Tier 3 — preclinical

Biological and catalytic functions of sirtuin 6 as targets for small-molecule modulators

Mark A. Klein, John M. Denu
Journal of Biological Chemistry 2020 Volume 295, issue 32, pages 11021–11041

Bibliography

PubMed
PMID 32518153
PubMed Central
PMC7415977
DOI
10.1074/jbc.REV120.011438
Funding
US National Institutes of Health grant GM065386 to J.M.D. M.A.K. supported by the Chemistry-Biology Interface Training Program (NIGMS, NIH grant T32GM008505).
Competing interests
J.M.D. is a consultant for Evrys Bio and cofounder of Galilei BioSciences. This is disclosed in the paper's Conflict of Interest statement. Both companies operate in the sirtuin therapeutics space, and the review's positive framing of SIRT6 as a small-molecule target aligns with these commercial interests. This does not invalidate the biochemistry catalogued but warrants reader awareness.

Study snapshot

DesignNarrative review covering SIRT6 biological functions (DNA repair, chromatin maintenance, metabolic regulation, aging and lifespan, cancer), molecular architecture (Rossmann fold, zinc-binding domain, hydrophobic pocket, N- and C-terminal extensions), catalytic mechanism, and the identified natural and synthetic small-molecule activators and inhibitors.
ModelReview scope covers in vitro biochemistry, X-ray crystal structures, mouse embryonic fibroblasts, murine knockout and transgenic models, human cell lines, and clinical observations from SIRT6-linked human disease across the SIRT6 literature through mid-2020.
SampleNot applicable — narrative review.
InterventionNot applicable — narrative review of SIRT6 substrates, catalytic mechanism, and modulator chemistry.
DurationNot applicable — narrative review.
EndpointsCataloguing of SIRT6 biological functions and validated substrates; Structural and mechanistic basis of SIRT6 catalysis and NAD dependence; Kinetic characterisation of small-molecule activators including free fatty acids, anthocyanidins, fucoidan, UBCS039, MDL-800, and CL5D; Identification of SIRT6 inhibitors and their translational potential; Framework for developing activity-selective SIRT6 probes to disentangle deacetylation, mono-ADP-ribosylation, and long-chain deacylation

What the study showed, in plain terms

This is a review, not a new experiment. Two University of Wisconsin biochemists — one a graduate student in the training programme, the other one of the field's most cited SIRT6 mechanism researchers — took every published SIRT6 paper up to mid-2020 and organised it around a single question: which of SIRT6's chemical activities produces which biological effect, and how do you drug it.

They start with what SIRT6 does inside a cell. SIRT6 mice die at four weeks of age from an ageing-like illness, they explain, and SIRT6 loss shows up naturally in many human cancers. The protein sits in the nucleus, mediates DNA damage repair by both recruiting repair factors and modifying the chromatin around break sites, and holds glucose and fat metabolism in check by silencing genes that would otherwise push a cell toward the Warburg-effect metabolism seen in tumours. Mice engineered to make extra SIRT6 live longer.

Then they tackle the biochemistry that has puzzled the field. SIRT6 has three known enzyme activities: it removes acetyl tags from histone lysines, it removes long-chain fatty acid tags, and it stitches ADP-ribose molecules onto other proteins. Its removal of acetyl tags is very slow in the test tube — roughly a thousand times slower than SIRT1 or SIRT3 — but is clearly biologically important. This puzzle was partially resolved by the discovery that certain fatty acids and small molecules can stimulate SIRT6 acetyl-removal activity by up to fifty-fold, apparently by filling a hydrophobic pocket that would otherwise sit empty.

The review closes on the practical side. As of publication, cellularly active SIRT6 activators including UBCS039 and MDL-800 had been reported, small-molecule SIRT6 inhibitors including OSS_128167 existed, and animal studies had begun to suggest that either activating or inhibiting SIRT6 could be therapeutically useful depending on the disease context. But the authors argue that better selectivity between the three catalytic activities is essential to properly disentangle SIRT6's biological roles. That call has largely defined the SIRT6 medicinal chemistry programme in the years since.

Key findings

  • SIRT6 has three biochemically validated enzymatic activities: NAD-dependent lysine deacetylation, NAD-dependent long-chain lysine defatty-acylation (removing myristoyl and palmitoyl groups), and mono-ADP-ribosylation of other proteins. Deacetylation is catalytically inefficient in vitro compared with other sirtuins, but long-chain defatty-acylation is several hundred-fold more efficient than SIRT6 deacetylation.
  • SIRT6 loss-of-function causes DNA repair failure, genomic instability, dysregulated glycolysis in a Warburg-like pattern, hypoglycaemia, and premature ageing with death by four weeks in mice. SIRT6 overexpression in mice extends lifespan approximately 15 per cent in males and protects against diet-induced obesity, LDL-cholesterol accumulation, and fatty liver.
  • The molecular architecture of SIRT6 differs from other sirtuins in three important ways: an extended hydrophobic pocket that accommodates long-chain acyl substrates, a missing salt bridge that keeps the two catalytic domains in a splayed-open conformation, and a ten-amino-acid extension in the zinc-binding domain unique to SIRT6.
  • Free fatty acids ranging from twelve to eighteen carbons in length activate SIRT6 deacetylation up to thirty-five-fold by binding the hydrophobic pocket, providing a candidate mechanism by which endogenous cellular fatty acid pools might regulate SIRT6 activity in vivo.
  • Synthetic SIRT6 activators identified as of 2020 include the flavonoids quercetin (concentration-dependent, dual behaviour), luteolin, and cyanidin; the fucoidan sulfated polysaccharide (355-fold activation at 100 micrograms per millilitre); UBCS039 (EC50 38 micromolar, structurally validated to bind the distal hydrophobic pocket); MDL-801 and MDL-800 (EC50 approximately 10 micromolar, cellularly active, dose-dependent decrease in H3K9 and H3K56 acetylation and cell-cycle arrest in cancer cells); and CL5D (EC50 15 micromolar). Kinetic profiles differ meaningfully between compounds.
  • The SIRT6 inhibitor OSS_128167 shows selectivity for SIRT6 over SIRT1 and SIRT2, improves glucose tolerance in a type 2 diabetes mouse model, and inhibits hepatitis B viral transcription in vivo despite a short serum half-life. Cyclic-peptide thioacyl-lysine inhibitors reach nanomolar potency in vitro but have not been translated to cellular activity.
  • The authors argue that combining activity-selective small molecules with SIRT6 amino acid substitutions from enzymology studies is the most promising path to disentangling which catalytic activity of SIRT6 drives which biological phenotype — including the apparently opposite roles of SIRT6 as tumour suppressor in some cancers and tumour driver in others.

What this study can and cannot tell us

This is a narrative review, not a systematic review. The authors did not use a pre-registered search strategy or apply a formal quality-assessment framework to the studies discussed. Readers should treat the synthesis as informed scholarly opinion rather than a statistical summary of the field.

The senior author (J.M.D.) discloses consultancy for Evrys Bio and co-founder status at Galilei BioSciences. Both companies operate in the sirtuin therapeutics space. The review's positive framing of SIRT6 as a small-molecule target aligns with these commercial interests. The disclosure is made openly in the Conflict of Interest statement, which is appropriate. Readers should nonetheless weigh the strength of individual claims — particularly around activator translational potential — against this context.

The review covers literature through mid-2020. Subsequent work has extended the SIRT6 activator landscape (for example, the compound 12q reported by Chen and colleagues; the fluvastatin repurposing described by You and Steegborn) and clarified the allosteric activation mechanism (Zhao et al. 2023). Readers assessing the current state of SIRT6 pharmacology should read this review in combination with the more recent primary literature.

The review advocates for activity-selective SIRT6 probes but does not itself provide such probes. As of publication, no activator was known to selectively stimulate one of SIRT6's three catalytic activities without affecting the others. The argument that this selectivity is achievable rests on the identification of the hydrophobic pocket as a pharmacologically tractable allosteric site and on preliminary evidence that different activators drive different Michaelis-Menten kinetic profiles, but the medicinal chemistry work to realise this potential remained a future project at the time of writing.

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