Functional Modulation of Peptide Structural Interaction Fingerprints upon Stereochemical Diversification

The total conformational search space of an l-amino acid in a polypeptide chain is limited to 21% with structural variation including helices, sheets, turns, and random coils. The conformational search space of a polypeptide will expand to astronomical propositions if both l- and d-chiral amino acids are used to design novel polypeptide chains with altogether new structures and functions. This possibility has been systematically investigated in this study by making designed mutations that result in novel architectures. We hypothesize that the electrostatic interaction fingerprints of these peptides are distinctly different with stereochemical mutations of the polypeptide chain, and this will consequently reflect in their ability to interact and penetrate the membrane. The designed peptide structures are examined for their ability to interact with bacterial and mammalian cell membranes by employing molecular dynamics simulations. Mammalian triple-negative breast cancer (MDA-MB-231) and noncancerous (MCF-10A) cell lines were treated with 5(6)-carboxyfluorescein-labeled peptides, and the cellular uptake was measured quantitatively by flow cytometry for objective comparison of their ability to be used as anticancer or drug delivery agents. Antibacterial properties of the peptides were tested for Gram-positive <i>Staphylococcus aureus</i> (<i>S. aureus</i>) and Gram-negative <i><i>Escherichia coli</i></i> (<i><i>E. coli</i></i>) species. Both in silico and in vitro experimental results are largely supportive of the hypothesis tested, and they further point to the possibility of expanding the polypeptide conformational space in the search for novel functional molecular constructs. Our study also identified two promising therapeutic peptides for further development: YRC03 as a viable antibacterial agent against Gram-negative bacteria and YRC01 as a promising drug delivery vehicle for breast cancer treatment.