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1.
Protein Sci ; 33(5): e4994, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38647411

RESUMEN

Sirtuin 2 (SIRT2) is a class III histone deacetylase that is highly conserved from bacteria to mammals. We prepared and characterized the wild-type (WT) and mutant forms of the histone deacetylase (HDAC) domain of human SIRT2 (hSIRT2) using various biophysical methods and evaluated their deacetylation activity. We found that WT hSIRT2 HDAC (residues 52-357) forms a homodimer in a concentration-dependent manner with a dimer-monomer dissociation constant of 8.3 ± 0.5 µM, which was determined by mass spectrometry. The dimer was disrupted into two monomers by binding to the HDAC inhibitors SirReal1 and SirReal2. We also confirmed dimer formation of hSIRT2 HDAC in living cells using a NanoLuc complementation reporter system. Examination of the relationship between dimer formation and deacetylation activity using several mutants of hSIRT2 HDAC revealed that some non-dimerizing mutants exhibited deacetylation activity for the N-terminal peptide of histone H3, similar to the wild type. The hSIRT2 HDAC mutant Δ292-306, which lacks a SIRT2-specific disordered loop region, was identified to exist as a monomer with slightly reduced deacetylation activity; the X-ray structure of the mutant Δ292-306 was almost identical to that of the WT hSIRT2 HDAC bound to an inhibitor. These results indicate that hSIRT2 HDAC forms a dimer, but this is independent of deacetylation activity. Herein, we discuss insights into the dimer formation of hSIRT2 based on our biophysical experimental results.


Asunto(s)
Multimerización de Proteína , Sirtuina 2 , Humanos , Sirtuina 2/metabolismo , Sirtuina 2/química , Sirtuina 2/genética , Acetilación , Células HEK293
2.
Biochemistry ; 62(23): 3383-3395, 2023 12 05.
Artículo en Inglés | MEDLINE | ID: mdl-37966275

RESUMEN

Human sirtuin isoform 2 (SIRT2) is an NAD+-dependent enzyme that functions as a lysine deacetylase and defatty-acylase. Here, we report that SIRT2 readily dimerizes in solution and in cells and that dimerization affects its ability to remove different acyl modifications from substrates. Dimerization of recombinant SIRT2 was revealed with analytical size exclusion chromatography and chemical cross-linking. Dimerized SIRT2 dissociates into monomers upon binding long fatty acylated substrates (decanoyl-, dodecanoyl-, and myristoyl-lysine). However, we did not observe dissociation of dimeric SIRT2 in the presence of acetyl-lysine. Analysis of X-ray crystal structures led us to discover a SIRT2 double mutant (Q142A/E340A) that is impaired in its ability to dimerize, which was confirmed with chemical cross-linking and in cells with a split-GFP approach. In enzyme assays, the SIRT2(Q142A/E340A) mutant had normal defatty-acylase activity and impaired deacetylase activity compared with the wild-type protein. These results indicate that dimerization is essential for optimal SIRT2 function as a deacetylase. Moreover, we show that SIRT2 dimers can be dissociated by a deacetylase and defatty-acylase inhibitor, ascorbyl palmitate. Our finding that its oligomeric state can affect the acyl substrate selectivity of SIRT2 is a novel mode of activity regulation by the enzyme that can be altered genetically or pharmacologically.


Asunto(s)
Sirtuina 2 , Humanos , Dimerización , Lisina/metabolismo , Sirtuina 2/química , Sirtuina 2/metabolismo
3.
J Chem Inf Model ; 63(15): 4780-4790, 2023 08 14.
Artículo en Inglés | MEDLINE | ID: mdl-37486605

RESUMEN

The sirtuin enzyme family members, SIRT1 and SIRT2, play both tumor-promoting and tumor-suppressing roles, depending on the context and experimental conditions. Compounds that inhibit either SIRT1 or SIRT2 show promising antitumor effects in several types of cancer models, both in vitro and in vivo. The simultaneous inhibition of SIRT1 and SIRT2 is helpful in treating cancer by completely blocking p53 deacetylation, leading to cell death. However, only a few SIRT1/2 dual inhibitors have been developed. Here, we report the discovery of a novel series of SIRT1/2 dual inhibitors via a rational drug design that involved virtual screening and a substructure search. Eleven of the derived compounds exhibited high inhibitory activities, with IC50 < 5 µM and high specificity for both SIRT1 and SIRT2. Compounds hsa55 and PS9 strongly induced apoptosis and showed antiproliferative effects against human leukemia cell lines, which could be due to their ability to increase of p53 and α-tubulin acetylation, as we observed in MOLM-13 cells. Therefore, the new scaffolds of these compounds and their efficacy in leukemia cell lines provide important clues for the further development of novel anti-leukemia drugs.


Asunto(s)
Neoplasias , Sirtuina 2 , Humanos , Sirtuina 2/química , Sirtuina 1 , Proteína p53 Supresora de Tumor/metabolismo , Apoptosis
4.
Int J Mol Sci ; 24(11)2023 May 27.
Artículo en Inglés | MEDLINE | ID: mdl-37298312

RESUMEN

Sirtuin isoform 2 (SIRT2) is one of the seven sirtuin isoforms present in humans, being classified as class III histone deacetylases (HDACs). Based on the high sequence similarity among SIRTs, the identification of isoform selective modulators represents a challenging task, especially for the high conservation observed in the catalytic site. Efforts in rationalizing selectivity based on key residues belonging to the SIRT2 enzyme were accompanied in 2015 by the publication of the first X-ray crystallographic structure of the potent and selective SIRT2 inhibitor SirReal2. The subsequent studies led to different experimental data regarding this protein in complex with further different chemo-types as SIRT2 inhibitors. Herein, we reported preliminary Structure-Based Virtual Screening (SBVS) studies using a commercially available library of compounds to identify novel scaffolds for the design of new SIRT2 inhibitors. Biochemical assays involving five selected compounds allowed us to highlight the most effective chemical features supporting the observed SIRT2 inhibitory ability. This information guided the following in silico evaluation and in vitro testing of further compounds from in-house libraries of pyrazolo-pyrimidine derivatives towards novel SIRT2 inhibitors (1-5). The final results indicated the effectiveness of this scaffold for the design of promising and selective SIRT2 inhibitors, featuring the highest inhibition among the tested compounds, and validating the applied strategy.


Asunto(s)
Sirtuina 2 , Sirtuina 2/antagonistas & inhibidores , Sirtuina 2/química , Dominio Catalítico , Bibliotecas de Moléculas Pequeñas , Conformación Proteica , Simulación del Acoplamiento Molecular
5.
J Chem Inf Model ; 62(10): 2571-2585, 2022 05 23.
Artículo en Inglés | MEDLINE | ID: mdl-35467856

RESUMEN

Considerations of binding pocket dynamics are one of the crucial aspects of the rational design of binders. Identification of alternative conformational states or cryptic subpockets could lead to the discovery of completely novel groups of the ligands. However, experimental characterization of pocket dynamics, besides being expensive, may not be able to elucidate all of the conformational states relevant for drug discovery projects. In this study, we propose the protocol for computational simulations of sirtuin 2 (SIRT2) binding pocket dynamics and its integration into the structure-based virtual screening (SBVS) pipeline. Initially, unbiased molecular dynamics simulations of SIRT2:inhibitor complexes were performed using optimized force field parameters of SIRT2 inhibitors. Time-lagged independent component analysis (tICA) was used to design pocket-related collective variables (CVs) for enhanced sampling of SIRT2 pocket dynamics. Metadynamics simulations in the tICA eigenvector space revealed alternative conformational states of the SIRT2 binding pocket and the existence of a cryptic subpocket. Newly identified SIRT2 conformational states outperformed experimentally resolved states in retrospective SBVS validation. After performing prospective SBVS, compounds from the under-represented portions of the SIRT2 inhibitor chemical space were selected for in vitro evaluation. Two compounds, NDJ18 and NDJ85, were identified as potent and selective SIRT2 inhibitors, which validated the in silico protocol and opened up the possibility for generalization and broadening of its application. The anticancer effects of the most potent compound NDJ18 were examined on the triple-negative breast cancer cell line. Results indicated that NDJ18 represents a promising structure suitable for further evaluation.


Asunto(s)
Simulación de Dinámica Molecular , Sirtuina 2 , Ligandos , Estudios Prospectivos , Estudios Retrospectivos , Sirtuina 2/química
6.
Sci Rep ; 11(1): 10169, 2021 05 13.
Artículo en Inglés | MEDLINE | ID: mdl-33986372

RESUMEN

Sirtuin 2 (Sirt2) nicotinamide adenine dinucleotide-dependent deacetylase enzyme has been reported to alter diverse biological functions in the cells and onset of diseases, including cancer, aging, and neurodegenerative diseases, which implicate the regulation of Sirt2 function as a potential drug target. Available Sirt2 inhibitors or modulators exhibit insufficient specificity and potency, and even partially contradictory Sirt2 effects were described for the available inhibitors. Herein, we applied computational screening and evaluation of FDA-approved drugs for highly selective modulation of Sirt2 activity via a unique inhibitory mechanism as reported earlier for SirReal2 inhibitor. Application of stringent molecular docking results in the identification of 48 FDA-approved drugs as selective putative inhibitors of Sirt2, but only top 10 drugs with docking scores > - 11 kcal/mol were considered in reference to SirReal2 inhibitor for computational analysis. The molecular dynamics simulations and post-simulation analysis of Sirt2-drug complexes revealed substantial stability for Fluphenazine and Nintedanib with Sirt2. Additionally, developed 3D-QSAR-models also support the inhibitory potential of drugs, which exclusively revealed highest activities for Nintedanib (pIC50 ≥ 5.90 µM). Conclusively, screened FDA-approved drugs were advocated as promising agents for Sirt2 inhibition and required in vitro investigation for Sirt2 targeted drug development.


Asunto(s)
Dominio Catalítico/efectos de los fármacos , Reposicionamiento de Medicamentos/métodos , Sirtuina 2/antagonistas & inhibidores , Acetamidas/química , Acetamidas/farmacología , Cristalografía por Rayos X , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Humanos , Ligandos , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Preparaciones Farmacéuticas/química , Unión Proteica , Relación Estructura-Actividad Cuantitativa , Sirtuina 2/química , Tiazoles/química , Tiazoles/farmacología
7.
J Chem Inf Model ; 61(3): 1105-1124, 2021 03 22.
Artículo en Inglés | MEDLINE | ID: mdl-33606530

RESUMEN

Sirt1-3 are the most studied sirtuins, playing a key role in caloric-dependent epigenetic modifications. Since they are localized in distinct cellular compartments and act differently under various pathological conditions, selective inhibition would be a promising strategy to understand their biological function and to discover effective therapeutics. Here, sirtuin's inhibitor Ex527* is used as a probe to speculate the possible root cause of selective inhibition and differential structural dynamics of Sirt1-3. Comparative energetics and mutational studies revealed the criticality of residues I279 and I316 for the Sirt1 selectivity toward Ex527*. Furthermore, essential dynamics and residue network analysis revealed that the side-chain reorientation in residue F190 due to nonconserved residue Y191 played a major role in the formation of an extended selectivity pocket in Sirt2. These changes at the dynamical and residual level, which impact the internal wiring significantly, might help in rationally designing selective inhibitors against Sirt1-3.


Asunto(s)
Sirtuina 1/química , Sirtuina 2/química , Sirtuina 3/química , Secuencia de Aminoácidos , Humanos , Conformación Proteica
8.
Biochemistry ; 59(40): 3869-3878, 2020 10 13.
Artículo en Inglés | MEDLINE | ID: mdl-32941003

RESUMEN

Sirtuin isoform 2 (SIRT2) is an enzyme that catalyzes the removal of acyl groups from lysine residues. SIRT2's catalytic domain has a hydrophobic tunnel where its substrate acyl groups bind. Here, we report that the fluorescent probe 1-aminoanthracene (AMA) binds within SIRT2's hydrophobic tunnel in a substrate-dependent manner. AMA's interaction with SIRT2 was characterized by its enhanced fluorescence upon protein binding (>10-fold). AMA interacted weakly with SIRT2 alone in solution (Kd = 37 µM). However, when SIRT2 was equilibrated with a decanoylated peptide substrate, AMA's affinity for SIRT2 was enhanced ∼10-fold (Kd = 4 µM). The peptide's decanoyl chain and AMA co-occupied SIRT2's hydrophobic tunnel when bound to the protein. In contrast, binding of AMA to SIRT2 was competitive with a myristoylated substrate whose longer acyl chain occluded the entire tunnel. AMA competitively inhibited SIRT2 demyristoylase activity with an IC50 of 21 µM, which was significantly more potent than its inhibition of other deacylase activities. Finally, binding and structural analysis suggests that the AMA binding site in SIRT2's hydrophobic tunnel was structurally stabilized when SIRT2 interacted with a decanoylated or 4-oxononanoylated substrate, but AMA's binding site was less stable when SIRT2 was bound to an acetylated substrate. Our use of AMA to explore changes in SIRT2's hydrophobic tunnel that are induced by interactions with specific acylated substrates has implications for developing ligands that modulate SIRT2's substrate specificity.


Asunto(s)
Antracenos/metabolismo , Colorantes Fluorescentes/metabolismo , Péptidos/metabolismo , Sirtuina 2/metabolismo , Antracenos/química , Colorantes Fluorescentes/química , Humanos , Ligandos , Simulación del Acoplamiento Molecular , Péptidos/química , Unión Proteica/efectos de los fármacos , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Sirtuina 2/química , Especificidad por Sustrato/efectos de los fármacos
9.
J Cell Mol Med ; 24(13): 7439-7450, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32515550

RESUMEN

SIRT2 is a NAD+ -dependent deacetylase that deacetylates a diverse array of protein substrates and is involved in many cellular processes, including regulation of inflammation. However, its precise role in the inflammatory process has not completely been elucidated. Here, we identify heat-shock protein 90α (Hsp90α) as novel substrate of SIRT2. Functional investigation suggests that Hsp90 is deacetylated by SIRT2, such that overexpression and knock-down of SIRT2 altered the acetylation level of Hsp90. This subsequently resulted in disassociation of Hsp90 with glucocorticoid receptor (GR), and translocation of GR to the nucleus. This observation was further confirmed by glucocorticoid response element (GRE)-driven reporter assay. Nuclear translocation of GR induced by SIRT2 overexpression repressed the expression of inflammatory cytokines, which were even more prominent under lipopolysaccharide (LPS) stimulation. Conversely, SIRT2 knock-down resulted in the up-regulation of cytokine expression. Mutation analysis indicated that deacetylation of Hsp90 at K294 is critical for SIRT2-mediated regulation of cytokine expression. These data suggest that SIRT2 reduces the extent of LPS-induced inflammation by suppressing the expression of inflammatory factors via SIRT2-Hsp90-GR axis.


Asunto(s)
Proteínas HSP90 de Choque Térmico/metabolismo , Inflamación/metabolismo , Receptores de Glucocorticoides/metabolismo , Transducción de Señal , Sirtuina 2/metabolismo , Acetilación/efectos de los fármacos , Secuencia de Aminoácidos , Animales , Línea Celular , Núcleo Celular/efectos de los fármacos , Núcleo Celular/metabolismo , Escherichia coli/metabolismo , Humanos , Lipopolisacáridos/farmacología , Modelos Biológicos , Unión Proteica/efectos de los fármacos , ARN Mensajero/genética , ARN Mensajero/metabolismo , ARN Interferente Pequeño/metabolismo , Ratas , Transducción de Señal/efectos de los fármacos , Sirtuina 2/química , Solubilidad
10.
Bioorg Med Chem ; 28(7): 115356, 2020 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-32067892

RESUMEN

Past few years have seen an active pursuit of the inhibitors for the deacylation catalyzed by the seven human sirtuins (i.e. SIRT1-7) as valuable chemical biological/pharmacological probes of this enzymatic deacylation and lead compounds for developing novel therapeutics for human diseases. In the current study, we prepared eight monocyclic and one bicyclic analogs of a linear pentapeptide-based potent (sub-µM IC50's) pan-SIRT1/2/3 inhibitor Zheng laboratory discovered recently that harbors the catalytic mechanism-based SIRT1/2/3 inhibitory warhead Nε-thioacetyl-lysine at its central position. We found that the bicyclic analog exhibited largely comparable SIRT1/2/3 inhibitory potencies to those of the parent linear pentapeptide, however, the former is proteolytically much more stable than the latter. Moreover, the bicyclic analog displayed very weak inhibition against SIRT5/6/7, was cell permeable, and exhibited an anti-proliferative effect on the human SK-MEL-2 melanoma cells. This bicyclic analog could be a lead for the future development of more potent and still selective pan-SIRT1/2/3 inhibitors whose use in studies on human sirtuin biology, pharmacology, and medicinal chemistry could complement with the use of the potent inhibitors selective for a single human sirtuin.


Asunto(s)
Lisina/análogos & derivados , Péptidos/farmacología , Sirtuina 1/antagonistas & inhibidores , Sirtuina 2/antagonistas & inhibidores , Sirtuina 3/antagonistas & inhibidores , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Regulación de la Expresión Génica/efectos de los fármacos , Humanos , Lisina/química , Modelos Moleculares , Estructura Molecular , Péptidos/química , Conformación Proteica , Sirtuina 1/química , Sirtuina 2/química , Sirtuina 3/química
11.
Theranostics ; 10(5): 2188-2200, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32104503

RESUMEN

Aldo-keto reductase family 1 member C1 (AKR1C1) promotes malignancy of Non-Small Cell Lung Cancer (NSCLC) by activating Signal Transducer and Activator of Transcription 3 (STAT3) pathway. However, how the pro-metastatic functions of AKR1C1 are switched on/off remains unknown. Methods: Immunoprecipitation and LC-MS/MS analyses were performed to identify the acetylation on AKR1C1 protein, and the functional analyses (in vitro and in vivo) were performed to depict the contribution of acetylation to the pro-metastatic effects of AKR1C1. Results: Here we report that acetylated AKR1C1 on two lysine residues K185 & K201 is critical to its pro-metastatic role. The acetylation modification has no impact on the canonical enzymatic activity of AKR1C1, while it is required for the interaction between AKR1C1 to STAT3, which triggers the downstream transduction events, ultimately mobilizing cells. Importantly, the deacetylase Sirtuin 2 (SIRT2) is capable of deacetylating AKR1C1, inhibiting the transactivation of STAT3 target genes, thus suppressing the migration of cells. Conclusion: Acetylation on Lysines 185 and 201 of AKR1C1 dictates its pro-metastatic potential both in vitro and in vivo, and the reverting of acetylation by Sirtuin 2 provides potential therapeutic targets for treatment against metastatic NSCLC patients with high AKR1C1 expression.


Asunto(s)
20-Hidroxiesteroide Deshidrogenasas/metabolismo , Carcinoma de Pulmón de Células no Pequeñas/metabolismo , Neoplasias Pulmonares/patología , Sirtuina 2/metabolismo , 20-Hidroxiesteroide Deshidrogenasas/química , Acetilación , Animales , Carcinógenos/metabolismo , Carcinoma de Pulmón de Células no Pequeñas/terapia , Movimiento Celular/efectos de los fármacos , Movimiento Celular/genética , Modelos Animales de Enfermedad , Femenino , Humanos , Ratones , Ratones Endogámicos BALB C , Metástasis de la Neoplasia/genética , Factor de Transcripción STAT3/metabolismo , Transducción de Señal , Sirtuina 2/química
12.
J Biomol Struct Dyn ; 38(2): 354-363, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-30789810

RESUMEN

Sirtuin 2 is a key enzyme in gene expression regulation that is often associated with tumor proliferation control and therefore is a relevant anticancer drug target. Anilinobenzamide derivatives have been discussed as selective sirtuin 2 inhibitors and can be developed further. In the present study, hologram and three-dimensional quantitative structure-activity relationship (HQSAR and 3D-QSAR) analyses were employed for determining structural contributions of a compound series containing human sirtuin-2-selective inhibitors that were then correlated with structural data from the literature. The final QSAR models were robust and predictive according to statistical validation (q2 and r2pred values higher than 0.85 and 0.75, respectively) and could be employed further to generate fragment contribution and contour maps. 3D-QSAR models together with information about the chemical properties of sirtuin 2 inhibitors can be useful for designing novel bioactive ligands.Communicated by Ramaswamy H. Sarma.


Asunto(s)
Benzamidas/farmacología , Relación Estructura-Actividad Cuantitativa , Sirtuina 2/antagonistas & inhibidores , Sirtuina 2/química , Acetilación/efectos de los fármacos , Dominio Catalítico , Epigénesis Genética/efectos de los fármacos , Humanos , Simulación del Acoplamiento Molecular , Reproducibilidad de los Resultados , Sirtuina 2/metabolismo
13.
Chembiochem ; 21(8): 1161-1166, 2020 04 17.
Artículo en Inglés | MEDLINE | ID: mdl-31692222

RESUMEN

We have discovered the sirtuin-rearranging ligands (SirReals) to be highly potent and selective inhibitors of the NAD+ -dependent lysine deacetylase Sirt2. Using a biotinylated SirReal in combination with biolayer interferometry, we previously observed a slow dissociation rate of the inhibitor-enzyme complex; this had been postulated to be the key to the high affinity and selectivity of SirReals. However, to attach biotin to the SirReal core, we introduced a triazole as a linking moiety; this was shown by X-ray co-crystallography to interact with Arg97 of the cofactor binding loop. Herein, we aim to elucidate whether the observed long residence time of the SirReals is induced mainly by triazole incorporation or is an inherent characteristic of the SirReal inhibitor core. We used the novel label-free switchSENSE® technology, which is based on electrically switchable DNA nanolevers, to prove that the long residence time of the SirReals is indeed caused by the core scaffold.


Asunto(s)
Electrónica/instrumentación , Inhibidores Enzimáticos/farmacología , Nanotecnología/métodos , Sirtuina 2/antagonistas & inhibidores , Tiazoles/química , Cristalografía por Rayos X , Inhibidores Enzimáticos/química , Humanos , Cinética , Ligandos , Modelos Moleculares , Simulación del Acoplamiento Molecular , Conformación Proteica , Sirtuina 2/química , Sirtuina 2/metabolismo , Relación Estructura-Actividad
14.
ACS Chem Biol ; 14(8): 1802-1810, 2019 08 16.
Artículo en Inglés | MEDLINE | ID: mdl-31373792

RESUMEN

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.


Asunto(s)
Glucósidos/farmacología , Inhibidores de Histona Desacetilasas/farmacología , Lipopéptidos/farmacología , Sirtuina 2/antagonistas & inhibidores , Antineoplásicos/síntesis química , Antineoplásicos/química , Antineoplásicos/farmacología , Línea Celular Tumoral , Cristalografía por Rayos X , Diseño de Fármacos , Glucósidos/síntesis química , Glucósidos/química , Inhibidores de Histona Desacetilasas/síntesis química , Inhibidores de Histona Desacetilasas/química , Humanos , Lipopéptidos/síntesis química , Lipopéptidos/química , Estructura Molecular , Sirtuina 1/antagonistas & inhibidores , Sirtuina 2/química , Solubilidad
15.
Molecules ; 24(15)2019 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-31357491

RESUMEN

Human sirtuin 2 (SIRT2), a member of the sirtuin family, has been considered as a promising drug target in cancer, neurodegenerative diseases, type II diabetes, and bacterial infections. Thus, SIRT2 inhibitors have been involved in effective treatment strategies for related diseases. Using previously established fluorescence-based assays for SIRT2 activity tests, the authors screened their in-house database and identified a compound, 4-(5-((3-(quinolin-5-yl)ureido)methyl)furan-2-yl)benzoic acid (20), which displayed 63 ± 5% and 35 ± 3% inhibition against SIRT2 at 100 µM and 10 µM, respectively. The structure-activity relationship (SAR) analyses of a series of synthesized (5-phenylfuran-2-yl)methanamine derivatives led to the identification of a potent compound 25 with an IC50 value of 2.47 µM, which is more potent than AGK2 (IC50 = 17.75 µM). Meanwhile, 25 likely possesses better water solubility (cLogP = 1.63 and cLogS = -3.63). Finally, the molecular docking analyses indicated that 25 fitted well with the induced hydrophobic pocket of SIRT2.


Asunto(s)
Descubrimiento de Drogas , Inhibidores de Histona Desacetilasas/química , Metilaminas/química , Sirtuina 2/química , Inhibidores de Histona Desacetilasas/farmacología , Humanos , Metilaminas/farmacología , Modelos Moleculares , Conformación Molecular , Estructura Molecular , Sirtuina 2/antagonistas & inhibidores , Relación Estructura-Actividad
16.
J Med Chem ; 62(12): 5844-5862, 2019 06 27.
Artículo en Inglés | MEDLINE | ID: mdl-31144814

RESUMEN

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.


Asunto(s)
Benzamidas/química , Dicetopiperazinas/química , Dicetopiperazinas/farmacología , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , NAD/metabolismo , Sirtuina 2/antagonistas & inhibidores , Sitios de Unión , Dicetopiperazinas/metabolismo , Inhibidores Enzimáticos/metabolismo , Humanos , Células MCF-7 , Simulación del Acoplamiento Molecular , Conformación Proteica , Sirtuina 1/antagonistas & inhibidores , Sirtuina 1/química , Sirtuina 1/metabolismo , Sirtuina 2/química , Sirtuina 2/metabolismo , Relación Estructura-Actividad , Especificidad por Sustrato
17.
J Mol Graph Model ; 89: 60-73, 2019 06.
Artículo en Inglés | MEDLINE | ID: mdl-30870650

RESUMEN

Sirtuins (SIRTs) are a class of NAD+-dependent protein histone deacetylases (HDACs) that catalyse the reversible deacetylation of lysine residues in the histones or non-histone substrates. Mammalian sirtuins consist of seven isoforms (SIRT1-7), which show different subcellular localizations and enzymatic functions. Among the seven human sirtuins, SIRT2 predominantly located in the cytoplasm but is enriched in the nucleus during mitosis. Its activity has been found to be modulate the pathophysiology of various diseases such as cancer, metabolic and neurodegenerative disorders. Therefore, selective SIRT2 inhibitors are of growing interest as potentially candidate therapeutic agents to treat SIRT2-driven pathologies as well as valuable tools to investigate and define the biological roles of SIRT2. Herein, in order to identify potent leads against SIRT2, a multi-step pharmacophore based-virtual screening campaign was performed and 31 predicted compounds were subjected to in vitro biological evaluation. Finally, compound 2 and 3 showing better SIRT2 inhibition potency were selected for further in vitro cytotoxic assays against a panel of three human cancer cell lines. This study will hopefully provide a basis for developing potent and selective SIRT2 inhibitors.


Asunto(s)
Antineoplásicos/química , Antineoplásicos/farmacología , Inhibidores de Histona Desacetilasas/química , Inhibidores de Histona Desacetilasas/farmacología , Modelos Moleculares , Sirtuina 2/química , Línea Celular , Simulación por Computador , Relación Dosis-Respuesta a Droga , Ensayos de Selección de Medicamentos Antitumorales , Humanos , Conformación Molecular , Estructura Molecular , Curva ROC , Sirtuina 2/antagonistas & inhibidores , Relación Estructura-Actividad
18.
Methods Mol Biol ; 1813: 225-234, 2018.
Artículo en Inglés | MEDLINE | ID: mdl-30097871

RESUMEN

Sirtuins are a class of enzymes that utilize nicotinamide adenine dinucleotide, NAD+, to remove various acyl groups from protein lysine residues. They have important biological functions and regulate numerous biological pathways. Small molecules that can modulate sirtuin enzymatic activities are potential therapeutic candidates to treat various human diseases. This protocol describes a high-performance liquid chromatography (HPLC)-based method to measure the enzyme kinetics for SIRT2 and SIRT6's demyristoylase activities and SIRT5's desuccinylase activity. This method uses peptide substrates that resemble physiological substrates and thus can give more reliable kinetic parameters (K m and k cat values) for these enzymes. The data obtained are useful for understanding the biological function of sirtuins and developing sirtuin modulators.


Asunto(s)
Cromatografía Líquida de Alta Presión/métodos , Pruebas de Enzimas/métodos , Sirtuina 2/aislamiento & purificación , Sirtuinas/aislamiento & purificación , Humanos , Cinética , Lisina/química , NAD/química , Péptidos/química , Sirtuina 2/química , Sirtuinas/química
19.
Chem Rec ; 18(12): 1701-1707, 2018 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-29931800

RESUMEN

Reversible lysine deacetylation is exerted by both zinc and NAD+ -dependent deacetylases. It is an important factor in epigenetic regulation and more generally in the posttranslational regulation of protein stability, association and activity. Some of these enzymes can also cleave off fatty acids or dicarboxylic acids from lysines in proteins. The NAD+ -dependent deacetylases are termed Sirtuins and are implicated in the pathogenesis of different diseases. For the isotype Sirt2 highly selective inhibitors have been identified in the last few years. Many of those Sirt2 selective compounds, like the Sirtuin rearranging ligands (SirReals) discovered in our group, have been shown or are postulated to bind to the so-called selectivity pocket. This binding site is not observed in crystal structures of the apo-enzyme but can be opened up by long chain fatty acid substrates respectively suitable inhibitors. Recently, this unique feature of Sirt2 was exploited to provide highly potent and selective tools for the chemical biology of Sirtuins. Here, we shortly review Sirtuin biology, present inhibitors that have either been confirmed or postulated to bind to the selectivity pocket, their applications and an outlook regarding mechanistic investigations.


Asunto(s)
Sirtuina 2/química , Sirtuina 2/metabolismo , Sitios de Unión , Epigenómica , Humanos , Ligandos , Lisina/química , Lisina/metabolismo , Simulación de Dinámica Molecular , Estructura Terciaria de Proteína , Pirimidinas/química , Pirimidinas/metabolismo , Sirtuina 2/antagonistas & inhibidores , Especificidad por Sustrato
20.
Artículo en Inglés | MEDLINE | ID: mdl-29685963

RESUMEN

Sirtuins are NAD+-dependent protein deacylases capable of cleaving off acetyl as well as other acyl groups from the ɛ-amino group of lysines in histones and other substrate proteins. They have been reported as promising drug targets, and thus modulators of their activity are needed as molecular tools to uncover their biological function and as potential therapeutics. Here, we present new assay formats that complement existing assays for sirtuin biochemistry and cellular target engagement. Firstly, we report the development of a homogeneous fluorescence-based activity assay using unlabelled acylated peptides. Upon deacylation, the free lysine residue reacts with fluorescamine to form a fluorophore. Secondly, using click chemistry with a TAMRA-azide on a propargylated sirtuin inhibitor, we prepared the first fluorescently labelled small-molecule inhibitor of Sirt2. This is used in a binding assay, which is based on fluorescence polarization. We used it successfully to map potential inhibitor-binding sites and also to show cellular Sirt2 engagement. By means of these new assays, we were able to identify and characterize novel Sirt2 inhibitors out of a focused library screen. The binding of the identified Sirt2 inhibitors was rationalized by molecular docking studies. These new chemical tools thus can enhance further sirtuin research.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.


Asunto(s)
Simulación del Acoplamiento Molecular , NAD/química , Sirtuina 2/química , Fluorescencia , Humanos
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