The selective detection of amino acid enantiomers can be achieved by considering chiral nanotubes used in a resonator configuration. We show that this enantioselectivity is appreciably increased when a peptide molecule is inserted in the tube. The chiral polarization of the nanotube at the linear and nonlinear levels due to the inserted polar peptide is very sensitive to the adsorption of left- or right-handed alanine molecules. This leads to a difference in the resonance frequency of the sensor which can increase to 12 MHz when the nanotube is not chiral (instead of 0 for the bare tube) and can reach 38 MHz for a chiral tube (instead of 14 MHz for the bare tube). The influence of the various parameters which are responsible for such a differential frequency shift, i.e., the tube hyperpolarizability, the polar electric properties of the peptide, and the screening effect due to the tube on the peptide-alanine interactions, is discussed and some general rules are given regarding the optimization of the enantioselectivity of these sensors.