Mechanism — how MOTS-c and SS-31 differ
MOTS-c is a 16-amino-acid mitochondrial-derived peptide encoded within the 12S rRNA region of the mitochondrial genome. In research models it has been characterised as a signalling peptide that influences nuclear gene expression and metabolic homeostasis, particularly through AMPK-axis activation.
SS-31 (elamipretide) is a synthetic four-amino-acid peptide (D-Arg-2',6'-dimethylTyr-Lys-Phe-NH2) that localises selectively to the inner mitochondrial membrane and binds to cardiolipin. The cardiolipin interaction is the proposed mechanism for its mitochondrial-protective effects in published research.
Receptor profile
MOTS-c does not act through a single canonical receptor in the conventional sense — its proposed mechanism centres on intracellular AMPK-axis activation and downstream effects on nuclear metabolic gene expression.
SS-31 does not act through a cell-surface receptor either; its proposed mechanism is the direct interaction with cardiolipin at the inner mitochondrial membrane, stabilising mitochondrial cristae structure and preserving electron-transport-chain function in research models.
Pharmacokinetics and half-life
MOTS-c is a 16-residue peptide with a short native half-life; research protocols typically use daily or sub-daily cadences with bacteriostatic-water reconstitution and refrigerated in-use storage.
SS-31 is a small tetrapeptide with sub-cellular targeting and a similarly short native half-life. Research cadences are typically daily; the small molecular size simplifies penetration in cell-culture models compared with larger peptides.
Research applications
MOTS-c is widely used in metabolic, exercise-physiology, insulin-sensitivity and longevity research models. The AMPK-axis activation profile makes it a common comparator against other metabolic-axis research compounds.
SS-31 is the leading research compound for mitochondrial-membrane and cardiolipin-interaction studies. It is widely used in ischaemia-reperfusion, neurodegeneration and mitochondrial-dysfunction research models where preserving electron-transport-chain function is the experimental endpoint.
Analytical specification on every Regena batch
Both MOTS-c and SS-31 ship from Regena only after independent third-party verification — Janoshik Analytical is the default verifier, with orthogonal independent laboratories used when batch chemistry calls for confirmation by a second method. Minimum release specification is ≥99.0% HPLC main-peak purity with matching mass-spectrometry molecular weight and water content within the published specification for the compound.
Batch COAs for both compounds are published on the Regena lab reports page so a research-peptide buyer can audit the analytical detail before purchase. The /trust/how-to-read-a-coa reference walks through every field on a modern Regena COA.
Handling, reconstitution and stability
Both compounds ship lyophilised under nitrogen. Hold the unopened vial at 2–8 °C; freeze at −20 °C for long-term storage. Reconstitution with bacteriostatic water (0.9% benzyl alcohol) supports a 28-day in-use stability window under refrigeration. SS-31 is particularly sensitive to repeat freeze-thaw cycling — aliquot before any freeze.
Aliquot before any freeze. The single most common cause of measurable potency loss in research peptides is repeat freeze-thaw cycling — both MOTS-c and SS-31 benefit from single-thaw aliquot workflows. Vortex gently, never shake aggressively, and keep reconstituted vials away from direct light. The /research/compound-storage-guide reference covers the per-compound stability windows in detail.
When researchers choose MOTS-c vs SS-31
Researchers choose MOTS-c when the protocol targets metabolic, exercise-physiology or AMPK-axis signalling outcomes. Researchers choose SS-31 when the protocol targets the inner mitochondrial membrane directly — cardiolipin interaction, electron-transport-chain preservation, ischaemia-reperfusion models — and when a small-molecule pharmacokinetic profile is preferred over a longer signalling peptide.
For multi-compound comparator studies, the Regena consultations team will reserve matched-batch inventory of both MOTS-c and SS-31 against a project timeline so the experimental panel is sourced under a single analytical specification window.
Regulatory and research-use framing
Both MOTS-c and SS-31 are supplied strictly for in-vitro and preclinical research use. They are not medicines, are not approved for human consumption in Spain, the United Kingdom, the European Union or the United States, and are not dispensed against a prescription. The research-use declaration ships with every package alongside the independent third-party COA.
Comparison pages on the Regena site exist for laboratory-research reference. Nothing on this page constitutes a recommendation for human use of either compound.
Frequently asked questions
What is the main difference between MOTS-c and SS-31?+
MOTS-c is a 16-amino-acid mitochondrial-derived peptide encoded within the 12S rRNA region of the mitochondrial genome.
Which has the longer half-life, MOTS-c or SS-31?+
MOTS-c is a 16-residue peptide with a short native half-life; research protocols typically use daily or sub-daily cadences with bacteriostatic-water reconstitution and refrigerated in-use storage.
Are MOTS-c and SS-31 the same compound class?+
Both sit in the mitochondrial-targeted peptides category but with distinct receptor profiles and pharmacokinetics — see the receptor-profile section above for the side-by-side detail.
What HPLC purity does Regena release each compound against?+
≥99.0% HPLC main-peak purity for both MOTS-c and SS-31, with matching mass-spectrometry molecular weight and water content within the published specification for each compound.
Who independently verifies the batches?+
Janoshik Analytical is the default independent verifier for both compounds; orthogonal independent laboratories are used when batch chemistry calls for second-method confirmation.
Can I order matched batches for a comparator study?+
Yes — the Regena consultations team will reserve matched-batch inventory of both compounds against a project timeline so the experimental panel is sourced under a single analytical specification window.
Are these peptides approved for human use?+
No. Both are supplied strictly for in-vitro and preclinical research use. They are not medicines, are not approved for human consumption, and are not dispensed against a prescription.
Where can I see the current batch COAs for both compounds?+
On the /coa lab reports page, indexed by compound and batch number. New batches appear within 24 hours of independent release.
Recommended next — keep comparing
Hand-picked links our research customers most often open after this page.