Identification of potential inhibitors of interleukin-2-inducible T-cell kinase: insights from docking, molecular dynamics, MMPBSA and free energy landscape studies
Abstract Interleukin-2-inducible T-cell kinase (ITK) is an essential enzyme that plays a key role in both the activation and differentiation of T-cells. As a member of the Tec family of non-receptor tyrosine kinases, ITK is predominantly expressed in T cells, exerting a critical influence on T-cell...
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Springer
2025-06-01
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| Series: | Amino Acids |
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| Online Access: | https://doi.org/10.1007/s00726-025-03457-2 |
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| author | Shazia Ahmed Arunabh Choudhury Mohammad Umar Saeed Taj Mohammad Afzal Hussain Mohamed F. Alajmi Dharmendra Kumar Yadav Anas Shamsi Md. Imtaiyaz Hassan |
| author_facet | Shazia Ahmed Arunabh Choudhury Mohammad Umar Saeed Taj Mohammad Afzal Hussain Mohamed F. Alajmi Dharmendra Kumar Yadav Anas Shamsi Md. Imtaiyaz Hassan |
| author_sort | Shazia Ahmed |
| collection | DOAJ |
| description | Abstract Interleukin-2-inducible T-cell kinase (ITK) is an essential enzyme that plays a key role in both the activation and differentiation of T-cells. As a member of the Tec family of non-receptor tyrosine kinases, ITK is predominantly expressed in T cells, exerting a critical influence on T-cell receptor signaling and downstream pathways. Moreover, ITK regulates cytokine production, notably interleukin-2 (IL-2), and the differentiation of Th2 cells. In the context of immunology, ITK has garnered significant attention, particularly for its potential to address immune-related conditions such as cancer and autoimmune diseases, including lymphoproliferative diseases. In this study, we performed a structure-based virtual screening utilizing a library of plant-based small molecules to identify inhibitors of ITK. The initial selection of phytochemicals was guided by adherence to the Lipinski rule of five. After molecular docking, top-ranked hits in terms of binding affinity underwent screening for physicochemical and pharmacokinetic properties and PASS analyses. The three selected phytochemicals, Withanolide A, Amorphispironon E, and 27-Deoxy-14-hydroxywithaferin A (27-DHA) demonstrated remarkable binding affinity to ITK with a docking score of − 9.2, − 9.1, and − 9.1 kcal/mol, respectively. All the phytochemicals showed specific binding to the ATP-binding site of ITK as revealed by protein structure network analysis. These selected phytoconstituents underwent all-atom molecular dynamics (MD) simulations, spanning 100 ns each. The simulation results showed that ITK with elucidated compounds exhibited stability with minimal dynamics. In addition, we performed an MM-PBSA analysis, which indicated a strong binding affinity. This study highlights the potential of Withanolide A, Amorphispironon E, and 27-DHA as preliminary leads for further experimental validation and preclinical investigation toward therapeutic development. |
| format | Article |
| id | doaj-art-7265344491984d2aba6e733f3c49a4f0 |
| institution | Kabale University |
| issn | 1438-2199 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Springer |
| record_format | Article |
| series | Amino Acids |
| spelling | doaj-art-7265344491984d2aba6e733f3c49a4f02025-08-20T03:25:19ZengSpringerAmino Acids1438-21992025-06-0157111710.1007/s00726-025-03457-2Identification of potential inhibitors of interleukin-2-inducible T-cell kinase: insights from docking, molecular dynamics, MMPBSA and free energy landscape studiesShazia Ahmed0Arunabh Choudhury1Mohammad Umar Saeed2Taj Mohammad3Afzal Hussain4Mohamed F. Alajmi5Dharmendra Kumar Yadav6Anas Shamsi7Md. Imtaiyaz Hassan8Department of Computer Science, Jamia Millia IslamiaCentre for Interdisciplinary Research in Basic Sciences, Jamia Millia IslamiaCentre for Interdisciplinary Research in Basic Sciences, Jamia Millia IslamiaCentre for Interdisciplinary Research in Basic Sciences, Jamia Millia IslamiaDepartment of Pharmacognosy, College of Pharmacy, King Saud UniversityDepartment of Pharmacognosy, College of Pharmacy, King Saud UniversityCollege of Pharmacy, Gachon UniversityCentre of Medical and Bio-Allied Health Sciences Research, Ajman UniversityCentre for Interdisciplinary Research in Basic Sciences, Jamia Millia IslamiaAbstract Interleukin-2-inducible T-cell kinase (ITK) is an essential enzyme that plays a key role in both the activation and differentiation of T-cells. As a member of the Tec family of non-receptor tyrosine kinases, ITK is predominantly expressed in T cells, exerting a critical influence on T-cell receptor signaling and downstream pathways. Moreover, ITK regulates cytokine production, notably interleukin-2 (IL-2), and the differentiation of Th2 cells. In the context of immunology, ITK has garnered significant attention, particularly for its potential to address immune-related conditions such as cancer and autoimmune diseases, including lymphoproliferative diseases. In this study, we performed a structure-based virtual screening utilizing a library of plant-based small molecules to identify inhibitors of ITK. The initial selection of phytochemicals was guided by adherence to the Lipinski rule of five. After molecular docking, top-ranked hits in terms of binding affinity underwent screening for physicochemical and pharmacokinetic properties and PASS analyses. The three selected phytochemicals, Withanolide A, Amorphispironon E, and 27-Deoxy-14-hydroxywithaferin A (27-DHA) demonstrated remarkable binding affinity to ITK with a docking score of − 9.2, − 9.1, and − 9.1 kcal/mol, respectively. All the phytochemicals showed specific binding to the ATP-binding site of ITK as revealed by protein structure network analysis. These selected phytoconstituents underwent all-atom molecular dynamics (MD) simulations, spanning 100 ns each. The simulation results showed that ITK with elucidated compounds exhibited stability with minimal dynamics. In addition, we performed an MM-PBSA analysis, which indicated a strong binding affinity. This study highlights the potential of Withanolide A, Amorphispironon E, and 27-DHA as preliminary leads for further experimental validation and preclinical investigation toward therapeutic development.https://doi.org/10.1007/s00726-025-03457-2Interleukin-2-inducible T-cell kinaseVirtual screeningLymphoproliferative diseasesPhytochemicalsMolecular dynamics simulation |
| spellingShingle | Shazia Ahmed Arunabh Choudhury Mohammad Umar Saeed Taj Mohammad Afzal Hussain Mohamed F. Alajmi Dharmendra Kumar Yadav Anas Shamsi Md. Imtaiyaz Hassan Identification of potential inhibitors of interleukin-2-inducible T-cell kinase: insights from docking, molecular dynamics, MMPBSA and free energy landscape studies Amino Acids Interleukin-2-inducible T-cell kinase Virtual screening Lymphoproliferative diseases Phytochemicals Molecular dynamics simulation |
| title | Identification of potential inhibitors of interleukin-2-inducible T-cell kinase: insights from docking, molecular dynamics, MMPBSA and free energy landscape studies |
| title_full | Identification of potential inhibitors of interleukin-2-inducible T-cell kinase: insights from docking, molecular dynamics, MMPBSA and free energy landscape studies |
| title_fullStr | Identification of potential inhibitors of interleukin-2-inducible T-cell kinase: insights from docking, molecular dynamics, MMPBSA and free energy landscape studies |
| title_full_unstemmed | Identification of potential inhibitors of interleukin-2-inducible T-cell kinase: insights from docking, molecular dynamics, MMPBSA and free energy landscape studies |
| title_short | Identification of potential inhibitors of interleukin-2-inducible T-cell kinase: insights from docking, molecular dynamics, MMPBSA and free energy landscape studies |
| title_sort | identification of potential inhibitors of interleukin 2 inducible t cell kinase insights from docking molecular dynamics mmpbsa and free energy landscape studies |
| topic | Interleukin-2-inducible T-cell kinase Virtual screening Lymphoproliferative diseases Phytochemicals Molecular dynamics simulation |
| url | https://doi.org/10.1007/s00726-025-03457-2 |
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