As mitochondria lack UPS and lysosomes, mitoTPD requires harnessing protein degradation machinery that is unique to mitochondria. Candidates include the following four ATP-dependent proteases: Lon, ClpXP (a complex of caseinolytic protease P (ClpP) and AAA+ATPase ClpX), the matrix-oriented AAA (m-AAA) protease, and the intermembrane space-oriented AAA (i-AAA) protease. ClpP is a serine protease resident in the matrix and is well conserved across species, being found in mitochondria, chloroplasts, and most bacteria. We hypothesized that mitoTPD could be achieved by using a chimeric small molecule consisting of a ClpP activator and a ligand of the target protein to bring the target protein into close proximity with activated ClpP (Figure ). Numerous activators of ClpP have already been reported and shown to degrade mitochondrial proteins non-specifically. We selected TR79, which has a primary amine in a pyrimidinedione scaffold, as a ClpP activator. Since this amino group has already been used to conjugate TR79 to agarose resin for ClpP pull-down, we thought that it would be suitable as a linker site for chimeric compound design. As a POI, we selected monomeric streptavidin (mSA) for the following two reasons: 1) biotin and desthiobiotin are well known and commercially available as mSA ligands with high affinity, and 2) mSA has a sufficiently small molecular weight (12 kDa) and has a track record as a fusion protein. We selected desthiobiotin as a ligand for mSA because it is thought to be bioorthogonal in mammals that lack avidin, as discussed later. Accordingly, we designed and synthesized compound 1, which connects TR79 and desthiobiotin via a tetraethylene glycol linker (Figure , Scheme S1, S2).