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Alsagaby SA, Iqbal D, Ahmad I, Patel H, Mir SA, Madkhali YA, Oyouni AAA, Hawsawi YM, Alhumaydhi FA, Alshehri B, Alturaiki W, Alanazi B, Mir MA, Al Abdulmonem W. In silico investigations identified Butyl Xanalterate to competently target CK2α (CSNK2A1) for therapy of chronic lymphocytic leukemia. Sci Rep 2022; 12:17648. [PMID: 36271116 PMCID: PMC9587039 DOI: 10.1038/s41598-022-21546-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/28/2022] [Indexed: 01/18/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is an incurable malignancy of B-cells. In this study, bioinformatics analyses were conducted to identify possible pathogenic roles of CK2α, which is a protein encoded by CSNK2A1, in the progression and aggressiveness of CLL. Furthermore, various computational tools were used to search for a competent inhibitor of CK2α from fungal metabolites that could be proposed for CLL therapy. In CLL patients, high-expression of CSNK2A1 was associated with early need for therapy (n = 130, p < 0.0001) and short overall survival (OS; n = 107, p = 0.005). Consistently, bioinformatics analyses showed CSNK2A1 to associate with/play roles in CLL proliferation and survival-dependent pathways. Furthermore, PPI network analysis identified interaction partners of CK2α (PPI enrichment p value = 1 × 10-16) that associated with early need for therapy (n = 130, p < 0.003) and have been known to heavily impact on the progression of CLL. These findings constructed a rational for targeting CK2α for CLL therapy. Consequently, computational analyses reported 35 fungal metabolites out of 5820 (filtered from 19,967 metabolites) to have lower binding energy (ΔG: - 10.9 to - 11.7 kcal/mol) and better binding affinity (Kd: 9.77 × 107 M-1 to 3.77 × 108 M-1) compared with the native ligand (ΔG: - 10.8, Kd: 8.3 × 107 M--1). Furthermore, molecular dynamics simulation study established that Butyl Xanalterate-CK2α complex continuously remained stable throughout the simulation time (100 ns). Moreover, Butyl Xanalterate interacted with most of the catalytic residues, where complex was stabilized by more than 65% hydrogen bond interactions, and a significant hydrophobic interaction with residue Phe113. Here, high-expression of CSNK2A1 was implicated in the progression and poor prognosis of CLL, making it a potential therapeutic target in the disease. Butyl Xanalterate showed stable and strong interactions with CK2α, thus we propose it as a competitive inhibitor of CK2α for CLL therapy.
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Affiliation(s)
- Suliman A. Alsagaby
- grid.449051.d0000 0004 0441 5633Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah, 11952 Kingdom of Saudi Arabia
| | - Danish Iqbal
- grid.449051.d0000 0004 0441 5633Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah, 11952 Kingdom of Saudi Arabia
| | - Iqrar Ahmad
- grid.412233.50000 0001 0641 8393Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 425405 India
| | - Harun Patel
- grid.412233.50000 0001 0641 8393Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra 425405 India
| | - Shabir Ahmad Mir
- grid.449051.d0000 0004 0441 5633Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah, 11952 Kingdom of Saudi Arabia
| | - Yahya Awaji Madkhali
- grid.449051.d0000 0004 0441 5633Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah, 11952 Kingdom of Saudi Arabia
| | - Atif Abdulwahab A. Oyouni
- grid.440760.10000 0004 0419 5685Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia ,grid.440760.10000 0004 0419 5685Genome and Biotechnology Unit, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia
| | - Yousef M. Hawsawi
- grid.415310.20000 0001 2191 4301Research Center, King Faisal Specialist Hospital and Research Center, P.O. Box 40047, Jeddah, 21499 Kingdom of Saudi Arabia ,grid.411335.10000 0004 1758 7207College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh, 11533 Kingdom of Saudi Arabia
| | - Fahad A. Alhumaydhi
- grid.412602.30000 0000 9421 8094Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Kingdom of Saudi Arabia
| | - Bader Alshehri
- grid.449051.d0000 0004 0441 5633Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah, 11952 Kingdom of Saudi Arabia
| | - Wael Alturaiki
- grid.449051.d0000 0004 0441 5633Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah, 11952 Kingdom of Saudi Arabia
| | - Bader Alanazi
- grid.415277.20000 0004 0593 1832Biomedical Research Administration, Research Center, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia ,Prince Mohammed bin Abdulaziz Medical City, AlJouf, Kingdom of Saudi Arabia
| | - Manzoor Ahmad Mir
- grid.412997.00000 0001 2294 5433Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Waleed Al Abdulmonem
- grid.412602.30000 0000 9421 8094Department of Pathology, College of Medicine, Qassim University, Qassim, Kingdom of Saudi Arabia
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