Small molecules targeting the eubacterial β-sliding clamp discovered by combined in silico and in vitro screening approaches
Antibiotic resistance stands as the foremost post-pandemic threat to public health. The urgent need for new, effective antibacterial treatments is evident. Protein-protein interactions (PPIs), owing to their pivotal role in microbial physiology, emerge as novel and attractive targets. Particularly p...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2025-12-01
|
| Series: | Journal of Enzyme Inhibition and Medicinal Chemistry |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/14756366.2024.2440861 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841560783588163584 |
|---|---|
| author | Alessia Caputo Gian Marco Elisi Elisabetta Levati Giulia Barotti Sara Sartini Jerome Wagner Dominique Y. Burnouf Simone Ottonello Silvia Rivara Barbara Montanini |
| author_facet | Alessia Caputo Gian Marco Elisi Elisabetta Levati Giulia Barotti Sara Sartini Jerome Wagner Dominique Y. Burnouf Simone Ottonello Silvia Rivara Barbara Montanini |
| author_sort | Alessia Caputo |
| collection | DOAJ |
| description | Antibiotic resistance stands as the foremost post-pandemic threat to public health. The urgent need for new, effective antibacterial treatments is evident. Protein-protein interactions (PPIs), owing to their pivotal role in microbial physiology, emerge as novel and attractive targets. Particularly promising is the α-subunit/β-sliding clamp interaction, crucial for the replicative competence of bacterial DNA polymerase III holoenzyme. Through pharmacophore-based virtual screening, we identified 4,000 candidate small molecule inhibitors targeting the β-clamp binding pocket. Subsequently, these candidates underwent evaluation using the BRET assay in yeast cells. Following this, three hits and 28 analogues were validated via Protein Thermal Shift and competitive ELISA assays. Among them, thiazolo[4,5-d]-pyrimidinedione and benzanilide derivatives exhibited micromolar potency in displacing the β-clamp protein partner and inhibiting DNA replication. This screening campaign unveiled new chemical classes of α/β-clamp PPI disruptors capable of inhibiting DNA polymerase III activity, which lend themselves for further optimisation to improve their antibacterial efficacy. |
| format | Article |
| id | doaj-art-74af6c7858974bb3993b6af9745bdcb8 |
| institution | Kabale University |
| issn | 1475-6366 1475-6374 |
| language | English |
| publishDate | 2025-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Journal of Enzyme Inhibition and Medicinal Chemistry |
| spelling | doaj-art-74af6c7858974bb3993b6af9745bdcb82025-01-03T13:20:00ZengTaylor & Francis GroupJournal of Enzyme Inhibition and Medicinal Chemistry1475-63661475-63742025-12-0140110.1080/14756366.2024.2440861Small molecules targeting the eubacterial β-sliding clamp discovered by combined in silico and in vitro screening approachesAlessia Caputo0Gian Marco Elisi1Elisabetta Levati2Giulia Barotti3Sara Sartini4Jerome Wagner5Dominique Y. Burnouf6Simone Ottonello7Silvia Rivara8Barbara Montanini9Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, ItalyDepartment of Food and Drug, University of Parma, Parma, ItalyLaboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, ItalyLaboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, ItalyLaboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, ItalyUniversité de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, FranceUniversité de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, FranceLaboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, ItalyDepartment of Food and Drug, University of Parma, Parma, ItalyLaboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, ItalyAntibiotic resistance stands as the foremost post-pandemic threat to public health. The urgent need for new, effective antibacterial treatments is evident. Protein-protein interactions (PPIs), owing to their pivotal role in microbial physiology, emerge as novel and attractive targets. Particularly promising is the α-subunit/β-sliding clamp interaction, crucial for the replicative competence of bacterial DNA polymerase III holoenzyme. Through pharmacophore-based virtual screening, we identified 4,000 candidate small molecule inhibitors targeting the β-clamp binding pocket. Subsequently, these candidates underwent evaluation using the BRET assay in yeast cells. Following this, three hits and 28 analogues were validated via Protein Thermal Shift and competitive ELISA assays. Among them, thiazolo[4,5-d]-pyrimidinedione and benzanilide derivatives exhibited micromolar potency in displacing the β-clamp protein partner and inhibiting DNA replication. This screening campaign unveiled new chemical classes of α/β-clamp PPI disruptors capable of inhibiting DNA polymerase III activity, which lend themselves for further optimisation to improve their antibacterial efficacy.https://www.tandfonline.com/doi/10.1080/14756366.2024.2440861Bacterial DNA polymeraseprotein–protein interaction inhibitorsvirtual screeningyeast Bioluminescence Resonance Energy Transfer (yBRET)antibiotics |
| spellingShingle | Alessia Caputo Gian Marco Elisi Elisabetta Levati Giulia Barotti Sara Sartini Jerome Wagner Dominique Y. Burnouf Simone Ottonello Silvia Rivara Barbara Montanini Small molecules targeting the eubacterial β-sliding clamp discovered by combined in silico and in vitro screening approaches Journal of Enzyme Inhibition and Medicinal Chemistry Bacterial DNA polymerase protein–protein interaction inhibitors virtual screening yeast Bioluminescence Resonance Energy Transfer (yBRET) antibiotics |
| title | Small molecules targeting the eubacterial β-sliding clamp discovered by combined in silico and in vitro screening approaches |
| title_full | Small molecules targeting the eubacterial β-sliding clamp discovered by combined in silico and in vitro screening approaches |
| title_fullStr | Small molecules targeting the eubacterial β-sliding clamp discovered by combined in silico and in vitro screening approaches |
| title_full_unstemmed | Small molecules targeting the eubacterial β-sliding clamp discovered by combined in silico and in vitro screening approaches |
| title_short | Small molecules targeting the eubacterial β-sliding clamp discovered by combined in silico and in vitro screening approaches |
| title_sort | small molecules targeting the eubacterial β sliding clamp discovered by combined in silico and in vitro screening approaches |
| topic | Bacterial DNA polymerase protein–protein interaction inhibitors virtual screening yeast Bioluminescence Resonance Energy Transfer (yBRET) antibiotics |
| url | https://www.tandfonline.com/doi/10.1080/14756366.2024.2440861 |
| work_keys_str_mv | AT alessiacaputo smallmoleculestargetingtheeubacterialbslidingclampdiscoveredbycombinedinsilicoandinvitroscreeningapproaches AT gianmarcoelisi smallmoleculestargetingtheeubacterialbslidingclampdiscoveredbycombinedinsilicoandinvitroscreeningapproaches AT elisabettalevati smallmoleculestargetingtheeubacterialbslidingclampdiscoveredbycombinedinsilicoandinvitroscreeningapproaches AT giuliabarotti smallmoleculestargetingtheeubacterialbslidingclampdiscoveredbycombinedinsilicoandinvitroscreeningapproaches AT sarasartini smallmoleculestargetingtheeubacterialbslidingclampdiscoveredbycombinedinsilicoandinvitroscreeningapproaches AT jeromewagner smallmoleculestargetingtheeubacterialbslidingclampdiscoveredbycombinedinsilicoandinvitroscreeningapproaches AT dominiqueyburnouf smallmoleculestargetingtheeubacterialbslidingclampdiscoveredbycombinedinsilicoandinvitroscreeningapproaches AT simoneottonello smallmoleculestargetingtheeubacterialbslidingclampdiscoveredbycombinedinsilicoandinvitroscreeningapproaches AT silviarivara smallmoleculestargetingtheeubacterialbslidingclampdiscoveredbycombinedinsilicoandinvitroscreeningapproaches AT barbaramontanini smallmoleculestargetingtheeubacterialbslidingclampdiscoveredbycombinedinsilicoandinvitroscreeningapproaches |