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El Fadili M, Er-Rajy M, Ali Eltayb W, Kara M, Imtara H, Zarougui S, Al-Hoshani N, Hamadi A, Elhallaoui M. An in-silico investigation based on molecular simulations of novel and potential brain-penetrant GluN2B NMDA receptor antagonists as anti-stroke therapeutic agents. J Biomol Struct Dyn 2024; 42:6174-6188. [PMID: 37428078 DOI: 10.1080/07391102.2023.2232024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023]
Abstract
GluN2B-induced activation of NMDA receptors plays a key function in central nervous system (CNS) disorders, including Parkinson, Alzheimer, and stroke, as it is strongly involved in excitotoxicity, which makes selective NMDA receptor antagonists one of the potential therapeutic agents for the treatment of neurodegenerative diseases, especially stroke. The present study aims to examine a structural family of thirty brain-penetrating GluN2B N-methyl-D-aspartate (NMDA) receptor antagonists, using virtual computer-assisted drug design (CADD) to discover highly candidate drugs for ischemic strokes. Initially, the physicochemical and ADMET pharmacokinetic properties confirmed that C13 and C22 compounds were predicted as non-toxic inhibitors of CYP2D6 and CYP3A4 cytochromes, with human intestinal absorption (HIA) exceeding 90%, and designed to be as efficient central nervous system (CNS) agents due to the highest probability to cross the blood-brain barrier (BBB). Compared to ifenprodil, a co-crystallized ligand complexed with the transport protein encoded as 3QEL.pdb, we have noticed that C13 and C22 chemical compounds were defined by good ADME-Toxicity profiles, meeting Lipinski, Veber, Egan, Ghose, and Muegge rules. The molecular docking results indicated that C22 and C13 ligands react specifically with the amino acid residues of the NMDA receptor subunit GluN1 and GluN2B. These intermolecular interactions produced between the candidate drugs and the targeted protein in the B chain remain stable over 200 nanoseconds of molecular dynamics simulation time. In conclusion, C22 and C13 ligands are highly recommended as anti-stroke therapeutic drugs due to their safety and molecular stability towards NMDA receptors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed El Fadili
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez, Morocco
| | - Mohammed Er-Rajy
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez, Morocco
| | - Wafa Ali Eltayb
- Biotechnology Department, Faculty of Sciences and Technology, Shendi University, Shendi, Sudan
| | - Mohammed Kara
- Laboratory of Biotechnology, Conservation and Valorisation of Naturals Resources, Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hamada Imtara
- Faculty of Arts and Sciences, Arab American University Palestine, Jenin, Palestine
| | - Sara Zarougui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez, Morocco
| | - Nawal Al-Hoshani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Abdullah Hamadi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Menana Elhallaoui
- LIMAS Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez, Morocco
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Zarougui S, Er-Rajy M, Faris A, Imtara H, El fadili M, Qurtam AA, Nasr FA, Al-Zharani M, Elhallaoui M. 3D computer modeling of inhibitors targeting the MCF-7 breast cancer cell line. Front Chem 2024; 12:1384832. [PMID: 38887699 PMCID: PMC11181028 DOI: 10.3389/fchem.2024.1384832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/11/2024] [Indexed: 06/20/2024] Open
Abstract
This study focused on developing new inhibitors for the MCF-7 cell line to contribute to our understanding of breast cancer biology and various experimental techniques. 3D QSAR modeling was used to design new tetrahydrobenzo[4, 5]thieno[2, 3-d]pyrimidine derivatives with good characteristics. Two robust 3D-QSAR models were developed, and their predictive capacities were confirmed through high correlations [CoMFA (Q2 = 0.62, R 2 = 0.90) and CoMSIA (Q2 = 0.71, R 2 = 0.88)] via external validations (R2 ext = 0.90 and R2 ext = 0.91, respectively). These successful evaluations confirm the potential of the models to provide reliable predictions. Six candidate inhibitors were discovered, and two new inhibitors were developed in silico using computational methods. The ADME-Tox properties and pharmacokinetic characteristics of the new derivatives were evaluated carefully. The interactions between the new tetrahydrobenzo[4, 5]thieno[2, 3-d]pyrimidine derivatives and the protein ERα (PDB code: 4XO6) were highlighted by molecular docking. Additionally, MM/GBSA calculations and molecular dynamics simulations provided interesting information on the binding stabilities between the complexes. The pharmaceutical characteristics, interactions with protein, and stabilities of the inhibitors were examined using various methods, including molecular docking and molecular dynamics simulations over 100 ns, binding free energy calculations, and ADME-Tox predictions, and compared with the FDA-approved drug capivasertib. The findings indicate that the inhibitors exhibit significant binding affinities, robust stabilities, and desirable pharmaceutical characteristics. These newly developed compounds, which act as inhibitors to mitigate breast cancer, therefore possess considerable potential as prospective drug candidates.
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Affiliation(s)
- Sara Zarougui
- Laboratory of Engineering, Modelisation and Systems Analysis, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Er-Rajy
- Laboratory of Engineering, Modelisation and Systems Analysis, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Abdelmoujoud Faris
- Laboratory of Engineering, Modelisation and Systems Analysis, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hamada Imtara
- Faculty of Medicine, Arab American University Palestine, Jenin, Palestine
| | - Mohamed El fadili
- Laboratory of Engineering, Modelisation and Systems Analysis, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ashraf Ahmed Qurtam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Fahd A. Nasr
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Mohammed Al-Zharani
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Menana Elhallaoui
- Laboratory of Engineering, Modelisation and Systems Analysis, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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Ahmad B, Saeed A, Al-Amery A, Celik I, Ahmed I, Yaseen M, Khan IA, Al-Fahad D, Bhat MA. Investigating Potential Cancer Therapeutics: Insight into Histone Deacetylases (HDACs) Inhibitions. Pharmaceuticals (Basel) 2024; 17:444. [PMID: 38675404 PMCID: PMC11054547 DOI: 10.3390/ph17040444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Histone deacetylases (HDACs) are enzymes that remove acetyl groups from ɛ-amino of histone, and their involvement in the development and progression of cancer disorders makes them an interesting therapeutic target. This study seeks to discover new inhibitors that selectively inhibit HDAC enzymes which are linked to deadly disorders like T-cell lymphoma, childhood neuroblastoma, and colon cancer. MOE was used to dock libraries of ZINC database molecules within the catalytic active pocket of target HDACs. The top three hits were submitted to MD simulations ranked on binding affinities and well-occupied interaction mechanisms determined from molecular docking studies. Inside the catalytic active site of HDACs, the two stable inhibitors LIG1 and LIG2 affect the protein flexibility, as evidenced by RMSD, RMSF, Rg, and PCA. MD simulations of HDACs complexes revealed an alteration from extended to bent motional changes within loop regions. The structural deviation following superimposition shows flexibility via a visual inspection of movable loops at different timeframes. According to PCA, the activity of HDACs inhibitors induces structural dynamics that might potentially be utilized to define the nature of protein inhibition. The findings suggest that this study offers solid proof to investigate LIG1 and LIG2 as potential HDAC inhibitors.
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Affiliation(s)
- Basharat Ahmad
- School of Life Science and Technology, Center for Informational Biology, University of Electronics Science and Technology of China, Chengdu 610056, China
| | - Aamir Saeed
- Department of Bioinformatics, Hazara University Mansehra, Mansehra 21120, Pakistan
| | - Ahmed Al-Amery
- Department of Physiology and Medical Physics, College of Medicine, University of Thi-Qar, Nasiriyah 64001, Iraq
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, 38280 Kayseri, Turkey;
| | - Iraj Ahmed
- Atta-Ur-Rehman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad 44000, Pakistan;
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Charbagh 19130, Pakistan;
| | - Imran Ahmad Khan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan;
| | - Dhurgham Al-Fahad
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Thi-Qar, Nasiriyah 64001, Iraq;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11421, Saudi Arabia
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Hago S, Lu T, Alzain AA, Abdelgadir AA, Yassin S, Ahmed EM, Xu H. Phytochemical constituents, in-vitro anticancer activity and computational studies of Cymbopogon schoenanthus. Nat Prod Res 2024; 38:1073-1079. [PMID: 37144384 DOI: 10.1080/14786419.2023.2208360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
The cytotoxic effects of Cymbopogon schoenanthus L. aerial part ethanol extract were examined against some cancer cell lines, and HUVEC normal cell lines using MTT assay. The ethanolic extract was prepared by ultrasonic-assisted extraction and analyzed by GC-MS and HPLC. The extract was found to be rich in terpene compounds. The extract proved to be highly selective and effective against breast and prostate cancer cell lines (MDA-MB-435, MCF-7, and DU 145) with IC50 as low as 0.7913 ± 0.14, 12.841 ± 0.21, and 30.51 ± 0.18 µg/ml, respectively. In silico modeling was performed to investigate the binding orientation and affinity of the major identified compounds against Polo-like kinase (PLK1 protein) a cancer molecular target using molecular docking and molecular dynamic whereas eudesm-5-en-11-ol, piperitone, and 2,3-dihydrobenzofuran displayed better binding affinity and stability against PLK1 compared to the reference drug. These findings encourage further in vivo studies to assess the anti-cancer effects of C. schoenanthus extract and its components.
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Affiliation(s)
- Salma Hago
- Department of Pharmacognosy, Faculty of Pharmacy, University of Gezira, Wad Madani, Gezira State, Sudan
| | - Tang Lu
- The Engineering Research Center of Peptide Drug Discovery and Development, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
| | - Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Gezira State, Sudan
| | - Abdelgadir A Abdelgadir
- Department of Pharmacognosy, Faculty of Pharmacy, University of Gezira, Wad Madani, Gezira State, Sudan
| | - Sitelbanat Yassin
- Department of Pharmaceutics, Faculty of Pharmacy, University of Gezira, Wad Madani, Gezira State, Sudan
| | - Elhadi M Ahmed
- Medicinal and Aromatic Plant Research Center, Faculty of Pharmacy, Gezira University, Wad Madani, Gezira State, Sudan
| | - Hanmei Xu
- The Engineering Research Center of Peptide Drug Discovery and Development, China Pharmaceutical University, Nanjing, Jiangsu, P.R. China
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Tayal S, Singh V, Bhatnagar S. 3D-QSAR and ADMET studies of morpholino-pyrimidine inhibitors of DprE1 from Mycobacterium tuberculosis. J Biomol Struct Dyn 2023:1-20. [PMID: 38112325 DOI: 10.1080/07391102.2023.2294496] [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: 07/18/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023]
Abstract
DprE1 is involved in the synthesis of Mycobacterium tuberculosis cell wall and is a potent drug target for Tuberculosis (TB) treatment. The structure and dynamics of the loops L-I and L-II flanking the inhibitor binding site was studied using molecular dynamics (MD) simulation and MMPBSA in Amber v18. Docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) of 55 Morpholino-pyrimidine (MP) inhibitors was carried out using Autodock v1.2.0 and Forge v10. ADMET analysis was done using SwissADME and pkCSM. All MP inhibitors docked in the DprE1 binding pocket, making contacts with L-II residues. MD studies showed that L-I and L-II unfold in the absence of the inhibitor but fold stably structure with reduced protein motions in the presence of MP-38, the highest affinity inhibitor. This was confirmed by k-means clustering and secondary structure analysis. L-II residues, L317, F320 and R325 contributed most towards the MMPBSA binding free energy of MP-38. A robust field-based 3D-QSAR model showed values of r2train = 0.982, r2test = 0.702 and q2 = 0.516. The MP inhibitor field points were broadly divided into negative electrostatics near the A, B rings and hydrophobic electrostatics near the D, E rings. Addition of negative groups at methanone position and ring B as well as addition of hydrophobic and bulky groups at ring E will improve activity. Highly active compounds 47, 49 and 50 of MP series exhibited highly favourable drug-like properties. SAR and ADMET insights attained from this model will help in the development of active DprE1 inhibitors in future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonali Tayal
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Vasundhara Singh
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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Lahyaoui M, El-Idrissi H, Saffaj T, Ihssane B, Saffaj N, Mamouni R, Kandri Rodi Y. QSAR modeling, molecular docking and Molecular Dynamic Simulation of phosphorus-substituted quinoline derivatives as topoisomerase I inhibitors. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
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