SUMMARYAmphotericin B is a powerful but toxic antifungal antibiotic that is used to treat systemic infections. It forms ionic membrane channels in fungal cells. These antibiotic/sterol channels are responsible for the leakage of ions, which causes cell destruction. The detailed molecular properties and structure of amphotericin B channels are still unknown. In the current study, two molecular dynamic simulations were performed of a particular model of amphotericin B/cholesterol channel. The water and phospholipid environment were included in our simulations, and the results obtained were compared with available experimental data. It was found that it is mainly the hydrogen bonding interactions that keep the channel stable in its open form. Our study also revealed the important role of the intermolecular interactions among the hydroxyl, amino, and carboxyl groups of the channel-forming molecules; in particular, some hydroxyl groups stand out as new "hot spots" that are potentially useful for chemotherapeutic investigations. Our results also help to clarify why certain antibiotic derivatives, with a blocked amino group, are less active. We present a hypothesis for the role of membrane lipids and cholesterol in the channel.AmB is a polyene macrolide antibiotic that is widely used in the treatment of systemic fungal infections (1) (Fig. 1, top). Despite its long clinical history, the molecular antifungal action of AmB is not well understood (2, 3). According to the most widely accepted mechanism, AmB molecules interact with membrane sterols to form channels (2-5). The channels are responsible for the leakage of monovalent ions, particularly K ϩ , and other small molecules from the cell. The resulting irregular ionic distribution eventually causes cell death. The chemotherapeutic use of AmB is based on the higher affinity of this antibiotic for ergosterol (principal sterol in fungal cells) than for cholesterol (sterol in mammalian cells) (6). Because it also has high affinity for cholesterol-containing membranes, AmB is quite toxic, and its use in clinical treatment is limited to rather severe cases.To reduce the toxic features of this powerful drug, its antifungal chemotherapeutic properties should be elucidated more precisely. Many experimental efforts (3, 7) designed to achieve a comprehensive understanding of the membranous AmB/sterol channels have shown that these channels are difficult to study; thus, there is little information available for the molecular level, and the channel structure remains unknown. In addition to experiments, in several recent theoretical studies (8 -14), the focus has been on the isolated molecular properties of AmB or sterols (8 -12). In some of these studies, the channel structure was also considered (13-15); however, only simple molecular mechanics or electrostatic calculations without proper treatment of the membrane/water environment were used. Ultimately, experimental efforts together with molecular modeling approaches should lead to a more complete understanding of the molecular ...