Virtual Screening, Molecular Docking, and Molecular Dynamics Simulation Studies on Potential Phytochemicals as Sphingosine Kinase 1 Inhibitors for Cancer Therapy

Sphingosine kinases (SphKs) as lipid kinases catalyze the phosphorylation of sphingosine (Sph) to sphingosine-1-phosphate (S1P). Targeting the S1P signaling pathway is a significant strategy for many human diseases. Herein, we evaluated main prenylated bioactive components of a medicinal plant and performed a virtual screening study with flavonoid compounds and then, molecular docking and molecular dynamics (MD) simulation for the targeted cancer therapy. In silico ADMET and drug-likeness results were determined by BIOVIA Discovery Studio (DS). Molecular docking and molecular dynamics (MD) simulations were carried out by using Glide/SP and Desmond of Maestro with the filtered ligands. Glide/SP docking results showed higher binding affinity with xanthohumol (XN), 8-prenylnaringenin (8-PN), and neobavaisoflavone against SphK1. Three hits displayed strong hydrogen binding between the specific amino acid residues of targeting SphK1. There were no significant structural changes between SphK1-XN and SphK1-neobavaisoflavone complexes during 200 ns MD simulation analysis performed by GROMACS. Root-mean square deviation (RMSD) average values of XN- and neobavaisoflavone-protein complexes were compared to free SphK1 and were found as 0.2626 nm, 0.2589 nm, and 0.2508 nm, respectively. As a result, XN and 8-PN, and neobavaisoflavone have been determined as potential inhibitor candidates of SphK1 to examine for further in vitro and in vivo studies.