Ionic liquid MIE-NH2 displays a new role in the development of modification of glycoproteins of lactoferrin through a reductive amination mechanism to synthesize versatile pharmaceuticals. This work introduces a new strategy of modification of lactoferrin by using methyl imidazolium N-ethylamine MIE-NH2, this ionic liquid linked to N-glycans in lactoferrin derivatives in simple method. The modification of lactoferrin with MIE-NH2 as a novel small molecule (SM-IL-Lf) contains active amino groups is confirmed by UPLC/ESI-QTOF and MALDI-TOF mass spectrometry. Molecular docking disclosed the bioactivity of modifying glycoproteins - small IL-Lf-molecules by elucidating its interactions with the inspected targets. This providing of small molecules IL-Lf released a wide display with different functions as significantly important drug candidates inhibiting the targets of main protease (Mpro), RNA dependent RNA polymerase (RdRp), transmembrane protease serine 2 (TMPRSS2), and Papain-like protease (PLpro). The probability of the modeling N-glycans from lactoferrin modified and designed as small IL-Lf-molecules to inhibit any of these targets was investigated to find out its potency inhibitor of SARS-CoV-2.