SIRT2-selective Inhibitors Research Articles

Hit evaluation results in 5-benzyl-1,3,4-thiadiazole-2-carboxamide based SIRT2-selective inhibitor with improved affinity and selectivity

Sirtuin 2 (SIRT2), member of sirtuin family, belongs to class III histone deacetylases (HDACs) and is majorly cytosolic with occasional nuclear translocation. The enzymatic activity of SIRT2 is dependent on nicotinamide adenine dinucleotide (NAD+) and SIRT2 regulates post-translational modifications that are responsible for deacetylation of lysine residues in histone and non-histone substrates. SIRT2, thus affects most likely multiple cellular processes, such as signaling, gene expression, aging, autophagy, and has been identified as potential drug target in relation to inflammation, neurodegenerative diseases and cancer. Therefore, probing potential selective inhibitors is essential for the accurate understanding of enzyme functions. Here, we report a series of heteroaryl-2-carboxamide hybrids bearing substituted benzyl or substituted phenoxy group at the 5-position of the central heterocyclic ring. The synthesized compounds were screened against SIRT1-3 and MCF-7 human breast cancer cell line to evaluate their biological activity. The best SIRT2 inhibition profiles were displayed by ST29 (SIRT2 IC50 = 38.69 μM) and ST30 (SIRT2 IC50 = 43.29 μM) with excellent selectivity against SIRT2 over SIRT1 and SIRT3. Molecular docking study of the synthesized compounds into SIRT2 active site was performed to rationalize the remarkable SIRT2 inhibitory activity. Furthermore, we performed all-atom, explicit-solvent molecular dynamics (MD) simulations and end-point binding free energy calculations using molecular mechanics/generalized Born surface area (MM/GBSA) method to evaluate whether this design strategy was successfully deployed. The results implied that the binding poses and ligand affinities were predicted without significant loss of accuracy. Conclusively, the developed chemotypes were advocated as promising leads for SIRT2 inhibition and required further investigation for SIRT2-targeted drug discovery and development.

Abstract 1635: Sirt2 blockade promotes T cell metabolism and restores the anti-tumor immunity

Abstract Background: The majority of cancer patients remain refractory to existing cancer immunotherapies. Despite the growing evidence that dysregulated metabolism contributes to the exhaustion of tumor-infiltrating T lymphocytes (TILs) and the loss of their effector functions within the metabolically restricted tumor microenvironment (TME), actionable targets to rescue metabolic fitness and anti-tumor activity of TILs remain elusive. Sirt2 is an NAD+ dependent histone deacetylase and conflicting evidences suggest its tumor-suppressor and oncogenic roles. In inflammatory response, Sirt2 suppresses inflammation via negative regulation of NF-κB subunit; however, the role of Sirt2 in tumor immunity has not been described. Method: Human TILs from non-small cell lung cancer (NSCLC) tumor samples and matched peripheral blood T cells were analyzed for Sirt2 expression by flow cytometry. The role of Sirt2 in anti-tumor immunity was studied by in vivo B16F10 tumor challenge in Wild-type (Wt) and Sirt2 knockout (Sirt2KO) mice. The role of Sirt2 in T cell effector functions was investigated ex vivo by CFSE proliferation assay, IFN-γ ELISpot assay, intracellular staining of effector markers and LDH cytotoxicity assay on Wt versus Sirt2KO T cells. Sirt2 targets were identified using mass spectrometry (MS) and Co-immunoprecipitation analyses. T cells metabolic changes were investigated using seahorse bioanalyzer and LC-MS/MS Metabolomic profiling. Sirt2 blockade in human T cells was performed using AGK2, a Sirt2 selective inhibitor. Result: We show that Sirt2 expression is upregulated within the TME, and its upregulation in human TILs is associated with a poor clinical response to immunotherapy in a phase I clinical trial in advanced NSCLC. We also show that, Sirt2 deficiency in mice boosts T cell effector functions and tumor rejection in vivo. Our molecular and metabolomic studies revealed multiple metabolic pathways as Sirt2 targets including glycolysis, TCA-cycle, FAO and glutaminolysis. We found that Sirt2 deacetylase deficiency increased acetylation and enzymatic activity of key metabolic enzymes leading to a hyper metabolic status of T cells. Finally pharmacologic inhibition of Sirt2 in human TILs isolated from NSCLC patients enhances their metabolic fitness and effector functions. Conclusion Our findings indicate Sirt2 as a master suppressor of T cell metabolism amenable to therapeutic targeting and Sirt2 inhibition reprograms T cell metabolic fitness to optimally sustain their effector function within the metabolically challenging TME, thus, leading to an effective anti-tumor immune response. Citation Format: Imene Hamaidi, Lin Zhang, Nayoung Kim, Min Hsuan Wang, Cristina Iclozan, Bin Fang, Min Liu, John M. Koomen, Anders E. Berglund, Sean J. Yoder, Jiqiang Yao, Robert W. Engelman, Ben C. Creelan, Jose R. Conejo-Garcia, James J. Mulé, Scott J. Antonia, Sungjune Kim. Sirt2 blockade promotes T cell metabolism and restores the anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1635.

Pharmacological Advantage of SIRT2-Selective versus pan-SIRT1-3 Inhibitors.

Because of their involvement in various biological pathways, the sirtuin enzyme family members SIRT1, SIRT2, and SIRT3 play both tumor-promoting and tumor-suppressing roles, based on the context and experimental conditions. Thus, an interesting question is whether inhibiting one of them or inhibiting all of them would be better for treating cancers. Pharmacologically, this is difficult to address, due in part to potential off-target effects of different compounds. Compounds with almost identical properties but differing in SIRT1-3 selectivity will be useful for addressing this question. Here, we have developed a pan SIRT1-3 inhibitor (NH4-6) and a SIRT2-selective inhibitor (NH4-13) with very similar chemical structures, with the only difference being the substitution of an ester bond to an amide bond. Such a minimal difference allows us to accurately compare the anticancer effect of pan SIRT1-3 inhibition and SIRT2-selective inhibition in cellular and mouse models. NH4-6 showed stronger cytotoxicity than NH4-13 in cancer cell lines. In mice, both inhibitors showed similar anticancer efficacy. However, NH4-6 is toxic to mice, which hinders the use of higher dosages. These results highlight the advantage of SIRT2-selective inhibitors as potential anticancer therapeutics.

Molecular dynamics simulations reveal the mechanism of the interactions between the inhibitors and SIRT2 at atom level

ABSTRACTThe sirtuins are members of the histone deacetylase family of proteins that participate in a variety of cellular functions and play a close role in cancers. Exploring the proper inhibitors for SIRT2 has attracted great interest in the experiment. However, the detail of the interaction mechanisms between inhibitors and SIRT2 is not well understood. In our study, we synthesised SIRT2 selective inhibitor TPN0_C7 as a model of the proper inhibitor of SIRT2. With the molecular dynamics (MD) simulations, we found that the hydrophobic interactions play the important roles between the inhibitors and SIRT2. According to the conformation character of the inhibitor TPN0_C7, we also explored the natural product, Ge Gen (Puerarol is one of the components.), which is a very effective herb for cancer described in Traditional Chinese Medicine (TCMs) library. Dramatically, we found that the structurally similar inhibitors, Puerarol and TPN0_C7, have the similar binding sites on SIRT2. The hydrophobic and π-π interactions between inhibitors and SIRT2 are important during the progress of the dynamic simulations. In summary, our study uncovers the interaction mechanisms between the inhibitors and SIRT2 at atom level, which may provide clues to explore more proper inhibitors from TCMs.

Unexpected small molecules as novel SIRT2 suicide inhibitors

A series of sirtuin inhibitor candidates were assembled based on an intermediate ester (1a) our accidently discovered. After screening and evaluation, several SIRT2 selective inhibitors were identified, which can inhibit all the deacetylation, defatty-acylation and debenzoylation of SIRT2. Among these inhibitors, compound 1e was the best SIRT2 selective inhibitors. The primary study on the inhibitory mechanism indicated that compound 1e may be a suicide inhibitor acting as an irreversible way. Given almost all reported sirtuin inhibitors are non-covalent, sirtuin covalent inhibitors are still need to be developed. These findings will facilitate for further development of SIRT2 selective and suicide inhibitors.

Early sirtuin 2 inhibition prevents age-related cognitive decline in a senescence-accelerated mouse model.

The senescence-accelerated mouse prone-8 (SAMP8) model has been considered as a good model for aged-related cognitive decline and Alzheimer's disease (AD). Since epigenetic alterations represent a crucial mechanism during aging, in the present study we tested whether the inhibition of the histone deacetylase sirtuin 2 (SIRT2) could ameliorate the age-dependent cognitive impairments and associated neuropathology shown by SAMP8 mice. To this end, the potent SIRT2-selective inhibitor, 33i (5 mg/kg i.p. 8 weeks) was administered to 5-month-old (early treatment) and 8-month-old (late treatment) SAMP8 and aged matched control, senescence-accelerated mouse resistant-1 (SAMR1) mice. 33i administration to 5-month-old SAMP8 mice improved spatial learning and memory impairments shown by this strain in the Morris water maze. SAMP8 showed hyperphosphorylation of tau protein and decrease levels of SIRT1 in the hippocampus, which were not altered by 33i treatment. However, this treatment upregulated the glutamate receptor subunits GluN2A, GluN2B, and GluA1 in both SAMR1 and SAMP8. Moreover, early SIRT2 inhibition prevented neuroinflammation evidenced by reduced levels of GFAP, IL-1β, Il-6, and Tnf-α, providing a plausible explanation for the improvement of cognitive deficits shown by 33i-treated SAMP8 mice. When 33i was administered to 8-month-old SAMP8 with a severe established pathology, increases in GluN2A, GluN2B, and GluA1 were observed; however, it was not able to reverse the cognitive decline or the neuroinflammation. These results suggest that early SIRT2 inhibition might be beneficial in preventing age-related cognitive deficits, neuroinflammation, and AD progression and could be an emerging candidate for the treatment of other diseases linked to dementia.

A Glycoconjugated SIRT2 Inhibitor with Aqueous Solubility Allows Structure-Based Design of SIRT2 Inhibitors.

Small molecule inhibitors for SIRT2, a member of the sirtuin family of nicotinamide adenine dinucleotide-dependent protein lysine deacylases, have shown promise in treating cancer and neurodegenerative diseases. Developing SIRT2-selective inhibitors with better pharmacological properties is key to further realize the therapeutic potential of targeting SIRT2. One of the best SIRT2-selective inhibitors reported is a thiomyristoyl lysine compound called TM, which showed promising anticancer activity in mouse models without much toxicity to normal cells. The main limitations of TM, however, are the low aqueous solubility and lack of X-ray crystal structures to aid future drug design. Here, we designed and synthesized a glucose-conjugated TM (glucose-TM) analog with superior aqueous solubility. Although glucose-TM is not cell permeable, the excellent aqueous solubility allowed us to obtain a crystal structure of SIRT2 in complex with it. The structure enabled us to design several new TM analogs, one of which, NH4-6, showed superior water solubility and better anticancer activity in cell culture. The results of these studies provided important insights that will further fuel the future development of improved SIRT2 inhibitors as promising therapeutics for treating cancer and neurodegeneration.

Identification of Diketopiperazine-Containing 2-Anilinobenzamides as Potent Sirtuin 2 (SIRT2)-Selective Inhibitors Targeting the “Selectivity Pocket”, Substrate-Binding Site, and NAD+-Binding Site

The NAD+-dependent deacetylase SIRT2 represents an attractive target for drug development. Here, we designed and synthesized drug-like SIRT2-selective inhibitors based on an analysis of the putative binding modes of recently reported SIRT2-selective inhibitors and evaluated their SIRT2-inhibitory activity. This led us to develop a more drug-like diketopiperazine structure as a "hydrogen bond (H-bond) hunter" to target the substrate-binding site of SIRT2. Thioamide 53, a conjugate of diketopiperazine and 2-anilinobenzamide which is expected to occupy the "selectivity pocket" of SIRT2, exhibited potent SIRT2-selective inhibition. Inhibition of SIRT2 by 53 was mediated by the formation of a 53-ADP-ribose conjugate, suggesting that 53 is a mechanism-based inhibitor targeting the "selectivity pocket", substrate-binding site, and NAD+-binding site. Furthermore, 53 showed potent antiproliferative activity toward breast cancer cells and promoted neurite outgrowth of Neuro-2a cells. These findings should pave the way for the discovery of novel therapeutic agents for cancer and neurological disorders.

Identification of the Binding Site of Chroman-4-one-Based Sirtuin 2-Selective Inhibitors using Photoaffinity Labeling in Combination with Tandem Mass Spectrometry.

Photoaffinity labeling (PAL) was used to identify the binding site of chroman-4-one-based SIRT2-selective inhibitors. The photoactive diazirine 4, a potent SIRT2 inhibitor, was subjected to detailed photochemical characterization. In PAL experiments with SIRT2, a tryptic peptide originating from the covalent attachment of photoactivated 4 was identified. The peptide covers both the active site of SIRT2 and the proposed binding site of chroman-4-one-based inhibitors. A high-power LED was used as source for the monochromatic UV light enabling rapid photoactivation.

A SIRT2-Selective Inhibitor Promotes c-Myc Oncoprotein Degradation and Exhibits Broad Anticancer Activity

Targeting sirtuins for cancer treatment has been a topic of debate due to conflicting reports and lack of potent and specific inhibitors. We have developed a thiomyristoyl lysine compound, TM, as a potent SIRT2-specific inhibitor with a broad anticancer effect in various human cancer cells and mouse models of breast cancer. Mechanistically, SIRT2 inhibition promotes c-Myc ubiquitination and degradation. The anticancer effect of TM correlates with its ability to decrease c-Myc level. TM had limited effects on non-cancerous cells and tumor-free mice, suggesting that cancer cells have an increased dependency on SIRT2 that can be exploited for therapeutic benefit. Our studies demonstrate that SIRT2-selective inhibitors are promising anticancer agents and may represent a general strategy to target certain c-Myc-driven cancers.

Sirtuin modulators control reactive gliosis in an in vitro model of Alzheimer's disease.

Among neurodegenerative disorders, Alzheimer’s disease (AD) represents the most common cause of dementia in the elderly. Several genetic and environmental factors have been identified; however, aging represents the most important risk factor in the development of AD. To date, no effective treatments to prevent or slow this dementia are available. Sirtuins (SIRTs) are a family of NAD+-dependent enzymes, implicated in the control of a variety of biological processes that have the potential to modulate neurodegeneration. Here we tested the hypothesis that activation of SIRT1 or inhibition of SIRT2 would prevent reactive gliosis which is considered one of the most important hallmark of AD. Primary rat astrocytes were activated with beta amyloid 1-42 (Aβ 1-42) and treated with resveratrol (RSV) or AGK-2, a SIRT1 activator and a SIRT2-selective inhibitor, respectively. Results showed that both RSV and AGK-2 were able to reduce astrocyte activation as well as the production of pro-inflammatory mediators. These data disclose novel findings about the therapeutic potential of SIRT modulators, and suggest novel strategies for AD treatment.

Identification of novel SIRT2-selective inhibitors using a click chemistry approach

A series of 114 SIRT inhibitor candidates was assembled using ‘click chemistry’, by reacting two alkynes bearing 2-anilinobenzamide pharmacophore with 57 azide building blocks in the presence of Cu(I) catalyst. Screening identified two SIRT2-selective inhibitors, which were more SIRT2-selective than AGK2, a known SIRT2 inhibitor. These findings will be useful for further development of SIRT2-selective inhibitors.

Discovery of Salermide-Related Sirtuin Inhibitors: Binding Mode Studies and Antiproliferative Effects in Cancer Cells Including Cancer Stem Cells

Chemical changes performed on 1a (sirtinol) led to a series of SIRT1/2 inhibitors, in some cases more potent than 1a mainly against SIRT1. Tested in human leukemia U937 cells, the benzamide and anilide derivatives 1b, 1c, 2b, and 2c as well as the 4-(2-phenylpropyl)thioanalogue 4c showed huge apoptosis induction, while some sulfinyl and sulfonyl derivatives (5b, 5c, and 6a-c) were highly efficient in granulocytic differentiation. When assayed in human leukemia MOLT4 as well as in human breast MDA-MB-231 and colon RKO cancer cell lines, the anilide 2b (salermide) and the phenylpropylthio analogue 4b emerged as the most potent antiproliferative agents. Tested on colorectal carcinoma and glioblastoma multiforme cancer stem cells (CSCs) from patients, 2b was particularly potent against colorectal carcinoma CSCs, while 4b, 6a, and the SIRT2-selective inhibitor AGK-2 showed the highest effect against glioblastoma multiforme CSCs. Such compounds will be further explored for their broad-spectrum anticancer properties.

Design, Synthesis, and Biological Activity of a Novel Series of Human Sirtuin-2-Selective Inhibitors

Selective inhibitors of human sirtuin 2 (SIRT2), a deacetylase, are candidate therapeutic agents for neurodegenerative diseases such as Parkinson's disease and Huntington's disease as well as potential tools for elucidating the biological functions of SIRT2. On the basis of homology models of SIRT1 and SIRT2, we designed and prepared a series of 2-anilinobenzamide analogues. Enzyme assays using recombinant SIRT1 and SIRT2 revealed that 3'-phenethyloxy-2-anilinobenzamide analogues such as 33a and 33i are potent and selective SIRT2 inhibitors, showing more than 3.5-fold greater SIRT2-inhibitory activity and more than 35-fold greater SIRT2-selectivity compared with AGK2 (3), a previously reported SIRT2-selective inhibitor. Compound 33a also induced a dose-dependent selective increase of α-tubulin acetylation in human colon cancer HCT116 cells, indicating selective inhibition of SIRT2 in the cells. These 3'-phenethyloxy-2-anilinobenzamide derivatives represent an entry into a new class of SIRT2-selective inhibitors.