Rational search of a ligand for a specific receptor is a cornerstone of a typical drug discovery process. However, to make it more “rational” one would appreciate having detailed information on the functional groups involved in ligand-receptor interaction. Typically, the 3D structure of a ligand-receptor complex can be built on the basis of time-consuming X-ray crystallography data. Here, a combination of FTIR and fluorescence methods, together with appropriate processing, yields valuable information about the functional groups of both the ligand and receptor involved in the interaction, with the simplicity of conventional spectrophotometry. We have synthesized the “molecular containers” based on cyclodextrins, polyethyleneimines (PEI) or spermine with mannose-rich side-chains of different molecular architecture (reticulated, star-shaped and branched) with variable parameters to facilitate delivery to alveolar macrophages. We have shown that synthetic mannose-rich conjugates are highly affine to the model mannose receptor ConA: Kd ≈ 10−5–10−7 M vs. natural ligand trimannoside (10−5 M). Further, it was shown that molecular containers effectively load levofloxacin (dissociation constants are 5·10−4–5·10−6 M) and the eugenol adjuvant (up to 15–80 drug molecules for each conjugate molecule) by including them in the cyclodextrins cavities, as well as by interacting with polymer chains. Promising formulations of levofloxacin and its enhancer (eugenol) in star-shaped and polymer conjugates of high capacity were obtained. UV spectroscopy demonstrated a doubling of the release time of levofloxacin into the external solution from the complexes with conjugates, and the effective action time (time of 80% release) was increased from 0.5 to 20–70 h. The synergy effect of antibacterial activity of levofloxacin and its adjuvants eugenol and apiol on Escherichia coli was demonstrated: the minimum effective concentration of the antibiotic was approximately halved.