Hydrophobicity modulated antibacterial small molecule eradicates biofilm with potent efficacy against skin-infections

The role of molecular arrangement of hydrophobic and hydrophilic groups for designing membrane-active molecules remains largely ambiguous. To explore this aspect, herein we report a series of membrane-active small molecules by varying the spatial distribution of hydrophobic groups. The two terminal amino groups of linear triamines such as diethylene triamine, bis(trimethylene)triamine and bis(hexamethylene)triamine were conjugated with cationic amino acids bearing variable side chain hydrophobicity (such as diaminobutyric acid, ornithine and lysine). The hydrophobicity was also modulated through conjugation of different long chain fatty acids with the central secondary amino group of the triamine. Molecules with constant backbone hydrophobicity displayed an enhanced antibacterial activity and decreased hemolytic activity upon increasing the side chain hydrophobicity of amino acids. On the other hand, increased hydrophobicity in the backbone introduced a slight hemolytic activity but a higher increment in antibacterial activity resulting in better selective antibacterial compounds. The optimized lead compound derived from structure-activity-relationship (SAR) studies was the dodecanoyl analogue of lysine series of compounds consisting of bis(hexamethylene)triamine as the backbone. This compound was active against various Gram-positive and Gram-negative bacteria at a low concentration (MIC ranged between 3.1-6.3 µg/mL) and displayed low toxicity towards mammalian cells (HC50 = 890 µg/mL and EC50 against HEK = 85 µg/mL). Additionally, it was able to kill metabolically inactive bacterial cells and eradicate preformed biofilms of MRSA. This compound showed excellent activity in a mouse model of skin-infection with reduction of ~4 log MRSA burden at 40 mg/kg dose without any sign of skin-toxicity even at 200 mg/kg. More importantly, it revealed potent efficacy in an ex-vivo model of human skin-infection (with reduction of 85% MRSA burden at 50 μg/mL), which indicates great potential of the compound as an antibacterial agent to treat skin-infections.