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Mesoporous silica nanoparticles (MSNs) are of significant interest as vehicles for different drugs. The main route to their producing is a gelsol synthesis using “inert” surfactant micelles as a template. After the synthesis is completed, a micellar template is removed, while the obtained MSNs are loaded with a targeted substance. This route results in low drug uptake and its burst release that are insufficient for the most applications. We propose a new approach that overcomes these drawbacks. This approach is based on the use of targeted drug itself (instead of inert surfactant ones) as templating agent at MSNs synthesis. As a result, it becomes possible to combine the stages of silica nanocontainers synthesis and their loading with the targeted drug. The prospects and benefits of the approach are exemplified by the encapsulation of surface active bactericidal drug benzyldimethyl[3-(miristoilamino)propyl]ammonium chloride, known under the trade name of Myramistin. It is shown that the synthesized mesoporous nanocontainers are characterized by an extremely high drug content (about 1 g and over per 1 g of SiO2) and are also pH-sensitive. The release of the encapsulated drug from the silica nanocontainers is studied and some features of this process are discussed. The bactericidal activity of encapsulated Myramistin against the Staphylococcus aureus is evaluated. Moreover, it is shown that it is possible to create the so-called protocells by self-assembly of lipid bilayers on the surface of nanocontainers in which the drug is loaded.