Virtual Screening Strategy and In Vitro Tests to Identify New Inhibitors of the Immunoproteasome
Immunoproteasome inhibition is a promising strategy for the treatment of hematological malignancies, autoimmune diseases, and inflammatory diseases. The design of non-covalent inhibitors of the immunoproteasome β1i/β5i catalytic subunits could be a novel approach to avoid the drawbacks of the known...
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MDPI AG
2023-06-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/13/10504 |
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| author | Giulia Culletta Marco Tutone Roberta Ettari Ugo Perricone Carla Di Chio Anna Maria Almerico Maria Zappalà |
| author_facet | Giulia Culletta Marco Tutone Roberta Ettari Ugo Perricone Carla Di Chio Anna Maria Almerico Maria Zappalà |
| author_sort | Giulia Culletta |
| collection | DOAJ |
| description | Immunoproteasome inhibition is a promising strategy for the treatment of hematological malignancies, autoimmune diseases, and inflammatory diseases. The design of non-covalent inhibitors of the immunoproteasome β1i/β5i catalytic subunits could be a novel approach to avoid the drawbacks of the known covalent inhibitors, such as toxicity due to off-target binding. In this work, we report the biological evaluation of thirty-four compounds selected from a commercially available collection. These hit compounds are the outcomes of a virtual screening strategy including a dynamic pharmacophore modeling approach onto the β1i subunit and a pharmacophore/docking approach onto the β5i subunit. The computational studies were first followed by in vitro enzymatic assays at 100 μM. Only compounds capable of inhibiting the enzymatic activity by more than 50% were characterized in detail using Tian continuous assays, determining the dissociation constant (<i>K</i><sub>i</sub>) of the non-covalent complex where <i>K</i><sub>i</sub> is also the measure of the binding affinity. Seven out of thirty-four hits showed to inhibit β1i and/or β5i subunit. Compound <b>3</b> is the most active on the β1i subunit with <i>K</i><sub>i</sub> = 11.84 ± 1.63 µM, and compound <b>17</b> showed <i>K</i><sub>i</sub> = 12.50 ± 0.77 µM on the β5i subunit. Compound <b>2</b> showed inhibitory activity on both subunits (<i>K</i><sub>i</sub> = 12.53 ± 0.18 and <i>K</i><sub>i</sub> = 31.95 ± 0.81 on the β1i subunit and β5i subunit, respectively). The induced fit docking analysis revealed interactions with Thr1 and Phe31 of β1i subunit and that represent new key residues as reported in our previous work. Onto β5i subunit, it interacts with the key residues Thr1, Thr21, and Tyr169. This last hit compound identified represents an interesting starting point for further optimization of β1i/β5i dual inhibitors of the immunoproteasome. |
| first_indexed | 2024-03-11T01:40:34Z |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T01:40:34Z |
| publishDate | 2023-06-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-f1bfabbe98874a53bfbba4a8d4b735962023-11-18T16:39:15ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-06-0124131050410.3390/ijms241310504Virtual Screening Strategy and In Vitro Tests to Identify New Inhibitors of the ImmunoproteasomeGiulia Culletta0Marco Tutone1Roberta Ettari2Ugo Perricone3Carla Di Chio4Anna Maria Almerico5Maria Zappalà6Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, ItalyDipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, ItalyDipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale Annunziata, 98168 Messina, ItalyDrug Discovery Unit, Fondazione Ri.MED, 90133 Palermo, ItalyDipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale Annunziata, 98168 Messina, ItalyDipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, ItalyDipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale Annunziata, 98168 Messina, ItalyImmunoproteasome inhibition is a promising strategy for the treatment of hematological malignancies, autoimmune diseases, and inflammatory diseases. The design of non-covalent inhibitors of the immunoproteasome β1i/β5i catalytic subunits could be a novel approach to avoid the drawbacks of the known covalent inhibitors, such as toxicity due to off-target binding. In this work, we report the biological evaluation of thirty-four compounds selected from a commercially available collection. These hit compounds are the outcomes of a virtual screening strategy including a dynamic pharmacophore modeling approach onto the β1i subunit and a pharmacophore/docking approach onto the β5i subunit. The computational studies were first followed by in vitro enzymatic assays at 100 μM. Only compounds capable of inhibiting the enzymatic activity by more than 50% were characterized in detail using Tian continuous assays, determining the dissociation constant (<i>K</i><sub>i</sub>) of the non-covalent complex where <i>K</i><sub>i</sub> is also the measure of the binding affinity. Seven out of thirty-four hits showed to inhibit β1i and/or β5i subunit. Compound <b>3</b> is the most active on the β1i subunit with <i>K</i><sub>i</sub> = 11.84 ± 1.63 µM, and compound <b>17</b> showed <i>K</i><sub>i</sub> = 12.50 ± 0.77 µM on the β5i subunit. Compound <b>2</b> showed inhibitory activity on both subunits (<i>K</i><sub>i</sub> = 12.53 ± 0.18 and <i>K</i><sub>i</sub> = 31.95 ± 0.81 on the β1i subunit and β5i subunit, respectively). The induced fit docking analysis revealed interactions with Thr1 and Phe31 of β1i subunit and that represent new key residues as reported in our previous work. Onto β5i subunit, it interacts with the key residues Thr1, Thr21, and Tyr169. This last hit compound identified represents an interesting starting point for further optimization of β1i/β5i dual inhibitors of the immunoproteasome.https://www.mdpi.com/1422-0067/24/13/10504immunoproteasomeβ1i subunitβ5i subunitdockinginduced fit dockingpharmacophore modeling |
| spellingShingle | Giulia Culletta Marco Tutone Roberta Ettari Ugo Perricone Carla Di Chio Anna Maria Almerico Maria Zappalà Virtual Screening Strategy and In Vitro Tests to Identify New Inhibitors of the Immunoproteasome International Journal of Molecular Sciences immunoproteasome β1i subunit β5i subunit docking induced fit docking pharmacophore modeling |
| title | Virtual Screening Strategy and In Vitro Tests to Identify New Inhibitors of the Immunoproteasome |
| title_full | Virtual Screening Strategy and In Vitro Tests to Identify New Inhibitors of the Immunoproteasome |
| title_fullStr | Virtual Screening Strategy and In Vitro Tests to Identify New Inhibitors of the Immunoproteasome |
| title_full_unstemmed | Virtual Screening Strategy and In Vitro Tests to Identify New Inhibitors of the Immunoproteasome |
| title_short | Virtual Screening Strategy and In Vitro Tests to Identify New Inhibitors of the Immunoproteasome |
| title_sort | virtual screening strategy and in vitro tests to identify new inhibitors of the immunoproteasome |
| topic | immunoproteasome β1i subunit β5i subunit docking induced fit docking pharmacophore modeling |
| url | https://www.mdpi.com/1422-0067/24/13/10504 |
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