephalin analogs by replacing the glycine residues with N-(2-thioethyl)glycines and opening the cyclisation potential is presented. The cyclization (stapling) was achieved using bifunctional reagents (hexafluorobenzene and trithiocyanuric acid derivatives). The CD conformational studies of the stapled analogs suggest that the peptides adopt the type I β-turn conformation, which is in agreement with the theoretical analysis. The analog containing a trithiocyanuric acid derivative with a benzyl substituent shows potent analgesic activity.
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Affiliation(s)
- Monika Kijewska
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Grzegorz Wołczański
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Piotr Kosson
- Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106 Warszawa, Poland
| | - Robert Wieczorek
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Marek Lisowski
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - Piotr Stefanowicz
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland.
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Kaganovich M, Taha M, Zig U, Tshuva EY, Shalev DE, Gamliel A, Reches M. Self-Assembly of a Dipeptide with a Reduced Amount of Copper into Antifungal and Antibacterial Particles. Biomacromolecules 2024; 25:1018-1026. [PMID: 38252413 DOI: 10.1021/acs.biomac.3c01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
With the growing concern over the environmental impact and health risks associated with conventional pesticides, there is a great need for developing safer and more sustainable alternatives. This study demonstrates the self-assembly of antimicrobial and antifungal spherical particles by a dipeptide utilizing a reduced amount of copper salt compared to the commonly employed formulation. The particles can be sprayed on a surface and form an antimicrobial coating. The effectiveness of the coating against the bacteria Pectobacterium brasiliense, a common pathogen affecting potato crops, was demonstrated, as the coating reduced the bacterial load by 7.3 log. Moreover, a comprehensive field trial was conducted, where the formulation was applied to potato seeds. Remarkably, it exhibited good efficacy against three prevalent potato pathogens (P. brasiliense, Pythium spp., and Spongospora subterranea) while demonstrating no phytotoxic effects on the potatoes. These findings highlight the tremendous potential of this formulation as a nonphytotoxic alternative to replace hazardous pesticides currently available in the market.
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Affiliation(s)
- Michaela Kaganovich
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Mohammad Taha
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Uri Zig
- Hevel Maon Enterprises, Negev 8551900, Israel
| | - Edit Y Tshuva
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Deborah E Shalev
- Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 9190500, Israel
- Department of Pharmaceutical Engineering, Azrieli College of Engineering, Jerusalem 9103501, Israel
| | - Abraham Gamliel
- Laboratory for Pest Management Research, Institute of Agricultural Engineering, ARO─The Volcani Center, Rishon LeZion 7505001, Israel
| | - Meital Reches
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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4
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Baral B, Panigrahi B, Kar A, Tulsiyan KD, Suryakant U, Mandal D, Subudhi U. Peptide nanostructures-based delivery of DNA nanomaterial therapeutics for regulating gene expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:493-510. [PMID: 37583574 PMCID: PMC10424151 DOI: 10.1016/j.omtn.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/14/2023] [Indexed: 08/17/2023]
Abstract
Self-assembled branched DNA (bDNA) nanomaterials have exhibited their functionality in various biomedical and diagnostic applications. However, the anionic cellular membrane has restricted the movement of bDNA nanostructures. Recently, amphiphilic peptides have been investigated as cationic delivery agents for nucleic acids. Herein, we demonstrate a strategy for delivering functional bDNA nanomaterials into mammalian cells using self-assembled linear peptides. In this study, antisense oligonucleotides of vascular endothelial growth factor (VEGF) were inserted in the overhangs of bDNAs. Novel linear peptides have been synthesized and the peptide-bound bDNA complex formation was examined using various biophysical experiments. Interestingly, the W4R4-bound bDNAs were found to be exceptionally stable against DNase I compared to other complexes. The delivery of fluorescent-labeled bDNAs into the mammalian cells confirmed the potential of peptide transporters. Furthermore, the functional efficacy of the peptide-bound bDNAs has been examined through RT-PCR and western blot analysis. The observed results revealed that W4R4 peptides exhibited excellent internalization of antisense bDNAs and significantly suppressed (3- to 4-fold) the transcripts and translated product of VEGF compared to the control. In summary, the results highlight the potential use of peptide-based nanocarrier for delivering bDNA nanostructures to regulate the gene expression in cell lines.
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Affiliation(s)
- Bineeth Baral
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bijayananda Panigrahi
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
- Biopioneer Private Limited, Bhubaneswar 751024, Odisha, India
| | - Avishek Kar
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kiran D. Tulsiyan
- School of Chemical Sciences, National Institute of Science Education & Research, Bhubaneswar 752050, India
- Homi Bhaba National Institute, Mumbai 400094, India
| | - Uday Suryakant
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
| | - Dindyal Mandal
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
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Caramiello A, Bellucci MC, Cristina G, Castellano C, Meneghetti F, Mori M, Secundo F, Viani F, Sacchetti A, Volonterio A. Synthesis and Conformational Analysis of Hydantoin-Based Universal Peptidomimetics. J Org Chem 2023; 88:10381-10402. [PMID: 36226862 PMCID: PMC10407853 DOI: 10.1021/acs.joc.2c01903] [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: 08/10/2022] [Indexed: 11/30/2022]
Abstract
The synthesis of a collection of enantiomerically pure, systematically substituted hydantoins as structural privileged universal mimetic scaffolds is presented. It relies on a chemoselective condensation/cyclization domino process between isocyanates of quaternary or unsubstituted α-amino esters and N-alkyl aspartic acid diesters followed by standard hydrolysis/coupling reactions with amines, using liquid-liquid acid/base extraction protocols for the purification of the intermediates. Besides the nature of the α carbon on the isocyanate moiety, either a quaternary carbon or a more flexible methylene group, conformational studies in silico (molecular modeling), in solution (NMR, circular dichroism (CD), Fourier transform infrared (FTIR)), and in solid state (X-ray) showed that the presented hydantoin-based peptidomimetics are able to project their substituents in positions superimposable to the side chains of common protein secondary structures such as α-helix and β-turn, being the open α-helix conformation slightly favorable according to molecular modeling, while the closed β-turn conformation preferred in solution and in solid state.
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Affiliation(s)
- Alessio
M. Caramiello
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Maria Cristina Bellucci
- Department
of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133Milano, Italy
| | - Gaetano Cristina
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Carlo Castellano
- Department
of Chemistry, Università degli Studi
di Milano, via Golgi
19, 20133Milano, Italy
| | - Fiorella Meneghetti
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Matteo Mori
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Francesco Secundo
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Fiorenza Viani
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Alessandro Sacchetti
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Alessandro Volonterio
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
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Stereochemistry of Chiral 2-Substituted Chromanes: Twist of the Dihydropyran Ring and Specific Optical Rotation. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28010439. [PMID: 36615631 PMCID: PMC9823451 DOI: 10.3390/molecules28010439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023]
Abstract
Chiral 2-substituted chromanes are important substructures in organic synthesis and appear in numerous natural products. Herein, the correlation between specific optical rotations (SORs) and the stereochemistry at C2 of chiral 2-substituted chromanes was investigated through data mining, quantum-chemical calculations using density functional theory (DFT), and mechanistic analyses. For 2-aliphatic (including acyloxy and alkenyl) chromanes, the P-helicity of the dihydropyran ring usually corresponds to a positive SOR; however, 2-aryl chromanes with P-helicity tend to exhibit negative SORs. 2-Carboxyl (including alkoxycarbonyl and carbonyl) chromanes often display small experimental SORs, and theoretical calculations for them are prone to error because of the fluctuating conformational distribution with computational parameters. Several typical compounds were discussed, including detailed descriptions of the asymmetric synthesis, absolute configuration (AC) assignment methods, and systematic conformational analysis. We hope this work will enrich the knowledge of the stereochemistry of chiral 2-substituted chromanes.
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Pereira MR, dos Santos VR, de Oliveira WC, Duque C, da Silva BF, Santos-Filho NA, Carneiro VA, Lorenzón EN, Cilli EM. Effects of Conjugation of Ferrocene and Gallic Acid On desCys 11/Lys 12/Lys 13-(p-BthTX-I) 2K Peptide: Structure, Permeabilization and Antibacterial Activity. Protein Pept Lett 2023; 30:690-698. [PMID: 37488753 DOI: 10.2174/0929866530666230721112129] [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: 04/17/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND Antimicrobial resistance is an emerging global health challenge that has led researchers to study alternatives to conventional antibiotics. A promising alternative is antimicrobial peptides (AMPs), produced as the first line of defense by almost all living organisms. To improve its biological activity, the conjugation of AMPs is a promising approach. OBJECTIVE In this study, we evaluated the N-terminal conjugation of p-Bt (a peptide derived from Bothrops Jararacuçu`s venom) with ferrocene (Fc) and gallic acid (GA). Acetylated and linear versions of p-Bt were also synthesized to evaluate the importance of N-terminal charge and dimeric structure. METHODS The compounds were obtained using solid-phase peptide synthesis. Circular dichroism, vesicle permeabilization, antimicrobial activity, and cytotoxicity studies were conducted. RESULTS No increase in antibacterial activity against Escherichia coli was observed by adding either Fc or GA to p-Bt. However, Fc-p-Bt and GA-p-Bt exhibited improved activity against Staphylococcus aureus. No cytotoxicity upon fibroblast was observed for GA-p-Bt. On the other hand, conjugation with Fc increased cytotoxicity. This toxicity may be related to the membrane permeabilization capacity of this bioconjugate, which showed the highest carboxyfluorescein leakage in vesicle permeabilization experiments. CONCLUSION Considering these observations, our findings highlight the importance of adding bioactive organic compounds in the N-terminal position as a tool to modulate the activity of AMPs.
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Affiliation(s)
- Marina Rodrigues Pereira
- Departamento de Bioquímica e Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), SP, 14800-060, São Paulo, Araraquara, Brasil
| | - Vanessa Rodrigues dos Santos
- Departamento de Odontologia Preventiva e Restauradora, Faculdade de Odontologia de Araçatuba, Universidade Estadual Paulista (UNESP), Araçatuba 16015-050, SP, Brasil
| | - Warlley Campos de Oliveira
- Departamento de Odontologia Preventiva e Restauradora, Faculdade de Odontologia de Araçatuba, Universidade Estadual Paulista (UNESP), Araçatuba 16015-050, SP, Brasil
| | - Cristiane Duque
- Departamento de Odontologia Preventiva e Restauradora, Faculdade de Odontologia de Araçatuba, Universidade Estadual Paulista (UNESP), Araçatuba 16015-050, SP, Brasil
- Dental Research Institute, Faculdade de Odontologia, Universidade de Toronto, Toronto, ONM5G 1G6, Canadá
| | - Benise Ferreira da Silva
- Núcleo de Bioprospecção e Experimentação Molecular Aplicada (NUBEM), Centro Universitário INTA - UNINTA, Sobral, 62050-100, Ceará, Brasil
| | - Norival Alves Santos-Filho
- Departamento de Bioquímica e Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), SP, 14800-060, São Paulo, Araraquara, Brasil
| | - Victor Alves Carneiro
- Núcleo de Bioprospecção e Experimentação Molecular Aplicada (NUBEM), Centro Universitário INTA - UNINTA, Sobral, 62050-100, Ceará, Brasil
| | | | - Eduardo Maffud Cilli
- Departamento de Bioquímica e Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), SP, 14800-060, São Paulo, Araraquara, Brasil
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Xiao S, Wang Z, Zhang H, Zhao L, Chang Q, Zhang X, Yan R, Wu X, Jin Y. Photoinduced Synthesis of Methylated Marine Cyclopeptide Galaxamide Analogs with Isoindolinone as Anticancer Agents. Mar Drugs 2022; 20:md20060379. [PMID: 35736182 PMCID: PMC9227305 DOI: 10.3390/md20060379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/16/2022] Open
Abstract
The methylation of amino acid residues has played an important role in the biological function of bioactive peptides. In this paper, various methyl-modified and stereostructural-modified marine cyclopeptide galaxamide analogs with isoindolinone were synthesized by a photoinduced single electron transfer cyclization reaction. It was found that the single-methyl substitution was beneficial for the bioactivity of cyclic analogs with isoindolinone fragments, and the influence of methylation on bioactivity is uncertain and is sometimes case-specific. The compound with a single methyl group at Gly5 (compound 8) showed the strongest antiproliferative activity against HepG-2 cells. The tumor cell apoptosis, cell cycle, mitochondrial membrane potential, intracellular Ca2+ concentration and lactate dehydrogenase activity have been studied extensively to evaluate the antitumor potential of compound 8. Western blotting tests showed that compound 8 could decrease the MDM2 level and increase p53 levels efficiently. Careful molecular docking suggested that cyclic peptide 8 could bind firmly with MDM2 oncoprotein, indicating that MDM2 may be a potential drug target of the prepared peptides.
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Hameed DS, Ovaa H, van der Heden van Noort GJ, Sapmaz A. Inhibiting UCH-L5: Rational Design of a Cyclic Ubiquitin-Based Peptide Inhibitor. Front Mol Biosci 2022; 9:866467. [PMID: 35720124 PMCID: PMC9204298 DOI: 10.3389/fmolb.2022.866467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
The ubiquitin-proteasome system is an essential regulator of many cellular processes including controlling protein homeostasis. The degradation of proteins by the multi-subunit proteasome complex is tightly regulated through a series of checkpoints, amongst which are a set of deubiquitinating proteases (DUBs). The proteasome-associated DUBs, UCH-L5 (Ubiquitin carboxyl-terminal hydrolase isozyme L5) and USP14 (Ubiquitin-specific protease 14), and the integral-DUB in the proteasome, Rpn11, is known to regulate proteasomal degradation by deubiquitination of distinct substrates. Although selective inhibitors for USP14 and Rpn11 have been recently developed, there are no known inhibitors that selectively bind to UCH-L5. The X-ray structure of the Ubiquitin (Ub) bound to UCH-L5 shows a β-sheet hairpin in Ub that contains a crucial hydrophobic patch involved in the interaction with UCH-L5. Herein, we designed and developed both a Ub sequence-based linear- and cyclic- β-sheet hairpin peptide that was found to preferably inhibit UCH-L5. We show that these peptides have low micromolar IC50 values and the cyclic peptide competes with the activity-based UbVME (Ubiquitin-Vinyl-Methyl-Ester) probe for UCH-L5, binding in a concentration-dependent manner. We further establish the selectivity profile of the cyclic peptide for UCH-L5 compared to other members of the UCH-DUB family and other cysteine DUBs in cell lysate. Furthermore, the cyclic peptide infiltrated cells resulting in the accumulation of polyUb chains, and was found to be non-toxic at the concentrations used here. Taken together, our data suggest that the cyclic peptide permeates the cell membrane, inhibits UCH-L5 by possibly blocking its deubiquitinating function, and contributes to the accumulation of polyubiquitinated substrates. The implications of inhibiting UCH-L5 in the context of the 26S proteasome render it an attractive candidate for further development as a potential selective inhibitor for therapeutic purposes.
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Affiliation(s)
| | | | | | - Aysegul Sapmaz
- *Correspondence: Gerbrand J. van der Heden van Noort, ; Aysegul Sapmaz,
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10
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Saemi Yokomichi MA, Leite Silva HR, Eivazian Vianna Nogueira Brandao L, Festozo Vicente E, Batista Junior JM. Conformational preferences induced by cyclization in orbitides: a vibrational CD study. Org Biomol Chem 2022; 20:1306-1314. [DOI: 10.1039/d1ob02170b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Orbitides are bioactive head-to-tail natural cyclic peptides from plant species. Their bioactivity is intrinsically related to the main conformations adopted in solution, whose correct characterization represents an important bottleneck for...
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11
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Gupta MK, Jena CK, Balachandra C, Sharma NK. Unusual Pseudopeptides: Syntheses and Structural Analyses of Ethylenediprolyl Peptides and Their Metal Complexes with Cu(II) Ion. J Org Chem 2021; 86:16327-16336. [PMID: 34783560 DOI: 10.1021/acs.joc.1c01676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthetic unnatural amino acids and their peptides as peptidomimetics have shown remarkable structural and functional properties. In the repertoire of synthetic peptides, pseudopeptides have emerged as attractive small peptidomimetics that are capable of forming the characteristic secondary structures in the solid/solution phase, as in natural peptides. This report describes the synthesis and structural analyses of novel pseudopeptides as ethylenediprolyl (etpro) tetra/hexapeptides, comprising a chiral diaminedicarboxylate scaffold. Their NMR and CD spectral analyses strongly support the formation of the β-turn-type structures in organic solvents (ACN/MeOH). Further, the single-crystal X-ray studies of tetrapseudopeptide confirm the formation of a unique self-assembly structure as β-strand type in the solid state through hydrogen bonding. Importantly, their diamine moiety influences the formation of Cu-complexes with Cu(II) ions. A tetrapseudopeptide monocarboxylate-Cu(II) complex forms the single crystal that is studied by the single-crystal X-ray diffractometer. The crystal structure of the tetrapseudopeptide-Cu(II) complex confirms the formation of the distorted square planar geometry structure, almost like the amyloid β(Aβ)-peptide-Cu(II) complex structural geometry. Hence, these etpro-pseudopeptides are emerging peptidomimatics that form β-turn types of structures and metal complexes mainly with Cu(II) ions. These molecules could be considered for the development of peptide-based catalysts and peptide-based therapeutic drug candidates.
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Affiliation(s)
- Manish K Gupta
- National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni Campus, Bhubaneswar 752050, India.,Homi Bhabha National Institute (HBNI), Mumbai 400094, India
| | - Chinmay K Jena
- National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni Campus, Bhubaneswar 752050, India.,Homi Bhabha National Institute (HBNI), Mumbai 400094, India
| | - Chenikkayala Balachandra
- National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni Campus, Bhubaneswar 752050, India.,Homi Bhabha National Institute (HBNI), Mumbai 400094, India
| | - Nagendra K Sharma
- National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni Campus, Bhubaneswar 752050, India.,Homi Bhabha National Institute (HBNI), Mumbai 400094, India
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Kieserling H, Giefer P, Uttinger MJ, Lautenbach V, Nguyen T, Sevenich R, Lübbert C, Rauh C, Peukert W, Fritsching U, Drusch S, Maria Wagemans A. Structure and adsorption behavior of high hydrostatic pressure-treated β-lactoglobulin. J Colloid Interface Sci 2021; 596:173-183. [PMID: 33839350 DOI: 10.1016/j.jcis.2021.03.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/24/2021] [Accepted: 03/09/2021] [Indexed: 12/18/2022]
Abstract
HYPOTHESIS High hydrostatic pressure treatment causes structural changes in interfacial-active β-lactoglobulin (β-lg). We hypothesized that the pressure-induced structural changes affect the intra- and intermolecular interactions which determine the interfacial activity of β-lg. The conducted experimental and numerical investigations could contribute to the mechanistic understanding of the adsorption behavior of proteins in food-related emulsions. EXPERIMENTS We treated β-lg in water at pH 7 with high hydrostatic pressures up to 600 MPa for 10 min at 20 °C. The secondary structure was characterized with Fourier-transform infrared spectroscopy (FTIR) and circular dichroism (CD), the surface hydrophobicity and charge with fluorescence-spectroscopy and ζ-potential, and the quaternary structure with membrane-osmometry, analytical ultracentrifugation (AUC) and mass spectrometry (MS). Experimental analyses were supported through molecular dynamic (MD) simulations. The adsorption behavior was investigated with pendant drop analysis. FINDINGS MD simulation revealed a pressure-induced molten globule state of β-lg, confirmed by an unfolding of β-sheets with FTIR, a stabilization of α-helices with CD and loss in tertiary structure induced by an increase in surface hydrophobicity. Membrane-osmometry, AUC and MS indicated the formation of non-covalently linked dimers that migrated slower through the water phase, adsorbed more quickly due to hydrophobic interactions with the oil, and lowered the interfacial tension more strongly than reference β-lg.
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Affiliation(s)
- Helena Kieserling
- Technische Universität Berlin, Department of Food Colloids, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Patrick Giefer
- Leibniz Institute for Materials Engineering-IWT, Particles and Process Engineering, Badgasteiner Str. 3, 28359 Bremen, Germany.
| | - Maximilian J Uttinger
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Haberstrasse 9a, 91058 Erlangen, Germany.
| | - Vanessa Lautenbach
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Haberstrasse 9a, 91058 Erlangen, Germany.
| | - Thu Nguyen
- Technische Universität Berlin, Department of Food Colloids, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Robert Sevenich
- Technische Universität Berlin, Department of Food Biotechnology and Process Engineering, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Christian Lübbert
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Haberstrasse 9a, 91058 Erlangen, Germany.
| | - Cornelia Rauh
- Technische Universität Berlin, Department of Food Biotechnology and Process Engineering, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Wolfgang Peukert
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Haberstrasse 9a, 91058 Erlangen, Germany.
| | - Udo Fritsching
- Leibniz Institute for Materials Engineering-IWT, Particles and Process Engineering, Badgasteiner Str. 3, 28359 Bremen, Germany; University of Bremen, Particles and Process Engineering, Bibliothekstraße 1, 28359 Bremen, Germany.
| | - Stephan Drusch
- Technische Universität Berlin, Department of Food Technology and Food Material Science, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Anja Maria Wagemans
- Technische Universität Berlin, Department of Food Colloids, Straße des 17. Juni 135, 10623 Berlin, Germany.
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13
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Shmool TA, Martin LK, Bui-Le L, Moya-Ramirez I, Kotidis P, Matthews RP, Venter GA, Kontoravdi C, Polizzi KM, Hallett JP. An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid. Chem Sci 2021; 12:9528-9545. [PMID: 34349928 PMCID: PMC8278930 DOI: 10.1039/d1sc02520a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/26/2021] [Indexed: 12/26/2022] Open
Abstract
Understanding protein folding in different environmental conditions is fundamentally important for predicting protein structures and developing innovative antibody formulations. While the thermodynamics and kinetics of folding and unfolding have been extensively studied by computational methods, experimental methods for determining antibody conformational transition pathways are lacking. Motivated to fill this gap, we prepared a series of unique formulations containing a high concentration of a chimeric immunoglobin G4 (IgG4) antibody with different excipients in the presence and absence of the ionic liquid (IL) choline dihydrogen phosphate. We determined the effects of different excipients and IL on protein thermal and structural stability by performing variable temperature circular dichroism and bio-layer interferometry analyses. To further rationalise the observations of conformational changes with temperature, we carried out molecular dynamics simulations on a single antibody binding fragment from IgG4 in the different formulations, at low and high temperatures. We developed a methodology to study the conformational transitions and associated thermodynamics of biomolecules, and we showed IL-induced conformational transitions. We showed that the increased propensity for conformational change was driven by preferential binding of the dihydrogen phosphate anion to the antibody fragment. Finally, we found that a formulation containing IL with sugar, amino acids and surfactant is a promising candidate for stabilising proteins against conformational destabilisation and aggregation. We hope that ultimately, we can help in the quest to understand the molecular basis of the stability of antibodies and protein misfolding phenomena and offer new candidate formulations with the potential to revive lost therapeutic candidates.
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Affiliation(s)
- Talia A Shmool
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Laura K Martin
- Department of Engineering Science, University of Oxford Parks Road Oxford OX1 3PJ UK
| | - Liem Bui-Le
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Ignacio Moya-Ramirez
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Pavlos Kotidis
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Richard P Matthews
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Gerhard A Venter
- Scientific Computing Research Unit, Department of Chemistry, University of Cape Town Rondebosch Cape Town 7701 South Africa
| | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Karen M Polizzi
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
| | - Jason P Hallett
- Department of Chemical Engineering, Imperial College London South Kensington Campus London SW7 2AZ UK +44 (0)20 7594 5388
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Clarke DE, Wu G, Wu C, Scherman OA. Host-Guest Induced Peptide Folding with Sequence-Specific Structural Chirality. J Am Chem Soc 2021; 143:6323-6327. [PMID: 33860670 PMCID: PMC8154536 DOI: 10.1021/jacs.1c00342] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Controlling the spatial and temporal behavior of peptide segments is essential in the fabrication of functional peptide-based materials and nanostructures. To achieve a desired structure, complex sequence design is often required, coupled with the inclusion of unnatural amino acids or synthetic modifications. Herein, we investigate the structural properties of 1:1 inclusion complexes between specific oligopeptides and cucurbit[8]uril (CB[8]), inducing the formation of turns, and by alteration of the peptide sequence, tunable structural chirality. We also explore extended peptide sequence binding with CB[8], demonstrating a simple approach to construct a peptide hairpin.
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Affiliation(s)
- David E Clarke
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Guanglu Wu
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Ce Wu
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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15
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Halat M, Klimek-Chodacka M, Orleanska J, Baranska M, Baranski R. Electronic Circular Dichroism of the Cas9 Protein and gRNA:Cas9 Ribonucleoprotein Complex. Int J Mol Sci 2021; 22:2937. [PMID: 33805827 PMCID: PMC8002190 DOI: 10.3390/ijms22062937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/26/2022] Open
Abstract
The Streptococcus pyogenes Cas9 protein (SpCas9), a component of CRISPR-based immune system in microbes, has become commonly utilized for genome editing. This nuclease forms a ribonucleoprotein (RNP) complex with guide RNA (gRNA) which induces Cas9 structural changes and triggers its cleavage activity. Here, electronic circular dichroism (ECD) spectroscopy was used to confirm the RNP formation and to determine its individual components. The ECD spectra had characteristic features differentiating Cas9 and gRNA, the former showed a negative/positive profile with maxima located at 221, 209 and 196 nm, while the latter revealed positive/negative/positive/negative pattern with bands observed at 266, 242, 222 and 209 nm, respectively. For the first time, the experimental ECD spectrum of the gRNA:Cas9 RNP complex is presented. It exhibits a bisignate positive/negative ECD couplet with maxima at 273 and 235 nm, and it differs significantly from individual spectrum of each RNP components. Additionally, the Cas9 protein and RNP complex retained biological activity after ECD measurements and they were able to bind and cleave DNA in vitro. Hence, we conclude that ECD spectroscopy can be considered as a quick and non-destructive method of monitoring conformational changes of the Cas9 protein as a result of Cas9 and gRNA interaction, and identification of the gRNA:Cas9 RNP complex.
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Affiliation(s)
- Monika Halat
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (M.H.); (J.O.)
| | - Magdalena Klimek-Chodacka
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. 29 Listopada 54, 31-425 Krakow, Poland;
| | - Jagoda Orleanska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (M.H.); (J.O.)
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (M.H.); (J.O.)
- Jagiellonian Centre for Experimental Therapeutics (JCET), Bobrzyńskiego 14, 30-348 Krakow, Poland
| | - Rafal Baranski
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. 29 Listopada 54, 31-425 Krakow, Poland;
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Composition and in silico structural analysis of fibroin from liquid silk of non-mulberry silkworm Antheraea assamensis. Int J Biol Macromol 2020; 163:1947-1958. [PMID: 32910960 DOI: 10.1016/j.ijbiomac.2020.08.232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 11/24/2022]
Abstract
Silk is spun from the liquid precursor known as liquid silk secreted from the posterior part and stored in the silk gland lumen with occurrence of many momentary events. The liquid silk in the silk gland is transformed to the spun silk fibre. In this study the elucidation of the protein components of liquid silk from the posterior part of the silk gland (PSG) of saturniid silkworm Antheraea assamensis along with its structural characterization has been reported. The 3D model of the N-terminal amorphous portion with some repeat crystalline motifs (19-255) of core protein fibroin has also been constructed. 1D and 2D electrophoresis revealed the homo-dimeric structure of the silk protein. Secondary structure analysis by Circular dichroism, FTIR spectroscopy showed α helical structural component as predominant conformation in the liquid silk. The crystalline structure investigated through X ray diffraction (XRD) analysis also revealed the presence of less ordered amorphous α helical conformation in the liquid silk. The 3D structural model proposed of the residues from 19 to 255 has revealed structural stability throughout the molecular dynamics simulation process. This study will provide the detailed structural information and in silico analysis of the core protein present in the liquid silk of PSG.
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