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Abstract Background Cysteamine is the only disease-modifying therapy for nephropathic cystinosis and has shown promise in mitochondrial disorders, but its clinical utility is limited by poor tolerability due to high peak concentrations with existing formulations. TTI-0102 is a novel natural controlled-release cysteamine prodrug designed to provide sustained cysteamine exposure with improved tolerability. Methods A multi-center, randomized, single-blind, placebo-controlled Phase 2 trial enrolled 9 patients with MELAS syndrome caused by mtDNA m.3243A>G mutation (>50% heteroplasmy) and moderate disease severity (NMDAS score 15-45). Patients received placebo (n=3) or TTI-0102 at 2.75 g/day for one week then 5.5 g/day (n=6, equivalent to 2.5 g/day cysteamine base). Pharmacokinetic parameters, safety, and pharmacodynamic biomarkers including pyruvate, taurine, pantothenic acid, tryptophan, GSH/GSSG, lactate, GDF-15, and FGF-21 were assessed. Clinical efficacy was evaluated using the Modified Fatigue Impact Scale (MFIS) and 12-minute walk test. Results TTI-0102 demonstrated expected gastrointestinal side effects (nausea, vomiting, diarrhea) consistent with the cysteamine class, with dropout occurring in patients 50 kg receiving fixed 5.5 g/day dosing. Weight-based dosing at 60 ± 5 mg/kg TTI-0102 (~26 mg/kg cysteamine base equivalent) achieved sustained 24-hour cysteamine exposure with half the daily dose and peak concentrations lower than expected by dose proportionality, compared to approved formulations (Procysbi ® : 56 mg/kg, peak 2.5 mg/L vs. TTI-0102: 26 mg/kg, peak ~2 mg/L). TTI-0102 significantly elevated pantothenic acid (plateauing at 2 weeks) and taurine levels, providing mitochondrial cofactor support and antioxidant effects. Statistically significant pharmacodynamic effects included increased plasma pyruvate (p=0.03) without lactate elevation, suggesting enhanced glycolytic flux, and decreased tryptophan (p<0.01), potentially reducing oxidative stress from neurotoxic kynurenine pathway metabolites. Interestingly, increase in plasma pyruvate and decrease in tryptophan were negligible at doses up to 40 mg/kg/day, optimal at 60 mg/kg/day, and slightly less at 65 mg/kg/day. GSH/GSSG measurements were confounded by sample stability issues. GDF-15, FGF-21, and 12-minute walk distance showed no treatment-related changes. Most notably, MFIS total scores demonstrated significant improvement in TTI-0102-treated patients at 60 mg/kg/day average dose compared to placebo (p=0.04). Polynomial regression revealed therapeutic onset at ~4 weeks, maximal benefit at ~12 weeks, and subsequent plateau. Conclusions This Phase 2 trial provides proof-of-concept that TTI-0102 is safe and well-tolerated in MELAS patients while treated with less than 65 mg/kg/day, with efficacy signals in fatigue reduction, a cardinal symptom affecting 71-100% of mitochondrial disease patients. The drug’s tri-faceted mechanism through sustained cysteamine, taurine, and pantothenic acid delivery addresses oxidative stress, mitochondrial energy metabolism, and cofactor deficiency. Significant MFIS improvement coupled with favorable modulation of pyruvate and tryptophan supports advancing TTI-0102 to larger Phase 2b/3 trials in mitochondrial disease employing weight-based dosing (60 ± 5 mg/kg), validated patient-reported outcomes, and minimum 12-week treatment duration. The same mechanism of cysteamine/cystine thiol-disulfide exchange in lysosomes that may benefit mitochondrial diseases also supports cystinosis treatment. An investigator-initiated study in cystinosis will evaluate whether once-daily TTI-0102 at 60 ± 5 mg/kg can maintain therapeutic WBC cystine levels, potentially offering improved adherence and quality of life compared to current twice-daily or four-times-daily regimens, and this weight-adjusted dosing strategy and pharmacodynamic biomarkers identified in the MELAS study are going to be used to inform the design of the planned Phase 2 study in Leigh syndrome, another mitochondrial disorder, in collaboration with the Children’s Hospital of Philadelphia (CHOP), with particular attention to dose optimization and biomarker-based assessment of pharmacological activity.