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The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors. Sci Rep 2021; 11:9283. [PMID: 33927258 PMCID: PMC8085067 DOI: 10.1038/s41598-021-88630-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
The maturation of coronavirus SARS-CoV-2, which is the etiological agent at the origin of the COVID-19 pandemic, requires a main protease Mpro to cleave the virus-encoded polyproteins. Despite a wealth of experimental information already available, there is wide disagreement about the Mpro monomer-dimer equilibrium dissociation constant. Since the functional unit of Mpro is a homodimer, the detailed knowledge of the thermodynamics of this equilibrium is a key piece of information for possible therapeutic intervention, with small molecules interfering with dimerization being potential broad-spectrum antiviral drug leads. In the present study, we exploit Small Angle X-ray Scattering (SAXS) to investigate the structural features of SARS-CoV-2 Mpro in solution as a function of protein concentration and temperature. A detailed thermodynamic picture of the monomer-dimer equilibrium is derived, together with the temperature-dependent value of the dissociation constant. SAXS is also used to study how the Mpro dissociation process is affected by small inhibitors selected by virtual screening. We find that these inhibitors affect dimerization and enzymatic activity to a different extent and sometimes in an opposite way, likely due to the different molecular mechanisms underlying the two processes. The Mpro residues that emerge as key to optimize both dissociation and enzymatic activity inhibition are discussed.
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Maio A, Giallombardo D, Scaffaro R, Palumbo Piccionello A, Pibiri I. Synthesis of a fluorinated graphene oxide–silica nanohybrid: improving oxygen affinity. RSC Adv 2016. [DOI: 10.1039/c6ra02585d] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
An easy method to selectively introduce specific fluorotails into a graphene oxide–silica nanohybrid. Fluoro-functionalization increases the oxygen exchange at saturation.
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Affiliation(s)
- A. Maio
- Department of Civil, Aerospace, Environmental, Materials Engineering
- University of Palermo
- Palermo
- Italy
| | - D. Giallombardo
- Department of Civil, Aerospace, Environmental, Materials Engineering
- University of Palermo
- Palermo
- Italy
| | - R. Scaffaro
- Department of Civil, Aerospace, Environmental, Materials Engineering
- University of Palermo
- Palermo
- Italy
| | - A. Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies
- University of Palermo
- Palermo
- Italy
| | - I. Pibiri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies
- University of Palermo
- Palermo
- Italy
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Enhancement of premature stop codon readthrough in the CFTR gene by Ataluren (PTC124) derivatives. Eur J Med Chem 2015; 101:236-44. [PMID: 26142488 DOI: 10.1016/j.ejmech.2015.06.038] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/14/2015] [Accepted: 06/19/2015] [Indexed: 12/31/2022]
Abstract
Premature stop codons are the result of nonsense mutations occurring within the coding sequence of a gene. These mutations lead to the synthesis of a truncated protein and are responsible for several genetic diseases. A potential pharmacological approach to treat these diseases is to promote the translational readthrough of premature stop codons by small molecules aiming to restore the full-length protein. The compound PTC124 (Ataluren) was reported to promote the readthrough of the premature UGA stop codon, although its activity was questioned. The potential interaction of PTC124 with mutated mRNA was recently suggested by molecular dynamics (MD) studies highlighting the importance of H-bonding and stacking π-π interactions. To improve the readthrough activity we changed the fluorine number and position in the PTC124 fluoroaryl moiety. The readthrough ability of these PTC124 derivatives was tested in human cells harboring reporter plasmids with premature stop codons in H2BGFP and FLuc genes as well as in cystic fibrosis (CF) IB3.1 cells with a nonsense mutation. Maintaining low toxicity, three of these molecules showed higher efficacy than PTC124 in the readthrough of the UGA premature stop codon and in recovering the expression of the CFTR protein in IB3.1 cells from cystic fibrosis patient. Molecular dynamics simulations performed with mutated CFTR mRNA fragments and active or inactive derivatives are in agreement with the suggested interaction of PTC124 with mRNA.
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Lentini L, Melfi R, Di Leonardo A, Spinello A, Barone G, Pace A, Palumbo Piccionello A, Pibiri I. Toward a rationale for the PTC124 (Ataluren) promoted readthrough of premature stop codons: a computational approach and GFP-reporter cell-based assay. Mol Pharm 2014; 11:653-64. [PMID: 24483936 PMCID: PMC4167060 DOI: 10.1021/mp400230s] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 12/17/2013] [Accepted: 01/31/2014] [Indexed: 01/28/2023]
Abstract
The presence in the mRNA of premature stop codons (PTCs) results in protein truncation responsible for several inherited (genetic) diseases. A well-known example of these diseases is cystic fibrosis (CF), where approximately 10% (worldwide) of patients have nonsense mutations in the CF transmembrane regulator (CFTR) gene. PTC124 (3-(5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl)-benzoic acid), also known as Ataluren, is a small molecule that has been suggested to allow PTC readthrough even though its target has yet to be identified. In the lack of a general consensus about its mechanism of action, we experimentally tested the ability of PTC124 to promote the readthrough of premature termination codons by using a new reporter. The reporter vector was based on a plasmid harboring the H2B histone coding sequence fused in frame with the green fluorescent protein (GFP) cDNA, and a TGA stop codon was introduced in the H2B-GFP gene by site-directed mutagenesis. Additionally, an unprecedented computational study on the putative supramolecular interaction between PTC124 and an 11-codon (33-nucleotides) sequence corresponding to a CFTR mRNA fragment containing a central UGA nonsense mutation showed a specific interaction between PTC124 and the UGA codon. Altogether, the H2B-GFP-opal based assay and the molecular dynamics (MD) simulation support the hypothesis that PTC124 is able to promote the specific readthrough of internal TGA premature stop codons.
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Affiliation(s)
- Laura Lentini
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Raffaella Melfi
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Aldo Di Leonardo
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Centro di OncoBiologia
Sperimentale (COBS), via San Lorenzo
Colli, 90145 Palermo, Italy
| | - Angelo Spinello
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Giampaolo Barone
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Istituto EuroMediterraneo
di Scienza e Tecnologia (IEMEST), Via
Emerico Amari 123, 90139 Palermo, Italy
| | - Andrea Pace
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Istituto EuroMediterraneo
di Scienza e Tecnologia (IEMEST), Via
Emerico Amari 123, 90139 Palermo, Italy
| | - Antonio Palumbo Piccionello
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Ivana Pibiri
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
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Palumbo FS, Di Stefano M, Palumbo Piccionello A, Fiorica C, Pitarresi G, Pibiri I, Buscemi S, Giammona G. Perfluorocarbon functionalized hyaluronic acid derivatives as oxygenating systems for cell culture. RSC Adv 2014. [DOI: 10.1039/c4ra01502a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Piccionello AP, Pitarresi G, Pace A, Triolo D, Picone P, Buscemi S, Giammona G. Fluorinated and pegylated polyaspartamide derivatives to increase solubility and efficacy of Flutamide. J Drug Target 2012; 20:433-44. [DOI: 10.3109/1061186x.2012.680961] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Palumbo Piccionello A, Guarcello A, Calabrese A, Pibiri I, Pace A, Buscemi S. Synthesis of fluorinated oxadiazoles with gelation and oxygen storage ability. Org Biomol Chem 2012; 10:3044-52. [PMID: 22395126 DOI: 10.1039/c2ob07024c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new family of fluorinated low molecular weight (LMW) gelators has been synthesized through SNAr substitution of 5-polyfluoroaryl-3-perfluoroheptyl-1,2,4-oxadiazoles with glycine ester. The obtained compounds give thermal and pH-sensitive hydrogels or thermo-reversible organogels in DMSO. Oxygen solubility studies showed the ability to maintain high oxygen levels in solution and in gel blend with plate counter agar (PCA).
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Affiliation(s)
- Antonio Palumbo Piccionello
- Dipartimento di Scienze e Tecnologie Molecolari e Biomolecolari - Sez. Chimica Organica E. Paternò, Università degli Studi di Palermo, Viale delle Scienze - Parco d'Orleans II, Ed. 17, I-90128, Palermo, Italy.
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Pibiri I, Pace A, Buscemi S, Causin V, Rastrelli F, Saielli G. Oxadiazolyl-pyridines and perfluoroalkyl-carboxylic acids as building blocks for protic ionic liquids: crossing the thin line between ionic and hydrogen bonded materials. Phys Chem Chem Phys 2012; 14:14306-14. [DOI: 10.1039/c2cp42467c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bretanha LC, Teixeira VE, Ritter M, Siqueira GM, Cunico W, Pereira CMP, Freitag RA. Ultrasound-promoted synthesis of 3-trichloromethyl-5-alkyl(aryl)-1,2,4-oxadiazoles. ULTRASONICS SONOCHEMISTRY 2011; 18:704-7. [PMID: 21115383 DOI: 10.1016/j.ultsonch.2010.09.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 08/16/2010] [Accepted: 09/30/2010] [Indexed: 05/14/2023]
Abstract
The alternative synthesis of 12 1,2,4-oxadiazoles using ultrasound irradiation from trichloroacetoamidoxime and acyl chlorides is reported. Seven of them are novel compounds. The 3-trichloromethyl-5alkyl(aryl)-1,2,4-oxadiazoles have been synthesised in better yields and shorter reaction times compared to the conventional method. This protocol can be applicable for preparation of 1,2,4-oxadiazoles containing aryl or alkyl groups attached at their C-5 side-chain.
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Affiliation(s)
- Lizandra C Bretanha
- NuQuiA-Núcleo de Química Aplicada, Departamento de Química Orgânica, Universidade Federal de Pelotas, Brazil
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Pibiri I, Palumbo Piccionello A, Calabrese A, Buscemi S, Vivona N, Pace A. Fluorescent Hg2+ Sensors: Synthesis and Evaluation of a Tren-Based Starburst Molecule Containing Fluorinated 1,2,4-Oxadiazoles. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000763] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Pitarresi G, Piccionello AP, Calabrese R, Pace A, Buscemi S, Giammona G. Fluorinated derivatives of a polyaspartamide bearing polyethylene glycol chains as oxygen carriers. J Fluor Chem 2008. [DOI: 10.1016/j.jfluchem.2008.07.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Yu C, Lei M, Su W, Xie Y. Y(OTf)3‐Catalyzed, One‐Pot Synthesis of 1,2,4‐Oxadiazole Derivatives. SYNTHETIC COMMUN 2007. [DOI: 10.1080/00397910701577695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Mandracchia D, Piccionello AP, Pitarresi G, Pace A, Buscemi S, Giammona G. Fluoropolymer Based on a Polyaspartamide containing 1,2,4-Oxadiazole Units: A Potential Artificial Oxygen (O2) Carrier. Macromol Biosci 2007; 7:836-45. [PMID: 17541930 DOI: 10.1002/mabi.200600266] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this preliminary work we have prepared a fluorinated polymer capable of solubilizing an appreciable amount of O(2) and, at the same time, maintaining a higher water solubility than perfluoroalkanes investigated as injectable O(2) carriers. In particular, we describe the synthesis and characterization of a new macromolecular conjugate obtained by derivatization of alpha,beta-poly(N-2-hydroxyethyl)-DL-aspartamide (PHEA) with 5-pentafluorophenyl-3-perfluoroheptyl-1,2,4-oxadiazole, called PHEA-F. This new water soluble fluoropolymer was prepared in high yield using a simple procedure. It was characterized by FT-IR and UV-vis spectrophotometry, (19)F-NMR and SEC measurements. O(2) solubility studies on PHEA-F aqueous solutions were carried out at 25 degrees C and 37 degrees C at atmospheric pressure and showed that PHEA-F conjugate, despite its low degree of derivatization in fluorine containing groups (2.60 mol-%), is capable of dissolving 13-15% more O(2) than non-fluorinated PHEA. Moreover, O(2) release in simulated physiological conditions is faster for PHEA-F than for PHEA. The biocompatibility of this conjugate has been evaluated by performing an in vitro viability assay on human chronic myelogenous leukaemia cells (K-562) chosen as a model cell line and in vitro haemolysis experiments on human RBCs. All these properties suggest the potential use of PHEA-F as an artificial O(2) carrier.
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Affiliation(s)
- Delia Mandracchia
- Dipartimento Farmaco-Chimico, Università di Bari, Via Orabona 4, I-70125 Bari, Italy
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