In silico Identification of Novel SphK1 Inhibitors
Authors: Liu Jin , Zhao Hui-Lin , He Lei , Yu Ri-Lei , Kang Cong-Min 
Published: May 2023

Aims:

In silico Identification of Novel SphK1 Inhibitors.

Background:

A tumor is one of the major causes of death worldwide; the emergence of new targeted
drugs has changed the mode of tumor treatment and opened up the era of targeted therapy. Sphingosine
kinase 1 (SphK1) is a strictly conserved lipid checkpoint kinase, mainly located in the cytosol, and is
overexpressed and enhances the development and progression of various type of tumors, such as melanoma,
esophageal, gastric, and colon cancers. SphK1, consisting of 384 amino acid residues, has two
domains: C-terminal (CTD) and N-terminal (NTD). SphK1 phosphorylates sphingosine to generate
sphingosine-1-phosphate (S1P), which exists in high concentration in both the plasma and the lymph of
cancer patients. S1P has 5 receptors (S1PRs) and controls 5 signal pathways, Ras/Raf/MEK1/2,
PI3K/Akt, G-protein/PLC/PKC, Rho/Rock/NF-ĸB and PTEN; they are all related to cell growth, proliferation,
differentiation, apoptosis, migration, and stress fiber formation. The sphK1/S1P signal pathway
influences tumor cells' growth, proliferation, survival and angiogenesis, and SphK1 inhibitors can decrease
Treg cell recruitment at tumor location. In T cells, SphK1/S1P signal way activates NF-ĸB and
induces proliferator-activated receptor γ (PPARγ) transcription, which in turn regulates lipolysis in T
cells. SphK1 can induce T cell failure through excessive S1P in extracellular vesicles of the tumor microenvironment.
SphK1 inhibitors block S1P generation and inhibit cell growth, proliferation, differentiation,
apoptosis, migration, and stress fiber formation, leading to increased CD8+T cells and decreased Treg
cells in the tumor microenvironment. S1P also upregulates the expression of programmed cell death 1
ligand 1(PD-L1) through Early 2-factor transcription factor 1 (E2F1).

Objective:

The discovery of better Sphk1 inhibitors by pharmacophore model, ADMET, molecular docking,
MM/GBSA, and MD simulation.

Methods:

Here, SphK1 pharmacophore was created; first, it was used for virtual screening, ADMET
properties of screened-out molecules were predicted, and the obtained molecules were performed molecular
docking and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) calculation, then
molecular dynamics (MD) simulation was performed, and Molecular Mechanics Poisson-Boltzmann Surface
Area (MM/PBSA) were calculated.

Results:

Compounds 1, 2, and 3 were obtained through screening, and the binding energy of 1, 2, and 3
were better than that of the existing corresponding target inhibitors.

Conclusion:

The overexpression of Sphk1 is closely related to the occurrence, development, migration
and drug resistance of tumors and has a good prospect of drug development. Given the important role of
SphK1 inhibitors in treating tumors and the shortcomings of clinical application of SphK1 inhibitors,
small molecule targeting inhibition SphK1 was screened to overcome the low efficiency. Firstly, establishing
a pharmacophore model for virtual screening, and then ADMET prediction, sixty-seven molecules
were selected. And then, molecular docking and MM/GBSA calculation obtain three compounds with
lower Glide Score. In addition, they both have lower binding energy than PF-543. The docking result
shows that Asp167, Asp264, and Thr282 of SphK1 with ligand more easily form H-bonds interaction.
Next, in molecular dynamics simulation, compounds 1, 2, and 3 can stably bind with SphK1 and have a
high activity of inhibiting SphK1, with more research potential. In conclusion, compounds 1, 2, and 3
inhibit SphK1 laying a foundation for further compound synthesis and activity evaluation. Compounds 1,
2 and 3 can stably bind to the receptor protein, which is valuable for further experimental research.