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Abd Emoniem N, Mukhtar RM, Ghaboosh H, Elshamly EM, Mohamed MA, Elsaman T, Alzain AA. Turning down PI3K/AKT/mTOR signalling pathway by natural products: an in silico multi-target approach. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023; 34:163-182. [PMID: 36853097 DOI: 10.1080/1062936x.2023.2181392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The PI3K/AKT/mTOR pathway is a significant target for cancer drug discovery. Many efforts have focused on discovering new inhibitors against key kinase proteins involved in this pathway for cancer treatment. PI3K/mTOR dual inhibitors, such as PKI-179, have been reported to be more effective than agents that act only on a single protein target. The present computational study aimed to discover triple target inhibitors against PI3K, AKT, and mTOR proteins. Accordingly, the PI3K protein bound with the ligand was used as input for e-pharmacophore modelling to generate the pharmacophore hypothesis and then screened for a library of 270,540 natural products from the Zinc database resulting in 57,220 compounds that matched the hypothesis. These compounds were then docked into the active site of PI3K, resulting in 292 compounds with better docking scores than the co-crystallized ligand. These compounds were re-docked into AKT and mTOR proteins. Besides, MM-GBSA binding free energy calculations, MD simulations, and ADMET prediction were carried out, leading to 5 potential triple-target inhibitors namely, ZINC000014644152, ZINC000014760695, ZINC000014644839, ZINC000095099451, and ZINC000005998557. In conclusion, these inhibitors may be possible leads for inhibiting PI3K/AKT/mTOR pathway, and they may be further evaluated in vitro and clinically as anticancer agents.
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Affiliation(s)
- N Abd Emoniem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - R M Mukhtar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - H Ghaboosh
- Department of Pharmaceutics, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - E M Elshamly
- Department of Molecular Biotechnology, Hochschule Anhalt, Köthen, Germany
| | - M A Mohamed
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - T Elsaman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - A A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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Li Y, Zhang Y, Wu X, Gao Y, Guo J, Tian Y, Lin Z, Wang X. Discovery of natural 15-LOX small molecule inhibitors from Chinese herbal medicine using virtual Screening, biological evaluation and molecular dynamics studies. Bioorg Chem 2021; 115:105197. [PMID: 34426159 DOI: 10.1016/j.bioorg.2021.105197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 11/19/2022]
Abstract
Chinese herbal medicines (CHM) are frequently used to treat different types of inflammatory diseases and 15-Lipoxygenase (15-LOX) is a critical target enzyme for treating various inflammatory diseases. In this study, natural 15-LOX inhibitors were identified in CHM using an approach of virtual screening combined with the biological assays. First, an in-house Chinese medicine database containing 360 compounds was screened using a virtual screening approach based on pharmacophore and molecular docking to uncover several novel potential 15-LOX inhibitors. Secondly, the inhibitory effect of virtual screening hits against the 15-LOX enzyme was validated in an in vitro enzyme inhibition assay. Then, a tumor necrosis factor-α (TNF-α) release assay was carried out to explore the anti-inflammatory response of the active compounds. Furthermore, molecular dynamics (MD) simulation and binding free energy calculation were applied to analyze the process of inhibitors binding and also compared the mode of binding of the inhibitors by using the Molecular Mechanics-Generalized Born Surface Area (MM/GBSA) method. Finally, licochalcone B and eriodictyol were confirmed as inhibitors of the 15-LOX enzyme with IC50 values of 9.67 and 18.99 μM, respectively. In vitro cell-based assay showed that licochalcone B and eriodictyol inhibited the release of TNF-α factor in RAW264.7 cells stimulated by lipopolysaccharides (LPS) in a dose-dependent manner. Molecular dynamics and binding free energy analysis showed that the two 15-LOX-ligand systems immediately attained equilibrium with almost 1 Å fluctuation, the calculated binding free energies were found around -18.89 and -12.96 kcal/mol for licochalcone B and eriodictyol, respectively. Thr412, Arg415, Val420, Thr429, Ile602 and Trp606 were the main amino acid residues for the inhibition of 15-LOX enzyme activity. The current study confirms that licochalcone B and eriodictyol are 15-LOX inhibitors and can suppress the release of the TNF-α factor in RAW264.7 cells stimulated by LPS, thus providing a basis for the follow-up research and development for 15-LOX inhibitors.
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Affiliation(s)
- Yatong Li
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yuxin Zhang
- Key Laboratory of Ethnomedicine, School of Pharmacy, Ministry of Education, Minzu University of China, Haidian District, Beijing 100081, China
| | - Xia Wu
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yanbin Gao
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Junfang Guo
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yulang Tian
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Ziyue Lin
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Xing Wang
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China.
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