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Open AccessArticle

Virtual Screening Approach to Identify High-Affinity Inhibitors of Serum and Glucocorticoid-Regulated Kinase 1 among Bioactive Natural Products: Combined Molecular Docking and Simulation Studies

1
Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
2
Department of Biotechnology, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
3
Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Alejandro Speck-Planche
Molecules 2020, 25(4), 823; https://doi.org/10.3390/molecules25040823 (registering DOI)
Received: 17 January 2020 / Revised: 6 February 2020 / Accepted: 10 February 2020 / Published: 13 February 2020
Serum and glucocorticoid-regulated kinase 1 (SGK1) is a serine/threonine kinase that works under acute transcriptional control by several stimuli, including serum and glucocorticoids. It plays a significant role in the cancer progression and metastasis, as it regulates inflammation, apoptosis, hormone release, neuro-excitability, and cell proliferation. SGK1 has recently been considered as a potential drug target for cancer, diabetes, and neurodegenerative diseases. In the present study, we have performed structure-based virtual high-throughput screening of natural compounds from the ZINC database to find potential inhibitors of SGK1. Initially, hits were selected based on their physicochemical, absorption, distribution, metabolism, excretion, and toxicity (ADMET), and other drug-like properties. Afterwards, PAINS filter, binding affinities estimation, and interaction analysis were performed to find safe and effective hits. We found four compounds bearing appreciable binding affinity and specificity towards the binding pocket of SGK1. The docking results were complemented by all-atom molecular dynamics simulation for 100ns, followed by MM/PBSA, and principal component analysis to investigate the conformational changes, stability, and interaction mechanism of SGK1 in-complex with the selected compound ZINC00319000. Molecular dynamics simulation results suggested that the binding of ZINC00319000 stabilizes the SGK1 structure, and it leads to fewer conformational changes. In conclusion, the identified compound ZINC00319000 might be further exploited as a scaffold to develop promising inhibitors of SGK1 for the therapeutic management of associated diseases, including cancer.
Keywords: serum and glucocorticoid-regulated kinase 1; virtual screening; molecular docking; MD simulation; natural products; MM/PBSA serum and glucocorticoid-regulated kinase 1; virtual screening; molecular docking; MD simulation; natural products; MM/PBSA
MDPI and ACS Style

Mohammad, T.; Siddiqui, S.; Shamsi, A.; Alajmi, M.F.; Hussain, A.; Islam, A.; Ahmad, F.; Hassan, M.I. Virtual Screening Approach to Identify High-Affinity Inhibitors of Serum and Glucocorticoid-Regulated Kinase 1 among Bioactive Natural Products: Combined Molecular Docking and Simulation Studies. Molecules 2020, 25, 823.

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