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Di Micco S, Rahimova R, Sala M, Scala MC, Vivenzio G, Musella S, Andrei G, Remans K, Mammri L, Snoeck R, Bifulco G, Di Matteo F, Vestuto V, Campiglia P, Márquez JA, Fasano A. Rational design of the zonulin inhibitor AT1001 derivatives as potential anti SARS-CoV-2. Eur J Med Chem 2022; 244:114857. [PMID: 36332548 PMCID: PMC9579148 DOI: 10.1016/j.ejmech.2022.114857] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/26/2022] [Accepted: 10/14/2022] [Indexed: 11/28/2022]
Abstract
Although vaccines are greatly mitigating the worldwide pandemic diffusion of SARS-Cov-2, therapeutics should provide many distinct advantages as complementary approach to control the viral spreading. Here, we report the development of new tripeptide derivatives of AT1001 against SARS-CoV-2 Mpro. By molecular modeling, a small compound library was rationally designed and filtered for enzymatic inhibition through FRET assay, leading to the identification of compound 4. X-ray crystallography studies provide insights into its binding mode and confirm the formation of a covalent bond with Mpro C145. In vitro antiviral tests indicate the improvement of biological activity of 4 respect to AT1001. In silico and X-ray crystallography analysis led to 58, showing a promising activity against three SARS-CoV-2 variants and a valuable safety in Vero cells and human embryonic lung fibroblasts. The drug tolerance was also confirmed by in vivo studies, along with pharmacokinetics evaluation. In summary, 58 could pave the way to develop a clinical candidate for intranasal administration.
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Affiliation(s)
- Simone Di Micco
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125, Salerno, Italy,Corresponding author
| | - Rahila Rahimova
- European Molecular Biology Laboratory, EMBL, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9, 38042, France
| | - Marina Sala
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Maria C. Scala
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Giovanni Vivenzio
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Simona Musella
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125, Salerno, Italy,Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Graciela Andrei
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Kim Remans
- European Molecular Biology Laboratory, EMBL, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Léa Mammri
- European Molecular Biology Laboratory, EMBL, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9, 38042, France
| | - Robert Snoeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Giuseppe Bifulco
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Francesca Di Matteo
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Vincenzo Vestuto
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Pietro Campiglia
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125, Salerno, Italy,Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - José A. Márquez
- European Molecular Biology Laboratory, EMBL, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9, 38042, France,ALPX S.A.S. 71, Avenue des Martyrs, France
| | - Alessio Fasano
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125, Salerno, Italy,Mucosal Immunology and Biology Research Center, Massachusetts General Hospital–Harvard Medical School, Boston, MA, 02114, USA
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Di Micco S, Musella S, Sala M, Scala MC, Andrei G, Snoeck R, Bifulco G, Campiglia P, Fasano A. Peptide Derivatives of the Zonulin Inhibitor Larazotide (AT1001) as Potential Anti SARS-CoV-2: Molecular Modelling, Synthesis and Bioactivity Evaluation. Int J Mol Sci 2021; 22:ijms22179427. [PMID: 34502335 PMCID: PMC8431481 DOI: 10.3390/ijms22179427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/25/2022] Open
Abstract
A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been identified as the pathogen responsible for the outbreak of a severe, rapidly developing pneumonia (Coronavirus disease 2019, COVID-19). The virus enzyme, called 3CLpro or main protease (Mpro), is essential for viral replication, making it a most promising target for antiviral drug development. Recently, we adopted the drug repurposing as appropriate strategy to give fast response to global COVID-19 epidemic, by demonstrating that the zonulin octapeptide inhibitor AT1001 (Larazotide acetate) binds Mpro catalytic domain. Thus, in the present study we tried to investigate the antiviral activity of AT1001, along with five derivatives, by cell-based assays. Our results provide with the identification of AT1001 peptide molecular framework for lead optimization step to develop new generations of antiviral agents of SARS-CoV-2 with an improved biological activity, expanding the chance for success in clinical trials.
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Affiliation(s)
- Simone Di Micco
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125 Salerno, Italy; (S.M.); (A.F.)
- Correspondence:
| | - Simona Musella
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125 Salerno, Italy; (S.M.); (A.F.)
| | - Marina Sala
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (M.S.); (M.C.S.); (G.B.); (P.C.)
| | - Maria C. Scala
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (M.S.); (M.C.S.); (G.B.); (P.C.)
| | - Graciela Andrei
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (G.A.); (R.S.)
| | - Robert Snoeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (G.A.); (R.S.)
| | - Giuseppe Bifulco
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (M.S.); (M.C.S.); (G.B.); (P.C.)
| | - Pietro Campiglia
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (M.S.); (M.C.S.); (G.B.); (P.C.)
| | - Alessio Fasano
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125 Salerno, Italy; (S.M.); (A.F.)
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital–Harvard Medical School, Boston, MA 02114, USA
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3
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Di Micco S, Musella S, Scala MC, Sala M, Campiglia P, Bifulco G, Fasano A. In silico Analysis Revealed Potential Anti-SARS-CoV-2 Main Protease Activity by the Zonulin Inhibitor Larazotide Acetate. Front Chem 2021; 8:628609. [PMID: 33520943 PMCID: PMC7843458 DOI: 10.3389/fchem.2020.628609] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
The most severe outcome of COVID-19 infection is the development of interstitial pneumonia causing acute lung injury (ALI) and/or acute respiratory distress syndrome (ARDS), both responsible for the infected patients' mortality. ALI and ARDS are characterized by a leakage of plasma components into the lungs, compromising their ability to expand and optimally engage in gas exchange with blood, resulting in respiratory failure. We have previously reported that zonulin, a protein dictating epithelial and endothelial permeability in several districts, including the airways, is involved in ALI pathogenesis in mouse models, and that its peptide inhibitor Larazotide acetate (also called AT1001) ameliorated ALI and subsequent mortality by decreasing mucosal permeability to fluid and extravasation of neutrophils into the lungs. With the recent crystallographic resolution of the SARS-CoV-2 main protease (Mpro), an enzyme fundamental in the viral lifecycle, bound to peptidomimetic inhibitors N3 and 13b, we were able to perform molecular modeling investigation showing that AT1001 presents structural motifs similar to co-crystallized ligands. Specifically, molecular docking, MM-GBSA-based predictions and molecular dynamics showed that AT1001 docks extremely well in the Mpro catalytic domain through a global turn conformational arrangement without any unfavorable steric hindrance. Finally, we have observed that AT1001 can be superimposed onto the crystallized structures of N3 and 13b, establishing a higher number of interactions and accordingly a tighter binding. In vitro studies confirmed AT1001 anti-Mpro and preliminary investigation indicted an anti-viral activity. Combined, these studies suggest that AT1001, besides its well-demonstrated effect in ameliorating mucosal permeability in ALI/ARDS, may also exert a direct anti-SARS-CoV-2 effect by blocking the Mpro. AT1001 has been used extensively in a variety of animal models of ALI demonstrating robust safety and efficacy; it is currently in phase 3 trials in celiac subjects showing strong safety and efficacy profiles. We therefore propose its use as a specific anti-SARS-CoV-2 multitargeting treatment for the current pandemic.
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Affiliation(s)
- Simone Di Micco
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy
| | - Simona Musella
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy
| | - Maria C Scala
- Department of Pharmacy, University of Salerno, Salerno, Italy
| | - Marina Sala
- Department of Pharmacy, University of Salerno, Salerno, Italy
| | - Pietro Campiglia
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy.,Department of Pharmacy, University of Salerno, Salerno, Italy
| | | | - Alessio Fasano
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy.,Mucosal Immunology and Biology Research Center, Massachusetts General Hospital-Harvard Medical School, Boston, MA, United States
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Giordano A, Forte G, Terracciano S, Russo A, Sala M, Scala MC, Johansson C, Oppermann U, Riccio R, Bruno I, Di Micco S. Identification of the 2-Benzoxazol-2-yl-phenol Scaffold as New Hit for JMJD3 Inhibition. ACS Med Chem Lett 2019; 10:601-605. [PMID: 30996803 DOI: 10.1021/acsmedchemlett.8b00589] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/25/2019] [Indexed: 12/11/2022] Open
Abstract
JMJD3 is a member of the KDM6 subfamily and catalyzes the demethylation of lysine 27 on histone H3 (H3K27). This protein was identified as a useful tool in understanding the role of epigenetics in inflammatory conditions and in cancer as well. Guided by a virtual fragment screening approach, we identified the benzoxazole scaffold as a new hit suitable for the development of tighter JMJD3 inhibitors. Compounds were synthesized by a microwave-assisted one-pot reaction under catalyst and solvent-free conditions. Among these, compound 8 presented the highest inhibitory activity (IC50 = 1.22 ± 0.22 μM) in accordance with molecular modeling calculations. Moreover, 8 induced the cycle arrest in S-phase on A375 melanoma cells.
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Affiliation(s)
- Assunta Giordano
- Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale delle Ricerche (CNR), Via Campi Flegrei 34, I-80078 Pozzuoli, Napoli, Italy
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Giovanni Forte
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Alessandra Russo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Marina Sala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Maria C. Scala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Catrine Johansson
- Botnar Research Centre, Oxford NIHR BRU, Oxford University, Oxford Centre for Translational Myeloma Research, Oxford, OX3 7LD, U.K
| | - Udo Oppermann
- Botnar Research Centre, Oxford NIHR BRU, Oxford University, Oxford Centre for Translational Myeloma Research, Oxford, OX3 7LD, U.K
| | - Raffaele Riccio
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Ines Bruno
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Simone Di Micco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
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5
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Sala M, Spensiero A, Esposito F, Scala MC, Vernieri E, Bertamino A, Manfra M, Carotenuto A, Grieco P, Novellino E, Cadeddu M, Tramontano E, Schols D, Campiglia P, Gomez-Monterrey IM. Development and Identification of a Novel Anti-HIV-1 Peptide Derived by Modification of the N-Terminal Domain of HIV-1 Integrase. Front Microbiol 2016; 7:845. [PMID: 27375570 PMCID: PMC4901077 DOI: 10.3389/fmicb.2016.00845] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/22/2016] [Indexed: 11/16/2022] Open
Abstract
The viral enzyme integrase (IN) is essential for the replication of human immunodeficiency virus type 1 (HIV-1) and represents an important target for the development of new antiretroviral drugs. In this study, we focused on the N-terminal domain (NTD), which is mainly involved into protein oligomerization process, for the development and synthesis of a library of overlapping peptide sequences, with specific length and specific offset covering the entire native protein sequence NTD IN 1–50. The most potent fragment, VVAKEIVAH (peptide 18), which includes a His residue instead of the natural Ser at position 39, inhibits the HIV-1 IN activity with an IC50 value of 4.5 μM. Amino acid substitution analysis on this peptide revealed essential residues for activity and allowed us to identify two nonapeptides (peptides 24 and 25), that show a potency of inhibition similar to the one of peptide 18. Interestingly, peptide 18 does not interfere with the dynamic interplay between IN subunits, while peptides 24 and 25 modulated these interactions in different manners. In fact, peptide 24 inhibited the IN-IN dimerization, while peptide 25 promoted IN multimerization, with IC50 values of 32 and 4.8 μM, respectively. In addition, peptide 25 has shown to have selective anti-infective cell activity for HIV-1. These results confirmed peptide 25 as a hit for further development of new chemotherapeutic agents against HIV-1.
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Affiliation(s)
- Marina Sala
- Department of Pharmacy, University of Salerno Salerno, Italy
| | | | - Francesca Esposito
- Department of Life and Environmental Sciences, Cittadella Universitaria di Monserrato, University of Cagliari Cagliari, Italy
| | - Maria C Scala
- Department of Pharmacy, University of Salerno Salerno, Italy
| | | | | | - Michele Manfra
- Department of Sciences, University of Basilicata Potenza, Italy
| | - Alfonso Carotenuto
- Department of Pharmacy, Medicicnal Chemistry and Toxicologic, University of Naples Federico II Napoli, Italy
| | - Paolo Grieco
- Department of Pharmacy, Medicicnal Chemistry and Toxicologic, University of Naples Federico II Napoli, Italy
| | - Ettore Novellino
- Department of Pharmacy, Medicicnal Chemistry and Toxicologic, University of Naples Federico II Napoli, Italy
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, Cittadella Universitaria di Monserrato, University of Cagliari Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, Cittadella Universitaria di Monserrato, University of CagliariCagliari, Italy; Institute of Genetic and Biomedical Research, National Research Council, Citadella di MonserratoCagliari, Italy
| | - Dominique Schols
- Department of Microbiology and Immunology, Rega Institute for Medical Research Leuven, Belgium
| | | | - Isabel M Gomez-Monterrey
- Department of Pharmacy, Medicicnal Chemistry and Toxicologic, University of Naples Federico II Napoli, Italy
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