Integrative Network Pharmacology and Virtual Screening Reveal Amentoflavone from Selaginella bryopteris as a Potent HIV-2 Integrase Inhibitor

Abstract

Despite its medicinal properties, the molecular regulatory mechanisms and antiviral activity of Selaginella bryopteris are not well understood. The phytoconstituents (PCs) of S. bryopteris were analyzed using the Drug-Induced Gene Expression Profile Predictor (DIGEP-Pred) for gene expression profiling, WebGestalt and Cytoscape for pathway enrichment, and AntiVir-Pred for antiviral screening in this study. Analyzing 947 target proteins, myo-inositol and amentoflavone were identified as the main regulators, which were found to be significantly enriched in estrogen signaling and cancer pathways by important nodes calmodulin 1 (CALM1), guanine nucleotide-binding protein G(i) subunit alpha-1 (GNAI1), Kras proto-oncogene, GTPase (KRAS), nuclear receptor coactivator 1 (NCOA1), and SP1 transcription factor (SP1) in the network pharmacology. These compounds were screened for antiviral activity using antiviral tools and were found to be highly active against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicase, dengue virus type 2 polyprotein (6KR3), and human immunodeficiency virus (HIV)‑2 integrase (3F9K). Initial docking revealed high affinities between myo-inositol (–5.8 kcal mol-1) and amentoflavone (–11.0 and –11.1 kcal mol-1), while the 100 ns molecular dynamics simulations (MDS) and molecular mechanics Poisson-Boltzmann surface area (MMPBSA) results showed that only the 3F9K-amentoflavone complex exhibited low root mean square deviation (RMSD, 0.8-1.2 nm), a small radius of gyration, and a tendency to form hydrogen bonds. In conclusion, amentoflavone and myo-inositol possess strong gene-modulatory and antiviral activities, and amentoflavone can be considered a lead compound for the developing of antiviral therapeutic agents, with a specific focus on HIV-2 integrase.