Sphingosine kinase 1 (SphK1) is an
oncogenic lipid kinase that
catalyzes the formation of sphingosine-1-phosphate via phosphorylation
of sphingosine and known to play a crucial role in angiogenesis, lymphocyte
trafficking, signal transduction pathways, and response to apoptotic
stimuli. SphK1 has received attention because of its involvement in
varying types of cancer and inflammatory diseases such as rheumatoid
arthritis, diabetes, renal fibrosis, pulmonary fibrosis, asthma, and
neurodegenerative disorders. In the malignancies of breast, lung,
uterus, ovary, kidney, and leukemia, overexpression of SphK1 has been
reported and thus considered as a potential drug target. In this study,
we have performed virtual high-throughput screening of ∼90,000
natural products from the ZINC database to find potential SphK1-inhibitors.
Initially, the hits were selected by applying absorption, distribution,
metabolism, excretion, and toxicity properties, Lipinski’s
rule, and PAINS filters. Further, docking analysis was performed to
estimate the binding affinities and specificity to find safe and effective
preclinical leads against SphK1. Two compounds, ZINC05434006 and ZINC04260971,
bearing appreciable binding affinity and SphK1 selectivity were selected
for 100 ns molecular dynamics (MD) simulations under explicit water
conditions. The all-atom MD simulation results suggested that the
ZINC05434006 and ZINC04260971 binding induces a slight structural
change and stabilizes the SphK1 structure. In conclusion, we propose
natural compounds, ZINC05434006 and ZINC04260971, as potential inhibitors
of SphK1, which may be further exploited as potential leads to develop
effective therapeutics against SphK1-associated diseases including
cancer after in vitro and in vivo validations.