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Giugliano R, Della Sala G, Buonocore C, Zannella C, Tedesco P, Palma Esposito F, Ragozzino C, Chianese A, Morone MV, Mazzella V, Núñez-Pons L, Folliero V, Franci G, De Filippis A, Galdiero M, de Pascale D. New Imidazolium Alkaloids with Broad Spectrum of Action from the Marine Bacterium Shewanella aquimarina. Pharmaceutics 2023; 15:2139. [PMID: 37631353 PMCID: PMC10458398 DOI: 10.3390/pharmaceutics15082139] [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: 07/13/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
The continuous outbreak of drug-resistant bacterial and viral infections imposes the need to search for new drug candidates. Natural products from marine bacteria still inspire the design of pharmaceuticals. Indeed, marine bacteria have unique metabolic flexibility to inhabit each ecological niche, thus expanding their biosynthetic ability to assemble unprecedented molecules. The One-Strain-Many-Compounds approach and tandem mass spectrometry allowed the discovery of a Shewanella aquimarina strain as a source of novel imidazolium alkaloids via molecular networking. The alkaloid mixture was shown to exert bioactivities such as: (a) antibacterial activity against antibiotic-resistant Staphylococcus aureus clinical isolates at 100 µg/mL, (b) synergistic effects with tigecycline and linezolid, (c) restoration of MRSA sensitivity to fosfomycin, and (d) interference with the biofilm formation of S. aureus 6538 and MRSA. Moreover, the mixture showed antiviral activity against viruses with and without envelopes. Indeed, it inhibited the entry of coronavirus HcoV-229E and herpes simplex viruses into human cells and inactivated poliovirus PV-1 in post-infection assay at 200 µg/mL. Finally, at the same concentration, the fraction showed anthelminthic activity against Caenorhabditis elegans, causing 99% mortality after 48 h. The broad-spectrum activities of these compounds are partially due to their biosurfactant behavior and make them promising candidates for breaking down drug-resistant infectious diseases.
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Affiliation(s)
- Rosa Giugliano
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (R.G.); (C.Z.); (A.C.); (M.V.M.); (A.D.F.)
| | - Gerardo Della Sala
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy; (G.D.S.); (C.B.); (P.T.); (F.P.E.); (C.R.)
| | - Carmine Buonocore
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy; (G.D.S.); (C.B.); (P.T.); (F.P.E.); (C.R.)
| | - Carla Zannella
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (R.G.); (C.Z.); (A.C.); (M.V.M.); (A.D.F.)
| | - Pietro Tedesco
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy; (G.D.S.); (C.B.); (P.T.); (F.P.E.); (C.R.)
| | - Fortunato Palma Esposito
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy; (G.D.S.); (C.B.); (P.T.); (F.P.E.); (C.R.)
| | - Costanza Ragozzino
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy; (G.D.S.); (C.B.); (P.T.); (F.P.E.); (C.R.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres, 31, 98166 Messina, Italy
| | - Annalisa Chianese
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (R.G.); (C.Z.); (A.C.); (M.V.M.); (A.D.F.)
| | - Maria Vittoria Morone
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (R.G.); (C.Z.); (A.C.); (M.V.M.); (A.D.F.)
| | - Valerio Mazzella
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Ischia Marine Centre, Ischia, 80077 Naples, Italy;
- NBFC, National Biodiversity Future Center, 90133 Palermo, Italy;
| | - Laura Núñez-Pons
- NBFC, National Biodiversity Future Center, 90133 Palermo, Italy;
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Veronica Folliero
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (V.F.); (G.F.)
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (V.F.); (G.F.)
| | - Anna De Filippis
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (R.G.); (C.Z.); (A.C.); (M.V.M.); (A.D.F.)
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (R.G.); (C.Z.); (A.C.); (M.V.M.); (A.D.F.)
| | - Donatella de Pascale
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy; (G.D.S.); (C.B.); (P.T.); (F.P.E.); (C.R.)
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Blaas D. Individual subunits of a rhinovirus causing common cold exhibit largely different protein-RNA contact site conformations. Commun Biol 2020; 3:537. [PMID: 32994533 PMCID: PMC7525237 DOI: 10.1038/s42003-020-01269-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/27/2020] [Indexed: 11/09/2022] Open
Abstract
Rhinoviruses cause the common cold. They are icosahedral, built from sixty copies each of the capsid proteins VP1 through VP4 arranged in a pseudo T = 3 lattice. This shell encases a ss(+) RNA genome. Three-D classification of single and oligomeric asymmetric units computationally excised from a 2.9 Å cryo-EM density map of rhinovirus A89, showed that VP4 and the N-terminal extension of VP1 adopt different conformations within the otherwise identical 3D-structures. Analysis of up to sixty classes of single subunits and of six classes of subunit dimers, trimers, and pentamers revealed different orientations of the amino acid residues at the interface with the RNA suggesting that local asymmetry is dictated by disparities of the interacting nucleotide sequences. The different conformations escape detection by 3-D structure determination of entire virions with the conformational heterogeneity being only indicated by low density. My results do not exclude that the RNA follows a conserved assembly mechanism, contacting most or all asymmetric units in a specific way. However, as suggested by the gradual loss of asymmetry with increasing oligomerization and the 3D-structure of entire virions reconstructed by using Euler angles selected in the classification of single subunits, RNA path and/or folding likely differ from virion to virion. From analysis of up to sixty classes of single subunits and of six classes of subunit dimers, trimers, and pentamers, Dieter Blaas demonstrates different orientations of the amino acid residues at the interface with the RNA. This study suggests that RNA path and/or folding is likely to differ from virion to virion.
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Affiliation(s)
- Dieter Blaas
- Vienna Biocenter, Max Perutz Laboratories, Centre of Medical Biochemistry, Medical University of Vienna, Dr. Bohr Gasse 9/3, A-1030, Vienna, Austria.
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Upfold N, Ross C, Tastan Bishop Ö, Knox C. The In Silico Prediction of Hotspot Residues that Contribute to the Structural Stability of Subunit Interfaces of a Picornavirus Capsid. Viruses 2020; 12:v12040387. [PMID: 32244486 PMCID: PMC7232237 DOI: 10.3390/v12040387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/26/2020] [Accepted: 03/28/2020] [Indexed: 11/16/2022] Open
Abstract
The assembly of picornavirus capsids proceeds through the stepwise oligomerization of capsid protein subunits and depends on interactions between critical residues known as hotspots. Few studies have described the identification of hotspot residues at the protein subunit interfaces of the picornavirus capsid, some of which could represent novel drug targets. Using a combination of accessible web servers for hotspot prediction, we performed a comprehensive bioinformatic analysis of the hotspot residues at the intraprotomer, interprotomer and interpentamer interfaces of the Theiler’s murine encephalomyelitis virus (TMEV) capsid. Significantly, many of the predicted hotspot residues were found to be conserved in representative viruses from different genera, suggesting that the molecular determinants of capsid assembly are conserved across the family. The analysis presented here can be applied to any icosahedral structure and provides a platform for in vitro mutagenesis studies to further investigate the significance of these hotspots in critical stages of the virus life cycle with a view to identify potential targets for antiviral drug design.
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Affiliation(s)
- Nicole Upfold
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa;
- Correspondence:
| | - Caroline Ross
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (C.R.); (Ö.T.B.)
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (C.R.); (Ö.T.B.)
| | - Caroline Knox
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa;
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