Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions
The selectivity pocket is a key binding site for inhibitors of the NAD<sup>+</sup>-dependent lysine deacylase Sirtuin 2 (Sirt2), a promising drug target in diseases like cancer. While small-molecule soaking can advance inhibitor development, the selectivity pocket is absent in available...
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2025
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| _version_ | 1852020242028429312 |
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| author | Florian Friedrich (17304380) |
| author2 | Matthias Schiedel (1399321) Sören Swyter (3930095) Lin Zhang (8926) Wolfgang Sippl (169574) Mike Schutkowski (135091) Oliver Einsle (765955) Manfred Jung (26925) |
| author2_role | author author author author author author author |
| author_facet | Florian Friedrich (17304380) Matthias Schiedel (1399321) Sören Swyter (3930095) Lin Zhang (8926) Wolfgang Sippl (169574) Mike Schutkowski (135091) Oliver Einsle (765955) Manfred Jung (26925) |
| author_role | author |
| dc.creator.none.fl_str_mv | Florian Friedrich (17304380) Matthias Schiedel (1399321) Sören Swyter (3930095) Lin Zhang (8926) Wolfgang Sippl (169574) Mike Schutkowski (135091) Oliver Einsle (765955) Manfred Jung (26925) |
| dc.date.none.fl_str_mv | 2025-05-20T04:44:06Z |
| dc.identifier.none.fl_str_mv | 10.1021/acs.jmedchem.4c02896.s006 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Efficient_Crystallization_of_Apo_Sirt2_for_Small-Molecule_Soaking_and_Structural_Analysis_of_Ligand_Interactions/29106159 |
| dc.rights.none.fl_str_mv | CC BY-NC 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biophysics Biochemistry Medicine Cell Biology Molecular Biology Pharmacology Biotechnology Cancer Chemical Sciences not elsewhere classified unfavorable crystal packing promising drug target lysine channel entrance diseases like cancer free apo structure peptide inhibitor kt9 key binding site cofactor binding site advance inhibitor development sirtuin rearranging ligand sirt2 apo crystals rapidly generate high open selectivity pocket fragment library using hinders ligand binding selectivity pocket apo sirt2 inhibitor structures inhibitor optimization sirt2 ), ligand interactions throughput soaking structural analysis molecule soaking maybridge ro3 efficient crystallization accommodate ligands |
| dc.title.none.fl_str_mv | Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | The selectivity pocket is a key binding site for inhibitors of the NAD<sup>+</sup>-dependent lysine deacylase Sirtuin 2 (Sirt2), a promising drug target in diseases like cancer. While small-molecule soaking can advance inhibitor development, the selectivity pocket is absent in available Sirt2 apo structures, and existing soaking systems like Sirt2–ADPribose (ADPR) suffer from unfavorable crystal packing that hinders ligand binding. We developed a method to rapidly generate high-quality Sirt2 apo crystals with an open selectivity pocket, suitable for high-throughput soaking. The induced-fit pocket forms upon seeding with a Sirtuin Rearranging ligand (SirReal) and is retained in the ligand-free apo structure. Screening the Maybridge Ro3-fragment library using a fluorescence polarization assay yielded three novel Sirt2-fragment-inhibitor structures. Additionally, our Sirt2 apo crystals can accommodate ligands at the acyl-lysine channel entrance and the cofactor binding site, as confirmed by binding of the peptide inhibitor KT9 and NAD<sup>+</sup>, facilitating SAR studies and inhibitor optimization. |
| eu_rights_str_mv | openAccess |
| id | Manara_3e3e88f18870efe3cbaa49830350ecf1 |
| identifier_str_mv | 10.1021/acs.jmedchem.4c02896.s006 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/29106159 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY-NC 4.0 |
| spelling | Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand InteractionsFlorian Friedrich (17304380)Matthias Schiedel (1399321)Sören Swyter (3930095)Lin Zhang (8926)Wolfgang Sippl (169574)Mike Schutkowski (135091)Oliver Einsle (765955)Manfred Jung (26925)BiophysicsBiochemistryMedicineCell BiologyMolecular BiologyPharmacologyBiotechnologyCancerChemical Sciences not elsewhere classifiedunfavorable crystal packingpromising drug targetlysine channel entrancediseases like cancerfree apo structurepeptide inhibitor kt9key binding sitecofactor binding siteadvance inhibitor developmentsirtuin rearranging ligandsirt2 apo crystalsrapidly generate highopen selectivity pocketfragment library usinghinders ligand bindingselectivity pocketapo sirt2inhibitor structuresinhibitor optimizationsirt2 ),ligand interactionsthroughput soakingstructural analysismolecule soakingmaybridge ro3efficient crystallizationaccommodate ligandsThe selectivity pocket is a key binding site for inhibitors of the NAD<sup>+</sup>-dependent lysine deacylase Sirtuin 2 (Sirt2), a promising drug target in diseases like cancer. While small-molecule soaking can advance inhibitor development, the selectivity pocket is absent in available Sirt2 apo structures, and existing soaking systems like Sirt2–ADPribose (ADPR) suffer from unfavorable crystal packing that hinders ligand binding. We developed a method to rapidly generate high-quality Sirt2 apo crystals with an open selectivity pocket, suitable for high-throughput soaking. The induced-fit pocket forms upon seeding with a Sirtuin Rearranging ligand (SirReal) and is retained in the ligand-free apo structure. Screening the Maybridge Ro3-fragment library using a fluorescence polarization assay yielded three novel Sirt2-fragment-inhibitor structures. Additionally, our Sirt2 apo crystals can accommodate ligands at the acyl-lysine channel entrance and the cofactor binding site, as confirmed by binding of the peptide inhibitor KT9 and NAD<sup>+</sup>, facilitating SAR studies and inhibitor optimization.2025-05-20T04:44:06ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.1021/acs.jmedchem.4c02896.s006https://figshare.com/articles/dataset/Efficient_Crystallization_of_Apo_Sirt2_for_Small-Molecule_Soaking_and_Structural_Analysis_of_Ligand_Interactions/29106159CC BY-NC 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/291061592025-05-20T04:44:06Z |
| spellingShingle | Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions Florian Friedrich (17304380) Biophysics Biochemistry Medicine Cell Biology Molecular Biology Pharmacology Biotechnology Cancer Chemical Sciences not elsewhere classified unfavorable crystal packing promising drug target lysine channel entrance diseases like cancer free apo structure peptide inhibitor kt9 key binding site cofactor binding site advance inhibitor development sirtuin rearranging ligand sirt2 apo crystals rapidly generate high open selectivity pocket fragment library using hinders ligand binding selectivity pocket apo sirt2 inhibitor structures inhibitor optimization sirt2 ), ligand interactions throughput soaking structural analysis molecule soaking maybridge ro3 efficient crystallization accommodate ligands |
| status_str | publishedVersion |
| title | Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions |
| title_full | Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions |
| title_fullStr | Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions |
| title_full_unstemmed | Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions |
| title_short | Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions |
| title_sort | Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions |
| topic | Biophysics Biochemistry Medicine Cell Biology Molecular Biology Pharmacology Biotechnology Cancer Chemical Sciences not elsewhere classified unfavorable crystal packing promising drug target lysine channel entrance diseases like cancer free apo structure peptide inhibitor kt9 key binding site cofactor binding site advance inhibitor development sirtuin rearranging ligand sirt2 apo crystals rapidly generate high open selectivity pocket fragment library using hinders ligand binding selectivity pocket apo sirt2 inhibitor structures inhibitor optimization sirt2 ), ligand interactions throughput soaking structural analysis molecule soaking maybridge ro3 efficient crystallization accommodate ligands |