Shikonin is a major naphthoquinone compound found in the roots of Lithospermum erythrorhizon and exhibits powerful anticancer activities for various cancer cells. Shikonin and its derivatives are characterized by a wide spectrum of antibacterial activities: high antibacterial activity towards Gram-positive bacteria (Staphylococcus aureus et al.), a stable fungicidal effect towards Candida and Trichosporon fungi. Shikonin normalizes the production of the key mediators of inflammation IL-1 and IL-2, IFN-γ, reduces vascular permeability in the focus of inflammation, exhibiting a marked anti-inflammatory effect. Combined therapy with applications of a bio-polymeric film with shikonin and its esters (naphthoquinone derivatives) led to an obvious improvement of the clinical parameters and reduced the morphological signs of the buccal mucosal lesions. The drug was well tolerated by all patients and no side effects were recorded. Shikonin, as a naturally occurring, low-molecular-weight pan-chemokine receptor inhibitor, constitutes a basis for the development of novel anti-HIV therapeutic agents.