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Van Scoyk AN, Antelope O, Franzini A, Ayer DE, Peterson RT, Pomicter AD, Owen SC, Deininger MW. Bioluminescence Assay of Lysine Deacylase Sirtuin Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552871. [PMID: 37645727 PMCID: PMC10461969 DOI: 10.1101/2023.08.10.552871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Lysine acylation can direct protein function, localization, and interactions. Sirtuins deacylate lysine towards maintaining cellular homeostasis, and their aberrant expression contributes to the pathogenesis of multiple pathological conditions, including cancer. Measuring sirtuins' activity is essential to exploring their potential as therapeutic targets, but accurate quantification is challenging. We developed 'SIRTify', a high-sensitivity assay for measuring sirtuin activity in vitro and in vivo. SIRTify is based on a split-version of the NanoLuc® luciferase consisting of a truncated, catalytically inactive N-terminal moiety (LgBiT) that complements with a high-affinity C-terminal peptide (p86) to form active luciferase. Acylation of two lysines within p86 disrupts binding to LgBiT and abates luminescence. Deacylation by sirtuins reestablishes p86 and restores binding, generating a luminescence signal proportional to sirtuin activity. Measurements accurately reflect reported sirtuin specificity for lysine acylations and confirm the effects of sirtuin modulators. SIRTify effectively quantifies lysine deacylation dynamics and may be adaptable to monitoring additional post-translational modifications.
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Affiliation(s)
| | | | - Anca Franzini
- University of Utah, Department of Oncological Sciences
| | - Donald E Ayer
- University of Utah, Department of Oncological Sciences
| | | | | | - Shawn C Owen
- University of Utah, Department of Molecular Pharmaceutics
- University of Utah, Department of Medicinal Chemistry; Department of Biomedical Engineering
| | - Michael W Deininger
- Blood Research Institute, Versiti
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin
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Sharma C, Donu D, Curry AM, Barton E, Cen Y. Multifunctional activity-based chemical probes for sirtuins. RSC Adv 2023; 13:11771-11781. [PMID: 37063743 PMCID: PMC10103746 DOI: 10.1039/d3ra02133e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/18/2023] Open
Abstract
The sirtuin family of NAD+-dependent protein deacylases has gained significant attention during the last two decades, owing to their unique enzymatic activities as well as their critical roles in a broad array of cellular events. Innovative chemical probes are heavily pursued for the functional annotation and pharmacological perturbation of this group of "eraser" enzymes. We have developed several series of activity-based chemical probes (ABPs) to interrogate the functional state of active sirtuins in complex biological samples. They feature a simple Ala-Ala-Lys tripeptide backbone with a thioacyl "warhead", a photoaffinity group (benzophenone or diazirine), and a bioorthogonal group (terminal alkyne or azido) for conjugation to reporters. When applied in a comparative fashion, these probes reveal the changes of active sirtuin contents under different physiological conditions. Additionally, they can also be utilized in a competitive manner for inhibitor discovery. The Nobel-winning "click" conjugation to a fluorophore allows the visualization of the active enzymes, while the covalent adduct to a biotin leads to the affinity capture of the protein of interest. Furthermore, the "clickable" tag enables the easy access to proteolysis targeting chimeras (PROTACs) that effectively degrade human SIRT2 in HEK293 cells, albeit at micromolar concentrations. These small molecule probes offer unprecedented opportunities to investigate the biological functions and physiological relevance of the sirtuin family.
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Affiliation(s)
- Chiranjeev Sharma
- Department of Medicinal Chemistry, Virginia Commonwealth University Richmond VA 23219 USA +1-804-828-7405
| | - Dickson Donu
- Department of Medicinal Chemistry, Virginia Commonwealth University Richmond VA 23219 USA +1-804-828-7405
| | - Alyson M Curry
- Department of Medicinal Chemistry, Virginia Commonwealth University Richmond VA 23219 USA +1-804-828-7405
| | - Elizabeth Barton
- Department of Medicinal Chemistry, Virginia Commonwealth University Richmond VA 23219 USA +1-804-828-7405
| | - Yana Cen
- Department of Medicinal Chemistry, Virginia Commonwealth University Richmond VA 23219 USA +1-804-828-7405
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University Richmond VA 23219 USA
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Zhang Z, Lin J, Liu Z, Tian G, Li XM, Jing Y, Li X, Li XD. Photo-Cross-Linking To Delineate Epigenetic Interactome. J Am Chem Soc 2022; 144:20979-20997. [DOI: 10.1021/jacs.2c06135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhuoyuan Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Miller GM, Flynn EM, Tom J, Song A, Cochran AG. Trifluoroacetyl Lysine as a Bromodomain Binding Mimic of Lysine Acetylation. ACS Chem Biol 2022; 17:1022-1029. [PMID: 35467836 DOI: 10.1021/acschembio.2c00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic code expansion has proven invaluable to the elucidation of functions of defined protein modifications through the site-specific incorporation of noncanonical amino acids. The use of nonhydrolyzable derivatives of post-translational modifications can greatly increase site stoichiometry and half-life. Investigating acetyllysine reader domain (bromodomain) interactions with acetylated nonhistone proteins is challenging due to the limited tools available and dynamic nature of this post-translational modification. Here, we demonstrate that bromodomains bind acetyllysine peptides and those substituted with an acetyllysine derivative, trifluoroacetyllysine, with similar affinity and selectivity. Importantly, both trifluoroacetyllysine and acetyllysine can be site-specifically incorporated into proteins expressed in bacterial and mammalian cells, and the strong electron-withdrawing trifluoro substituent makes the latter resistant to deacetylation by sirtuins (SIRTs). The controlled expression of SIRT-resistant, site-specifically acetylated transcription factors expands the set of available tools for determining the function of acetylation, and it serves as a template for investigating bromodomain interactions with acetylated transcription factors.
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Affiliation(s)
- Gregory M. Miller
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco 94080, California, United States
| | - E. Megan Flynn
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco 94080, California, United States
| | - Jeffrey Tom
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco 94080, California, United States
| | - Aimin Song
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco 94080, California, United States
| | - Andrea G. Cochran
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco 94080, California, United States
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Shao X, Kong W, Li Y, Zhang S. Quantitative structure-activity relationship modeling reveals the minimal sequence requirement and amino acid preference of sirtuin-1's deacetylation substrates in diabetes mellitus. J Bioinform Comput Biol 2022; 20:2250008. [PMID: 35451939 DOI: 10.1142/s0219720022500081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD[Formula: see text]-dependent deacetylase involved in multiple glucose metabolism pathways and plays an important role in the pathogenesis of diabetes mellitus (DM). The enzyme specifically recognizes its deacetylation substrates' peptide segments containing a central acetyl-lysine residue as well as a number of amino acids flanking the central residue. In this study, we attempted to ascertain the minimal sequence requirement (MSR) around the central acetyl-lysine residue of SIRT1 substrate-recognition sites as well as the amino acid preference (AAP) at different residues of the MSR window through quantitative structure-activity relationship (QSAR) strategy, which would benefit our understanding of SIRT1 substrate specificity at the molecular level and is also helpful to rationally design substrate-mimicking peptidic agents against DM by competitively targeting SIRT1 active site. In this procedure, a large-scale dataset containing 6801 13-mer acetyl-lysine peptides (and their SIRT1-catalyized deacetylation activities) were compiled to train 10 QSAR regression models developed by systematic combination of machine learning methods (PLS and SVM) and five amino acids descriptors (DPPS, T-scale, MolSurf, [Formula: see text]-score, and FASGAI). The two best QSAR models (PLS+FASGAI and SVM+DPPS) were then employed to statistically examine the contribution of residue positions to the deacetylation activity of acetyl-lysine peptide substrates, revealing that the MSR can be represented by 5-mer acetyl-lysine peptides that meet a consensus motif X[Formula: see text]X[Formula: see text]X[Formula: see text](AcK)0X[Formula: see text]. Structural analysis found that the X[Formula: see text] and (AcK)0 residues are tightly packed against the enzyme active site and confer both stability and specificity for the enzyme-substrate complex, whereas the X[Formula: see text], X[Formula: see text] and X[Formula: see text] residues are partially exposed to solvent but can also effectively stabilize the complex system. Subsequently, a systematic deacetylation activity change profile (SDACP) was created based on QSAR modeling, from which the AAP for each residue position of MSR was depicted. With the profile, we were able to rationally design an SDACP combinatorial library with promising deacetylation activity, from which nine MSR acetyl-lysine peptides as well as two known SIRT1 acetyl-lysine peptide substrates were tested by using SIRT1 deacetylation assay. It is revealed that the designed peptides exhibit a comparable or even higher activity than the controls, although the former is considerably shorter than the latter.
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Affiliation(s)
- X Shao
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - W Kong
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - Y Li
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - S Zhang
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
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Kalous KS, Wynia-Smith SL, Smith BC. Sirtuin Oxidative Post-translational Modifications. Front Physiol 2021; 12:763417. [PMID: 34899389 PMCID: PMC8652059 DOI: 10.3389/fphys.2021.763417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/19/2021] [Indexed: 12/24/2022] Open
Abstract
Increased sirtuin deacylase activity is correlated with increased lifespan and healthspan in eukaryotes. Conversely, decreased sirtuin deacylase activity is correlated with increased susceptibility to aging-related diseases. However, the mechanisms leading to decreased sirtuin activity during aging are poorly understood. Recent work has shown that oxidative post-translational modification by reactive oxygen (ROS) or nitrogen (RNS) species results in inhibition of sirtuin deacylase activity through cysteine nitrosation, glutathionylation, sulfenylation, and sulfhydration as well as tyrosine nitration. The prevalence of ROS/RNS (e.g., nitric oxide, S-nitrosoglutathione, hydrogen peroxide, oxidized glutathione, and peroxynitrite) is increased during inflammation and as a result of electron transport chain dysfunction. With age, cellular production of ROS/RNS increases; thus, cellular oxidants may serve as a causal link between loss of sirtuin activity and aging-related disease development. Therefore, the prevention of inhibitory oxidative modification may represent a novel means to increase sirtuin activity during aging. In this review, we explore the role of cellular oxidants in inhibiting individual sirtuin human isoform deacylase activity and clarify the relevance of ROS/RNS as regulatory molecules of sirtuin deacylase activity in the context of health and disease.
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Affiliation(s)
- Kelsey S Kalous
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Sarah L Wynia-Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
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Curry AM, Barton E, Kang W, Mongeluzi DV, Cen Y. Development of Second Generation Activity-Based Chemical Probes for Sirtuins. Molecules 2020; 26:molecules26010011. [PMID: 33375102 PMCID: PMC7792806 DOI: 10.3390/molecules26010011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/10/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
NAD+ (nicotinamide adenine dinucleotide)-dependent protein deacylases, namely, the sirtuins, are important cell adaptor proteins that alter cell physiology in response to low calorie conditions. They are thought to mediate the beneficial effects of calorie restriction to extend longevity and improve health profiles. Novel chemical probes are highly desired for a better understanding of sirtuin’s roles in various biological processes. We developed a group of remarkably simple activity-based chemical probes for the investigation of active sirtuin content in complex native proteomes. These probes harbor a thioacyllysine warhead, a diazirine photoaffinity tag, as well as a terminal alkyne bioorthogonal functional group. Compared to their benzophenone-containing counterparts, these new probes demonstrated improved labeling efficiency and sensitivity, shortened irradiation time, and reduced background signal. They were applied to the labeling of individual recombinant proteins, protein mixtures, and whole cell lysate. These cell permeable small molecule probes also enabled the cellular imaging of sirtuin activity change. Taken together, our study provides new chemical biology tools and future drug discovery strategies for perturbing the activity of different sirtuin isoforms.
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Affiliation(s)
- Alyson M. Curry
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Elizabeth Barton
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Wenjia Kang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Daniel V. Mongeluzi
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
| | - Yana Cen
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA; (A.M.C.); (E.B.); (W.K.); (D.V.M.)
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
- Correspondence: ; Tel.: +1-804-828-7405
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