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Antoniou M, Papavasileiou KD, Melagraki G, Dondero F, Lynch I, Afantitis A. Development of a Robust Read-Across Model for the Prediction of Biological Potency of Novel Peroxisome Proliferator-Activated Receptor Delta Agonists. Int J Mol Sci 2024; 25:5216. [PMID: 38791255 PMCID: PMC11121726 DOI: 10.3390/ijms25105216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
A robust predictive model was developed using 136 novel peroxisome proliferator-activated receptor delta (PPARδ) agonists, a distinct subtype of lipid-activated transcription factors of the nuclear receptor superfamily that regulate target genes by binding to characteristic sequences of DNA bases. The model employs various structural descriptors and docking calculations and provides predictions of the biological activity of PPARδ agonists, following the criteria of the Organization for Economic Co-operation and Development (OECD) for the development and validation of quantitative structure-activity relationship (QSAR) models. Specifically focused on small molecules, the model facilitates the identification of highly potent and selective PPARδ agonists and offers a read-across concept by providing the chemical neighbours of the compound under study. The model development process was conducted on Isalos Analytics Software (v. 0.1.17) which provides an intuitive environment for machine-learning applications. The final model was released as a user-friendly web tool and can be accessed through the Enalos Cloud platform's graphical user interface (GUI).
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Affiliation(s)
- Maria Antoniou
- Department of Chemoinformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus; (M.A.); (K.D.P.)
- Department of ChemoInformatics, NovaMechanics MIKE, 18545 Piraeus, Greece
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
| | - Konstantinos D. Papavasileiou
- Department of Chemoinformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus; (M.A.); (K.D.P.)
- Department of ChemoInformatics, NovaMechanics MIKE, 18545 Piraeus, Greece
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, 16672 Vari, Greece;
| | - Francesco Dondero
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
- Department of Science and Technological Innovation, Università del Piemonte Orientale, 15121 Alessandria, Italy
| | - Iseult Lynch
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
- School of Geography, Earth and Environmental Sciences, University of Birmingham Edgbaston, Birmingham B15 2TT, UK
| | - Antreas Afantitis
- Department of Chemoinformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus; (M.A.); (K.D.P.)
- Department of ChemoInformatics, NovaMechanics MIKE, 18545 Piraeus, Greece
- Entelos Institute, Larnaca 6059, Cyprus; (F.D.); (I.L.)
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Adhikari N, Amin SA, Ghosh B, Jha T. Shedding light on designing potential meprin β inhibitors through ligand-based robust validated computational approaches: A proposal to chemists! J Biomol Struct Dyn 2017; 36:3003-3022. [DOI: 10.1080/07391102.2017.1374210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
| | - Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
| | - Balaram Ghosh
- Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
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Structural exploration of PPARγ modulators through pharmacophore mapping, fragment-based design, docking, and molecular dynamics simulation analyses. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1727-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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