1
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Palmioli A, Airoldi C. An NMR Toolkit to Probe Amyloid Oligomer Inhibition in Neurodegenerative Diseases: From Ligand Screening to Dissecting Binding Topology and Mechanisms of Action. Chempluschem 2024:e202400243. [PMID: 38712695 DOI: 10.1002/cplu.202400243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
The aggregation of amyloid peptides and proteins into toxic oligomers is a hallmark of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Machado-Joseph's disease, and transmissible spongiform encephalopathies. Inhibition of amyloid oligomers formation and interactions with biological counterparts, as well as the triggering of non-toxic amorphous aggregates, are strategies towards preventive interventions against these pathologies. NMR spectroscopy addresses the need for structural characterization of amyloid proteins and their aggregates, their binding to inhibitors, and rapid screening of compound libraries for ligand identification. Here we briefly discuss the solution experiments constituting the NMR spectroscopist's toolkit and provide examples of their application.
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Affiliation(s)
- Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, P.zza della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, P.zza della Scienza 2, 20126, Milan, Italy
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2
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Palmioli A, Moretti L, Vezzoni CA, Legnani L, Sperandeo P, Baldini L, Sansone F, Airoldi C, Casnati A. Multivalent calix[4]arene-based mannosylated dendrons as new FimH ligands and inhibitors. Bioorg Chem 2023; 138:106613. [PMID: 37224739 DOI: 10.1016/j.bioorg.2023.106613] [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] [Received: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023]
Abstract
We report the synthesis and biological characterization of a novel class of multivalent glycoconjugates as hit compounds for the design of new antiadhesive therapies against urogenital tract infections (UTIs) caused by uropathogenic E. coli strains (UPEC). The first step of UTIs is the molecular recognition of high mannose N-glycan expressed on the surface of urothelial cells by the bacterial lectin FimH, allowing the pathogen adhesion required for mammalian cell invasion. The inhibition of FimH-mediated interactions is thus a validated strategy for the treatment of UTIs. To this purpose, we designed and synthesized d-mannose multivalent dendrons supported on a calixarene core introducing a significant structural change from a previously described family of dendrimers bearing the same dendrons units on a flexible pentaerythritol scaffold core. The new molecular architecture increased the inhibitory potency against FimH-mediated adhesion processes by about 16 times, as assessed by yeast agglutination assay. Moreover, the direct molecular interaction of the new compounds with FimH protein was assessed by on-cell NMR experiments acquired in the presence of UPEC cells.
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Affiliation(s)
- Alessandro Palmioli
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy
| | - Luca Moretti
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy
| | - Carlo Alberto Vezzoni
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Laura Legnani
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy
| | - Paola Sperandeo
- Department of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti, 9/11/13, 20133 Milano, Italy
| | - Laura Baldini
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Francesco Sansone
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Cristina Airoldi
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy.
| | - Alessandro Casnati
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 17/a, 43124 Parma, Italy.
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3
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Jenkins CH, Scott AE, O’Neill PA, Norville IH, Prior JL, Ireland PM. The Arabinose 5-Phosphate Isomerase KdsD Is Required for Virulence in Burkholderia pseudomallei. J Bacteriol 2023; 205:e0003423. [PMID: 37458584 PMCID: PMC10448790 DOI: 10.1128/jb.00034-23] [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: 01/27/2023] [Accepted: 06/06/2023] [Indexed: 08/25/2023] Open
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis, which is endemic primarily in Southeast Asia and northern Australia but is increasingly being seen in other tropical and subtropical regions of the world. Melioidosis is associated with high morbidity and mortality rates, which is mediated by the wide range of virulence factors encoded by B. pseudomallei. These virulence determinants include surface polysaccharides such as lipopolysaccharide (LPS) and capsular polysaccharides (CPS). Here, we investigated a predicted arabinose-5-phosphate isomerase (API) similar to KdsD in B. pseudomallei strain K96243. KdsD is required for the production of the highly conserved 3-deoxy-d-manno-octulosonic acid (Kdo), a key sugar in the core region of LPS. Recombinant KdsD was expressed and purified, and API activity was determined. Although a putative API paralogue (KpsF) is also predicted to be encoded, the deletion of kdsD resulted in growth defects, loss of motility, reduced survival in RAW 264.7 murine macrophages, and attenuation in a BALB/c mouse model of melioidosis. Suppressor mutations were observed during a phenotypic screen for motility, revealing single nucleotide polymorphisms or indels located in the poorly understood CPS type IV cluster. Crucially, suppressor mutations did not result in reversion of attenuation in vivo. This study demonstrates the importance of KdsD for B. pseudomallei virulence and highlights further the complex nature of the polysaccharides it produces. IMPORTANCE The intrinsic resistance of B. pseudomallei to many antibiotics complicates treatment. This opportunistic pathogen possesses a wide range of virulence factors, resulting in severe and potentially fatal disease. Virulence factors as targets for drug development offer an alternative approach to combat pathogenic bacteria. Prior to initiating early drug discovery approaches, it is important to demonstrate that disruption of the target gene will prevent the development of disease. This study highlights the fact that KdsD is crucial for virulence of B. pseudomallei in an animal model of infection and provides supportive phenotypic characterization that builds a foundation for future therapeutic development.
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Affiliation(s)
- Christopher H. Jenkins
- Chemical, Biological and Radiological Division, Defence Science and Technology Laboratory, Salisbury, Wiltshire, United Kingdom
| | - Andrew E. Scott
- Chemical, Biological and Radiological Division, Defence Science and Technology Laboratory, Salisbury, Wiltshire, United Kingdom
| | - Paul A. O’Neill
- University of Exeter Sequencing Service, Exeter, United Kingdom
| | - Isobel H. Norville
- Chemical, Biological and Radiological Division, Defence Science and Technology Laboratory, Salisbury, Wiltshire, United Kingdom
- Biosciences Department, University of Exeter, Exeter, United Kingdom
| | - Joann L. Prior
- Chemical, Biological and Radiological Division, Defence Science and Technology Laboratory, Salisbury, Wiltshire, United Kingdom
- Biosciences Department, University of Exeter, Exeter, United Kingdom
- Southampton General Hospital, Southampton, United Kingdom
| | - Philip M. Ireland
- Chemical, Biological and Radiological Division, Defence Science and Technology Laboratory, Salisbury, Wiltshire, United Kingdom
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4
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Palmioli A, Sperandeo P, Bertuzzi S, Polissi A, Airoldi C. On-cell saturation transfer difference NMR for the identification of FimH ligands and inhibitors. Bioorg Chem 2021; 112:104876. [PMID: 33845337 DOI: 10.1016/j.bioorg.2021.104876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/14/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022]
Abstract
We describe the development of an on-cell NMR method for the rapid screening of FimH ligands and the structural identification of ligand binding epitopes. FimH is a mannose-binding bacterial adhesin expressed at the apical end of type 1 pili of uropathogenic bacterial strains and responsible for their d-mannose sensitive adhesion to host mammalian epithelial cells. Because of these properties, FimH is a key virulence factor and an attractive therapeutic target for urinary tract infection. We prepared synthetic d-mannose decorated dendrimers, we tested their ability to prevent the FimH-mediated yeast agglutination, and thus we used the compounds showing the best inhibitory activity as models of FimH multivalent ligands to set up our NMR methodology. Our experimental protocol, based on on-cell STD NMR techniques, is a suitable tool for the screening and the epitope mapping of FimH ligands aimed at the development of new antiadhesive and diagnostic tools against urinary tract infection pathogens. Notably, the study is carried out in a physiological environment, i.e. at the surface of living pathogen cells expressing FimH.
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Affiliation(s)
- Alessandro Palmioli
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy.
| | - Paola Sperandeo
- Department of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti, 9/11/13, 20133 Milano, Italy
| | - Sara Bertuzzi
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy; Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC-bioGUNE), 48160 Derio, Spain
| | - Alessandra Polissi
- Department of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti, 9/11/13, 20133 Milano, Italy
| | - Cristina Airoldi
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy.
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Dezanet C, Kempf J, Mingeot-Leclercq MP, Décout JL. Amphiphilic Aminoglycosides as Medicinal Agents. Int J Mol Sci 2020; 21:E7411. [PMID: 33049963 PMCID: PMC7583001 DOI: 10.3390/ijms21197411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 12/25/2022] Open
Abstract
The conjugation of hydrophobic group(s) to the polycationic hydrophilic core of the antibiotic drugs aminoglycosides (AGs), targeting ribosomal RNA, has led to the development of amphiphilic aminoglycosides (AAGs). These drugs exhibit numerous biological effects, including good antibacterial effects against susceptible and multidrug-resistant bacteria due to the targeting of bacterial membranes. In the first part of this review, we summarize our work in identifying and developing broad-spectrum antibacterial AAGs that constitute a new class of antibiotic agents acting on bacterial membranes. The target-shift strongly improves antibiotic activity against bacterial strains that are resistant to the parent AG drugs and to antibiotic drugs of other classes, and renders the emergence of resistant Pseudomonas aeruginosa strains highly difficult. Structure-activity and structure-eukaryotic cytotoxicity relationships, specificity and barriers that need to be crossed in their development as antibacterial agents are delineated, with a focus on their targets in membranes, lipopolysaccharides (LPS) and cardiolipin (CL), and the corresponding mode of action against Gram-negative bacteria. At the end of the first part, we summarize the other recent advances in the field of antibacterial AAGs, mainly published since 2016, with an emphasis on the emerging AAGs which are made of an AG core conjugated to an adjuvant or an antibiotic drug of another class (antibiotic hybrids). In the second part, we briefly illustrate other biological and biochemical effects of AAGs, i.e., their antifungal activity, their use as delivery vehicles of nucleic acids, of short peptide (polyamide) nucleic acids (PNAs) and of drugs, as well as their ability to cleave DNA at abasic sites and to inhibit the functioning of connexin hemichannels. Finally, we discuss some aspects of structure-activity relationships in order to explain and improve the target selectivity of AAGs.
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Affiliation(s)
- Clément Dezanet
- Molecular Pharmacochemistry Department, University Grenoble Alpes, CNRS, 470 Rue de la Chimie, F-38000 Grenoble, France; (C.D.); (J.K.)
| | - Julie Kempf
- Molecular Pharmacochemistry Department, University Grenoble Alpes, CNRS, 470 Rue de la Chimie, F-38000 Grenoble, France; (C.D.); (J.K.)
| | - Marie-Paule Mingeot-Leclercq
- Cellular and Molecular Pharmacology Unit, Louvain Drug Research Institute, Catholic University of Louvain, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium
| | - Jean-Luc Décout
- Molecular Pharmacochemistry Department, University Grenoble Alpes, CNRS, 470 Rue de la Chimie, F-38000 Grenoble, France; (C.D.); (J.K.)
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6
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On-cell saturation transfer difference NMR study of Bombesin binding to GRP receptor. Bioorg Chem 2020; 99:103861. [PMID: 32339813 DOI: 10.1016/j.bioorg.2020.103861] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/15/2023]
Abstract
We report the NMR characterization of the molecular interaction between Gastrin Releasing Peptide Receptor (GRP-R) and its natural ligand bombesin (BN). GRP-R is a transmembrane G-protein coupled receptor promoting the stimulation of cancer cell proliferation; in addition, being overexpressed on the surface of different human cancer cell lines, it is ideal for the development of new strategies for the selective targeted delivery of anticancer drugs and diagnostic devices to tumor cells. However, the design of new GRP-R binders requires structural information on receptor interaction with its natural ligands. The experimental protocol presented herein, based on on-cell STD NMR techniques, is a powerful tool for the screening and the epitope mapping of GRP-R ligands aimed at the development of new anticancer and diagnostic tools. Notably, the study can be carried out in a physiological environment, at the surface of tumoral cells overespressing GRP-R. Moreover, to the best of our knowledge, this is the first example of an NMR experiment able to detect and investigate the structural determinants of BN/GRP-R interaction.
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7
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Vacchini M, Edwards R, Guizzardi R, Palmioli A, Ciaramelli C, Paiotta A, Airoldi C, La Ferla B, Cipolla L. Glycan Carriers As Glycotools for Medicinal Chemistry Applications. Curr Med Chem 2019; 26:6349-6398. [DOI: 10.2174/0929867326666190104164653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 11/07/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022]
Abstract
Carbohydrates are one of the most powerful and versatile classes of biomolecules that nature
uses to regulate organisms’ biochemistry, modulating plenty of signaling events within cells, triggering
a plethora of physiological and pathological cellular behaviors. In this framework, glycan carrier
systems or carbohydrate-decorated materials constitute interesting and relevant tools for medicinal
chemistry applications. In the last few decades, efforts have been focused, among others, on the development
of multivalent glycoconjugates, biosensors, glycoarrays, carbohydrate-decorated biomaterials
for regenerative medicine, and glyconanoparticles. This review aims to provide the reader with a general
overview of the different carbohydrate carrier systems that have been developed as tools in different
medicinal chemistry approaches relying on carbohydrate-protein interactions. Given the extent of
this topic, the present review will focus on selected examples that highlight the advancements and potentialities
offered by this specific area of research, rather than being an exhaustive literature survey of
any specific glyco-functionalized system.
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Affiliation(s)
- Mattia Vacchini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Rana Edwards
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Roberto Guizzardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Carlotta Ciaramelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Alice Paiotta
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Barbara La Ferla
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Laura Cipolla
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
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8
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Multi-enzyme systems and recombinant cells for synthesis of valuable saccharides: Advances and perspectives. Biotechnol Adv 2019; 37:107406. [DOI: 10.1016/j.biotechadv.2019.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/30/2019] [Accepted: 06/08/2019] [Indexed: 02/07/2023]
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9
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Palmioli A, Sperandeo P, Polissi A, Airoldi C. Targeting Bacterial Biofilm: A New LecA Multivalent Ligand with Inhibitory Activity. Chembiochem 2019; 20:2911-2915. [DOI: 10.1002/cbic.201900383] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Alessandro Palmioli
- Department of Biotechnology and BiosciencesUniversity of Milano–Bicocca Piazza della Scienza 2 20126 Milano Italy
| | - Paola Sperandeo
- Department of Pharmacological and Biomolecular SciencesUniversity of Milano Via Balzaretti, 9/11/13 20133 Milano Italy
| | - Alessandra Polissi
- Department of Pharmacological and Biomolecular SciencesUniversity of Milano Via Balzaretti, 9/11/13 20133 Milano Italy
| | - Cristina Airoldi
- Department of Biotechnology and BiosciencesUniversity of Milano–Bicocca Piazza della Scienza 2 20126 Milano Italy
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10
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Sperandeo P, Polissi A, De Fabiani E. Fat Matters for Bugs: How Lipids and Lipid Modifications Make the Difference in Bacterial Life. EUR J LIPID SCI TECH 2019. [DOI: 10.1002/ejlt.201900204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
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11
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bioNMR-based identification of natural anti-Aβ compounds in Peucedanum ostruthium. Bioorg Chem 2019; 83:76-86. [DOI: 10.1016/j.bioorg.2018.10.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/07/2018] [Accepted: 10/09/2018] [Indexed: 01/20/2023]
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12
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Ciaramelli C, Palmioli A, De Luigi A, Colombo L, Sala G, Riva C, Zoia CP, Salmona M, Airoldi C. NMR-driven identification of anti-amyloidogenic compounds in green and roasted coffee extracts. Food Chem 2018; 252:171-180. [DOI: 10.1016/j.foodchem.2018.01.075] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/03/2018] [Accepted: 01/09/2018] [Indexed: 01/07/2023]
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13
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Palmioli A, Ciaramelli C, Tisi R, Spinelli M, De Sanctis G, Sacco E, Airoldi C. Natural Compounds in Cancer Prevention: Effects of Coffee Extracts and Their Main Polyphenolic Component, 5-O-Caffeoylquinic Acid, on Oncogenic Ras Proteins. Chem Asian J 2017; 12:2457-2466. [PMID: 28719146 DOI: 10.1002/asia.201700844] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/17/2017] [Indexed: 01/08/2023]
Abstract
Recent epidemiological studies have demonstrated that the consumption of healthy foods that are particularly rich in polyphenols might reduce the incidence of cancer and neurodegenerative diseases. In particular, chlorogenic acids (CGAs) occur ubiquitously in food and represent the most abundant polyphenols in the human diet. A number of beneficial biological effects of CGAs, such as anti-inflammatory activity, anti-carcinogenic activity, and protection against neurodegenerative diseases, have been reported. However, the molecular mechanisms at the base of these biological activities have not yet been investigated in depth. By combining NMR spectroscopy, molecular docking, surface plasmon resonance and ex vivo assays of the Ras-dependent breast cancer cell line MDA-MB-231, we contribute to the elucidation of the molecular basis of the activity of CGAs and natural extracts from green and roasted coffee beans as chemoprotective dietary supplements.
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Affiliation(s)
- Alessandro Palmioli
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Carlotta Ciaramelli
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Renata Tisi
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.,NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, 20126, Milano, Italy
| | - Michela Spinelli
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Gaia De Sanctis
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Elena Sacco
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.,SysBio Center of Systems Biology, Piazza della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.,NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, 20126, Milano, Italy.,SysBio Center of Systems Biology, Piazza della Scienza 2, 20126, Milan, Italy
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14
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Sperandeo P, Martorana AM, Polissi A. Lipopolysaccharide biogenesis and transport at the outer membrane of Gram-negative bacteria. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1451-1460. [PMID: 27760389 DOI: 10.1016/j.bbalip.2016.10.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 01/10/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer containing a unique glycolipid, lipopolysaccharide (LPS) in its outer leaflet. LPS molecules confer to the OM peculiar permeability barrier properties enabling Gram-negative bacteria to exclude many toxic compounds, including clinically useful antibiotics, and to survive harsh environments. Transport of LPS poses several problems to the cells due to the amphipatic nature of this molecule. In this review we summarize the current knowledge on the LPS transport machinery, discuss the challenges associated with this process and present the solutions that bacterial cells have evolved to address the problem of LPS transport and assembly at the cell surface. Finally, we discuss how knowledge on LPS biogenesis can be translated for the development of novel antimicrobial therapies. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Affiliation(s)
- Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy.
| | - Alessandra M Martorana
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy.
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15
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Airoldi C, D'Orazio G, Richichi B, Guzzi C, Baldoneschi V, Colombo L, Salmona M, Nativi C, Nicotra F, La Ferla B. Structural Modifications ofcis-Glycofused Benzopyran Compounds and Their Influence on the Binding to Amyloid-β Peptide. Chem Asian J 2015; 11:299-309. [DOI: 10.1002/asia.201501114] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Cristina Airoldi
- Department of Biotecnology and Bioscience (Btbs); University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
| | - Giuseppe D'Orazio
- Department of Biotecnology and Bioscience (Btbs); University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
| | - Barbara Richichi
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 I-50019 Sesto Fiorentino (FI) Italy
| | - Cinzia Guzzi
- Department of Biotecnology and Bioscience (Btbs); University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
| | - Veronica Baldoneschi
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 I-50019 Sesto Fiorentino (FI) Italy
| | - Laura Colombo
- Department Biochemistry and Molecular Pharmacology; IRCCS-Istituto di Ricerche Farmacologiche “Mario Negri”; Via Giuseppe La Masa, 19 20156 Milano Italy
| | - Mario Salmona
- Department Biochemistry and Molecular Pharmacology; IRCCS-Istituto di Ricerche Farmacologiche “Mario Negri”; Via Giuseppe La Masa, 19 20156 Milano Italy
| | - Cristina Nativi
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 I-50019 Sesto Fiorentino (FI) Italy
| | - Francesco Nicotra
- Department of Biotecnology and Bioscience (Btbs); University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
| | - Barbara La Ferla
- Department of Biotecnology and Bioscience (Btbs); University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
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Bonanomi M, Visentin C, Natalello A, Spinelli M, Vanoni M, Airoldi C, Regonesi ME, Tortora P. How Epigallocatechin-3-gallate and Tetracycline Interact with the Josephin Domain of Ataxin-3 and Alter Its Aggregation Mode. Chemistry 2015; 21:18383-93. [PMID: 26538519 DOI: 10.1002/chem.201503086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 12/17/2022]
Abstract
Epigallocatechin-3-gallate (EGCG) and tetracycline are two known inhibitors of amyloid aggregation able to counteract the fibrillation of most of the proteins involved in neurodegenerative diseases. We have recently investigated their effect on ataxin-3 (AT3), the polyglutamine-containing protein responsible for spinocerebellar ataxia type 3. We previously showed that EGCG and tetracycline can contrast the aggregation process and toxicity of expanded AT3, although by different mechanisms. Here, we have performed further experiments by using the sole Josephin domain (JD) to further elucidate the mechanism of action of the two compounds. By protein solubility assays and FTIR spectroscopy we have first observed that EGCG and tetracycline affect the JD aggregation essentially in the same way displayed when acting on the full-length expanded AT3. Then, by saturation transfer difference (STD) NMR experiments, we have shown that EGCG binds both the monomeric and the oligomeric JD form, whereas tetracycline can only interact with the oligomeric one. Surface plasmon resonance (SPR) analysis has confirmed the capability of the sole EGCG to bind monomeric JD, although with a KD value suggestive for a non-specific interaction. Our investigations provide new details on the JD interaction with EGCG and tetracycline, which could explain the different mechanisms by which the two compounds reduce the toxicity of AT3.
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Affiliation(s)
- Marcella Bonanomi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy)
| | - Cristina Visentin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy)
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR Milano-Bicocca, Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy)
| | - Michela Spinelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,SysBio Centre for Systems Biology, Milano and Rome (Italy)
| | - Marco Vanoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy).,SysBio Centre for Systems Biology, Milano and Rome (Italy)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy). .,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy). .,SysBio Centre for Systems Biology, Milano and Rome (Italy).
| | - Maria E Regonesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy). .,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy).
| | - Paolo Tortora
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy)
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Sironi E, Colombo L, Lompo A, Messa M, Bonanomi M, Regonesi ME, Salmona M, Airoldi C. Natural Compounds against Neurodegenerative Diseases: Molecular Characterization of the Interaction of Catechins from Green Tea with Aβ1–42, PrP106–126, and Ataxin‐3 Oligomers. Chemistry 2014; 20:13793-800. [DOI: 10.1002/chem.201403188] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Erika Sironi
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
| | - Laura Colombo
- Department Biochemistry and Molecular Pharmacology, IRCCS‐Istituto di Ricerche Farmacologiche “Mario Negri”, Via Giuseppe La Masa, 19 20156 Milano (Italy)
| | - Angela Lompo
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
| | - Massimo Messa
- Department Biochemistry and Molecular Pharmacology, IRCCS‐Istituto di Ricerche Farmacologiche “Mario Negri”, Via Giuseppe La Masa, 19 20156 Milano (Italy)
| | - Marcella Bonanomi
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
| | - Maria Elena Regonesi
- Department of Statistics and Quantitative Methods, University of Milano‐Bicocca, Via Bicocca degli Arcimboldi, 8, 20126, Milano (Italy)
| | - Mario Salmona
- Department Biochemistry and Molecular Pharmacology, IRCCS‐Istituto di Ricerche Farmacologiche “Mario Negri”, Via Giuseppe La Masa, 19 20156 Milano (Italy)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
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Merlo S, Sironi E, Colombo L, Cardona F, Martorana AM, Salmona M, La Ferla B, Airoldi C. Cis-Glyco-Fused Benzopyran Derivatives as Hit Compounds for the Development of Therapeutic and Diagnostic Tools against Neurodegenerative Diseases. Chempluschem 2014. [DOI: 10.1002/cplu.201400035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Cipolla L, Airoldi C, Sperandeo P, Gianera S, Polissi A, Nicotra F, Gabrielli L. Synthesis and biological evaluation of arabinose 5-phosphate mimics modified at position five. Carbohydr Res 2014; 389:186-91. [DOI: 10.1016/j.carres.2014.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/31/2013] [Accepted: 01/08/2014] [Indexed: 01/10/2023]
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Gabrielli L, Merlo S, Airoldi C, Sperandeo P, Gianera S, Polissi A, Nicotra F, Holler TP, Woodard RW, Cipolla L. Arabinose 5-phosphate isomerase as a target for antibacterial design: Studies with substrate analogues and inhibitors. Bioorg Med Chem 2014; 22:2576-83. [DOI: 10.1016/j.bmc.2013.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/18/2013] [Accepted: 08/05/2013] [Indexed: 01/25/2023]
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Gabrielli L, Airoldi C, Sperandeo P, Gianera S, Polissi A, Nicotra F, Cipolla L. Phosphonate Analogues of Arabinose 5-Phosphate: Putative Ligands for Arabinose 5-Phosphate Isomerases. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300887] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Airoldi C, Giovannardi S, La Ferla B, Jiménez-Barbero J, Nicotra F. Saturation Transfer Difference NMR Experiments of Membrane Proteins in Living Cells under HR-MAS Conditions: The Interaction of the SGLT1 Co-transporter with Its Ligands. Chemistry 2011; 17:13395-9. [DOI: 10.1002/chem.201102181] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Indexed: 12/13/2022]
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Airoldi C, Cardona F, Sironi E, Colombo L, Salmona M, Silva A, Nicotra F, La Ferla B. cis-Glyco-fused benzopyran compounds as new amyloid-β peptide ligands. Chem Commun (Camb) 2011; 47:10266-8. [DOI: 10.1039/c1cc13046c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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