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Faris A, Hadni H, Saleh BA, Khelfaoui H, Harkati D, Ait Ahsaine H, Elhallaoui M, El-Hiti GA. In silico screening of a series of 1,6-disubstituted 1 H-pyrazolo[3,4- d]pyrimidines as potential selective inhibitors of the Janus kinase 3. J Biomol Struct Dyn 2024; 42:4456-4474. [PMID: 37317996 DOI: 10.1080/07391102.2023.2220829] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/28/2023] [Indexed: 06/16/2023]
Abstract
Rheumatoid arthritis is a common chronic disabling inflammatory disease that is characterized by inflammation of the synovial membrane and leads to discomfort. In the current study, twenty-seven 1,6-disubstituted 1H-pyrazolo[3,4-d]pyrimidines were tested as potential selective inhibitors of the tyrosine-protein kinase JAK3 using a number of molecular modeling methods. The activity of the screened derivatives was statistically quantified using multiple linear regression and artificial neural networks. To assess the quality, robustness, and predictability of the generated models, the leave-one-out cross-validation method was applied with favorable results (Q2 = 0.75) and Y-randomization. In addition, the evaluation of the predictive ability of the established model was confirmed by means of an external validation using a composite test set and an applicability domain approach. The covalent docking indicated that the tested 1H-pyrazolo[3,4-d]pyrimidines containing the acrylic aldehyde moiety had irreversible interaction with the residue Cys909 in the active sites of the tyrosine-protein kinase JAK3 by Michael addition. The molecular dynamics for three selected derivatives (compounds 9, 12, and 18) were used to verify the covalent docking by determining the stability of hydrogen bonding interactions with active sites, which are needed to stop tyrosine-protein kinase JAK3. The results obtained showed that the tested compounds containing acrylic aldehyde moiety had favorable binding free energies, indicating a strong affinity for the JAK3 enzyme. Overall, this current study suggests that the tested compounds containing the acrylic aldehyde moiety have the potential to act as anti-JAK3 inhibitors. They could be explored further to be used as treatment options for rheumatoid arthritis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdelmoujoud Faris
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hanine Hadni
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Basil A Saleh
- Department of Chemistry, College of Science, University of Basrah, Basrah, Iraq
| | - Hadjer Khelfaoui
- Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, Faculty of Exact and Natural Sciences, Department of Matter Sciences, University of Biskra, Biskra, Algeria
| | - Dalal Harkati
- Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, Faculty of Exact and Natural Sciences, Department of Matter Sciences, University of Biskra, Biskra, Algeria
| | - Hassan Ait Ahsaine
- Laboratoire de Chimie Appliquée des Matériaux, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Menana Elhallaoui
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Gamal A El-Hiti
- Department of Optometry, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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Maji L, Sengupta S, Purawarga Matada GS, Teli G, Biswas G, Das PK, Panduranga Mudgal M. Medicinal chemistry perspective of JAK inhibitors: synthesis, biological profile, selectivity, and structure activity relationship. Mol Divers 2024:10.1007/s11030-023-10794-5. [PMID: 38236444 DOI: 10.1007/s11030-023-10794-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/07/2023] [Indexed: 01/19/2024]
Abstract
JAK-STAT signalling pathway was discovered more than quarter century ago. The JAK-STAT pathway protein is considered as one of the crucial hubs for cytokine secretion which mediates activation of different inflammatory, cellular responses and hence involved in different etiological factors. The various etiological factors involved are haematopoiesis, immune fitness, tissue repair, inflammation, apoptosis, and adipogenesis. The presence of the active mutation V617K plays a significant role in the progression of the JAK-STAT pathway-related disease. Consequently, targeting the JAK-STAT pathway could be a promising therapeutic approach for addressing a range of causative factors. In this current review, we provided a comprehensive discussion for the in-detail study of anatomy and physiology of the JAK-STAT pathway which contributes structural domain rearrangement, activation, and negative regulation associated with the downstream signaling pathway, relationship between different cytokines and diseases. This review also discussed the recent development of clinical trial entities. Additionally, this review also provides updates on FDA-approved drugs. In the current investigation, we have classified recently developed small molecule inhibitors of JAK-STAT pathway according to different chemical classes and we emphasized their synthetic routes, biological evaluation, selectivity, and structure-activity relationship.
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Affiliation(s)
- Lalmohan Maji
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
| | - Sindhuja Sengupta
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
| | | | - Ghanshyam Teli
- School of Pharmacy, Sangam University, Atoon, Bhilwara, 311001, Rajasthan, India
| | - Gourab Biswas
- Department of Pharmaceutical Technology, Brainware University, Kolkata, West Bengal, India
| | - Pronoy Kanti Das
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, Karnataka, India
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Faris A, Ibrahim IM, Alnajjar R, Hadni H, Bhat MA, Yaseen M, Chakraborty S, Alsakhen N, Shamkh IM, Mabood F, M Naglah A, Ullah I, Ziedan N, Elhallaoui M. QSAR-driven screening uncovers and designs novel pyrimidine-4,6-diamine derivatives as potent JAK3 inhibitors. J Biomol Struct Dyn 2023:1-30. [PMID: 38059345 DOI: 10.1080/07391102.2023.2283168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
This study presents a robust and integrated methodology that harnesses a range of computational techniques to facilitate the design and prediction of new inhibitors targeting the JAK3/STAT pathway. This methodology encompasses several strategies, including QSAR analysis, pharmacophore modeling, ADMET prediction, covalent docking, molecular dynamics (MD) simulations, and the calculation of binding free energies (MM/GBSA). An efficacious QSAR model was meticulously crafted through the employment of multiple linear regression (MLR). The initial MLR model underwent further refinement employing an artificial neural network (ANN) methodology aimed at minimizing predictive errors. Notably, both MLR and ANN exhibited commendable performance, showcasing R2 values of 0.89 and 0.95, respectively. The model's precision was assessed via leave-one-out cross-validation (CV) yielding a Q2 value of 0.65, supplemented by rigorous Y-randomization. , The pharmacophore model effectively differentiated between active and inactive drugs, identifying potential JAK3 inhibitors, and demonstrated validity with an ROC value of 0.86. The newly discovered and designed inhibitors exhibited high inhibitory potency, ranging from 6 to 8, as accurately predicted by the QSAR models. Comparative analysis with FDA-approved Tofacitinib revealed that the new compounds exhibited promising ADMET properties and strong covalent docking (CovDock) interactions. The stability of the new discovered and designed inhibitors within the JAK3 binding site was confirmed through 500 ns MD simulations, while MM/GBSA calculations supported their binding affinity. Additionally, a retrosynthetic study was conducted to facilitate the synthesis of these potential JAK3/STAT inhibitors. The overall integrated approach demonstrates the feasibility of designing novel JAK3/STAT inhibitors with robust efficacy and excellent ADMET characteristics that surpass Tofacitinib by a significant margin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdelmoujoud Faris
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Cairo, Egypt
| | - Radwan Alnajjar
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi, Libya
| | - Hanine Hadni
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh, Swat, Pakistan
| | - Souvik Chakraborty
- Department of Physiology, Bhairab Ganguly College, Belghoria, Kolkata, West Bengal, India
| | - Nada Alsakhen
- Department of Chemistry, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Israa M Shamkh
- Botany and Microbiology Department, Faculty of Science, Cairo University, Cairo, Egypt
| | - Fazal Mabood
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh, Swat, Pakistan
| | - Ahmed M Naglah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ihsan Ullah
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh, Swat, Pakistan
| | - Noha Ziedan
- Department of Physical, Mathematical and Engineering Science, Faculty of Science, Business and Enterprise, University of Chester, Chester, UK
| | - Menana Elhallaoui
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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