Doxycycline, a semi-synthetic tetracycline, is a widely used antibiotic for mild-to-moderate infections. However, its pleiotropic effects, such as anti-inflammatory and antioxidant properties, combined with its ability to interfere with α-synuclein inhibiting its aggregation, make it an attractive candidate for repositioning in Parkinson's disease treatment. Nevertheless, the antibiotic activity of doxycycline restricts its potential for long-term treatment of Parkinsonian patients. Eighteen novel doxycycline derivatives were designed with substitution at C9. Specifically, the dimethyl-amino group at C4 was reduced to significantly diminish the antibiotic activity, and several coupling reactions were performed at position C9 of the D ring. Using biophysical models, we found that seven compounds were more effective than the parent compound in inhibiting α-synuclein aggregation. Furthermore, two of these derivatives exhibited better anti-inflammatory effects at non-cytotoxic concentrations on microglial cell culture. Thus, we identified two design-based tetracyclines as the most promising candidates for further preclinical investigations. In addition, our study provides new insights into the structure-activity relationship of tetracyclines as neuroprotective molecules.