The Water-Soluble [60]Fullerene Derivatives as Binders of SARS-CoV‑2 Proteins

Water-soluble fullerene derivatives represent emerging molecular nanomaterials for antiviral drug discovery, yet their target selectivity against SARS-CoV-2 proteins remains insufficiently defined. Here, four functionalized [60]-fullerenes, C₆₀(OH)₂₄, C₆₀ser, C₆₀ALA, and C₆₀Trp, were evaluated as binders of key SARS-CoV-2 targets involved in viral entry and replication: spike glycoprotein, papain-like protease, 3CL main protease, and RNA-dependent RNA polymerase. Microscale thermophoresis revealed distinct target-dependent binding profiles governed by fullerene functionalization. The C₆₀Trp fullerene was the most active derivative, binding Spike with nanomolar affinity (K_d = 94.8 nM) and showing micromolar affinity toward papain-like protease and 3CL main protease. Docking and molecular dynamics simulations supported the preferential interaction of C₆₀Trp with the spike protein cavity through combined fullerene cage complementarity and polar interactions with lysine and arginine residues. The tested derivatives showed low cytotoxicity in A549 cells, and C₆₀Trp was efficiently internalized. These findings identify tryptophan-functionalized [60]-fullerene as a promising multivalent scaffold for SARS-CoV-2 protein targeting.