Mitochondrial permeability transition pore (MPTp) opening is a critical event in neurodegeneration, representing a point of no return in cell death cascades. Despite the neuroprotective potential of MPTp inhibitors, systematic structure–activity relationship (SAR) studies for this target remain scarce. Here we present the first standardized dataset of 57 γ-carboline derivatives evaluated for their ability to inhibit MPTp under uniform experimental conditions. Using complementary Free–Wilson and 2D-QSAR analyses, we expertly propose rational structure–activity relationships (SAR) for this scaffold. Based on the Free–Wilson analysis, we assume that increasing lipophilicity and steric bulk at all four substitution positions to a certain limit positively correlates with inhibitory activity. The R3 linker plays a critical role: the presence of positively ionizable amine groups and potentially hydrogen bond donors enhances activity, whereas non-ionizable amide linkers may be detrimental. The QSAR model based on physicochemical descriptors of substituents corroborates these findings, with positive contributions from cLogP and HBD descriptors. This integrated computational–experimental approach provides a predictive framework for the rational design of novel neuroprotective agents targeting MPTp, with potential implications for the treatment of neurodegenerative diseases.