scholarly journals In silico profiling of histone deacetylase inhibitory activity of compounds isolated from Cajanus cajan

2022 ◽  
Vol 11 (1) ◽  
Author(s):  
Kayode Adewole ◽  
Adebayo Ishola ◽  
Ige Olaoye
Keyword(s):  
Betulinic Acid ◽  
Hdac Inhibitor ◽  
In Silico ◽  
Histone Deacetylases ◽  
Cajanus Cajan ◽  
Molecular Mechanisms ◽  
Hdac Inhibitors ◽  
High Morbidity ◽  
Discovery Studio ◽  
Potential Inhibitors

Abstract Background Cancer is responsible for high morbidity and mortality globally. Because the overexpression of histone deacetylases (HDACs) is one of the molecular mechanisms associated with the development and progression of some diseases such as cancer, studies are now considering inhibition of HDAC as a strategy for the treatment of cancer. In this study, a receptor-based in silico screening was exploited to identify potential HDAC inhibitors among the compounds isolated from Cajanus cajan, since reports have earlier confirmed the antiproliferative properties of compounds isolated from this plant. Results Cajanus cajan-derived phytochemicals were docked with selected HDACs, with givinostat as the reference HDAC inhibitor, using AutodockVina and Discovery Studio Visualizer, BIOVIA, 2020. Furthermore, absorption, distribution, metabolism and excretion (ADME) drug-likeness analysis was done using the Swiss online ADME web tool. From the results obtained, 4 compounds; betulinic acid, genistin, orientin and vitexin, were identified as potential inhibitors of the selected HDACs, while only 3 compounds (betulinic acid, genistin and vitexin) passed the filter of drug-likeness. The molecular dynamic result revealed the best level of flexibility on HDAC1 and HDAC3 compared to the wild-type HDACs and moderate flexibility of HDAC7 and HDAC8. Conclusions The results of molecular docking, pharmacokinetics and molecular dynamics revealed that betulinic acid might be a suitable HDAC inhibitor worthy of further investigation in order to be used for regulating conditions associated with overexpression of HDACs. This knowledge can be used to guide experimental investigation on Cajanus cajan-derived compounds as potential HDAC inhibitors.

scholarly journals Cytoplasmic Interactions between the Glucocorticoid Receptor and HDAC2 Regulate Osteocalcin Expression in VPA-Treated MSCs

Cells ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 217 ◽  
Author(s):  
Marcella La Noce ◽  
Luigi Mele ◽  
Luigi Laino ◽  
Giovanni Iolascon ◽  
Gorizio Pieretti ◽  
...  
Keyword(s):  
Glucocorticoid Receptor ◽  
Hdac Inhibitor ◽  
Histone Deacetylases ◽  
Molecular Mechanisms ◽  
Severe Combined Immunodeficiency ◽  
Hdac Inhibitors ◽  
Stem Cell Differentiation ◽  
Mechanistic Explanation ◽  
Nonobese Diabetic

Epigenetic regulation has been considered an important mechanism for influencing stem cell differentiation. In particular, histone deacetylases (HDACs) have been shown to play a role in the osteoblast differentiation of mesenchymal stem cells (MSCs). In this study, the effect of the HDAC inhibitor, valproic acid (VPA), on bone formation in vivo by MSCs was determined. Surprisingly, VPA treatment, unlike other HDAC inhibitors, produced a well-organized lamellar bone tissue when MSCs–collagen sponge constructs were implanted subcutaneously into nonobese diabetic/severe combined immunodeficiency (NOD/SCID) mice, although a decrease of osteocalcin (OC) expression was observed. Consequently, we decided to investigate the molecular mechanisms by which VPA exerts such effects on MSCs. We identified the glucocorticoid receptor (GR) as being responsible for that downregulation, and suggested a correlation between GR and HDAC2 inhibition after VPA treatment, as evidenced by HDAC2 knockdown. Furthermore, using co-immunoprecipitation analysis, we showed for the first time in the cytoplasm, binding between GR and HDAC2. Additionally, chromatin immunoprecipitation (ChIP) assays confirmed the role of GR in OC downregulation, showing recruitment of GR to the nGRE element in the OC promoter. In conclusion, our results highlight the existence of a cross-talk between GR and HDAC2, providing a mechanistic explanation for the influence of the HDAC inhibitor (namely VPA) on osteogenic differentiation in MSCs. Our findings open new directions in targeted therapies, and offer new insights into the regulation of MSC fate determination.

Identification of potential histone deacetylase inhibitory biflavonoids from Garcinia kola (Guttiferae) using in silico protein-ligand interaction

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Kayode E. Adewole ◽  
Ahmed A. Ishola ◽  
Blessing O. Omolaso
Keyword(s):  
In Silico ◽  
Histone Deacetylases ◽  
Hdac Inhibitors ◽  
Intimate Relationship ◽  
Binding Affinities ◽  
Ligand Interaction ◽  
Garcinia Kola ◽  
Discovery Studio ◽  
Limited Success ◽  
Protein Ligand Interaction

Abstract Overactivity of histone deacetylases (HDACs) is the underlying cause of some cancers, thus, inhibiting their overactivities is a rational treatment option. However, endeavors to employ current anti-HDACs agents in cancer treatment have yielded limited success. Consequently, there is need to explore anti-HDACs natural products, especially from plants sources, because of the intimate relationship plant products and drug discovery have enjoyed over the centuries. To identify possible HDACs inhibitors, Garcinia kola (Guttiferae) seed-derived compounds were screened in silico for HDAC-inhibitory tendencies because of their reported anticancer potentials. Fifteen G. kola-derived compounds and givinostat were docked with five selected HDACs using AutodockVina, while the binding interactions of the compounds with high binding affinities for the five HDACs were viewed with Discovery Studio Visualizer BIOVIA, 2016. Results indicated that four of the compounds studied, including amentoflavone, Garcinia biflavonoid 1, Garcinia biflavonoid 2 and kolaflavanone have higher binding propensity for all the five HDACs relative to givinostat, the standard HDAC inhibitor. This study indicated that inhibition of HDAC might be another key mechanism accountable for the bioactivities of G. kola and its intrinsic compounds. The results from this study implied that the compounds could be further investigated as drugable HDAC inhibitors with potential pharmacological applications in the treatment of cancers.

scholarly journals Resistance to histone deacetylase inhibitors confers hypersensitivity to oncolytic reovirus therapy

2020 ◽  
Vol 4 (20) ◽  
pp. 5297-5310
Author(s):  
Shariful Islam ◽  
Claudia M. Espitia ◽  
Daniel O. Persky ◽  
Jennifer S. Carew ◽  
Steffan T. Nawrocki
Keyword(s):  
Histone Deacetylase ◽  
Hdac Inhibitor ◽  
Histone Deacetylase Inhibitors ◽  
Molecular Mechanisms ◽  
Hdac Inhibitors ◽  
Cross Resistance ◽  
Drug Resistant ◽  
In Vivo Models ◽  
Clinical Issue ◽  
Resistant Cells

Abstract Despite the promising antilymphoma activity of histone deacetylase (HDAC) inhibitors as a drug class, resistance is a significant clinical issue. Elucidating the molecular mechanisms driving HDAC inhibitor resistance and/or the specific targets that are altered in drug-resistant cells may facilitate the development of strategies that overcome drug resistance and are more effective for refractory patients. We generated novel T-cell lymphoma (TCL) cell line models of acquired resistance to the HDAC inhibitor belinostat to identify potential effective therapies. Belinostat-resistant cells displayed significant cross-resistance to other HDAC inhibitors including romidepsin, panobinostat, and vorinostat. Consistent with a lack of sensitivity to HDAC inhibitors, the resistant cells failed to induce increased acetylated histones. Drug-resistant cells featured significantly decreased expression of the key antiviral mediators IRF1 and STAT1. On the basis of these findings, we investigated the efficacy of the clinical formulation of reovirus (Reolysin) in parental and drug-resistant models. Our investigation revealed that HDAC inhibitor–resistant cells displayed enhanced vulnerability to reovirus replication and cell death in both in vitro and in vivo models compared with their parental counterparts. Importantly, Reolysin also significantly increased the antilymphoma activity of belinostat in HDAC inhibitor–resistant cells. Our data demonstrate that Reolysin alone or in combination with belinostat is a novel therapeutic strategy to treat TCL patients who develop resistance to HDAC inhibitors.

scholarly journals Cystathionine γ-lyase protects vascular endothelium: a role for inhibition of histone deacetylase 6

2017 ◽  
Vol 312 (4) ◽  
pp. H711-H720 ◽  
Author(s):  
Thorsten M. Leucker ◽  
Yohei Nomura ◽  
Jae Hyung Kim ◽  
Anil Bhatta ◽  
Victor Wang ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Histone Deacetylase ◽  
Vascular Endothelium ◽  
High Fat Diet ◽  
Histone Deacetylases ◽  
Molecular Mechanisms ◽  
Oxidized Ldl ◽  
Hdac Inhibitors ◽  
Histone Deacetylase 6 ◽  
High Fat

Endothelial cystathionine γ-lyase (CSEγ) contributes to cardiovascular homeostasis, mainly through production of H2S. However, the molecular mechanisms that control CSEγ gene expression in the endothelium during cardiovascular diseases are unclear. The aim of the current study is to determine the role of specific histone deacetylases (HDACs) in the regulation of endothelial CSEγ. Reduced CSEγ mRNA expression and protein abundance were observed in human aortic endothelial cells (HAEC) exposed to oxidized LDL (OxLDL) and in aortas from atherogenic apolipoprotein E knockout (ApoE−/−) mice fed a high-fat diet compared with controls. Intact murine aortic rings exposed to OxLDL (50 μg/ml) for 24 h exhibited impaired endothelium-dependent vasorelaxation that was blocked by CSEγ overexpression or the H2S donor NaHS. CSEγ expression was upregulated by pan-HDAC inhibitors and by class II-specific HDAC inhibitors, but not by other class-specific inhibitors. The HDAC6 selective inhibitor tubacin and HDAC6-specific siRNA increased CSEγ expression and blocked OxLDL-mediated reductions in endothelial CSEγ expression and CSEγ promoter activity, indicating that HDAC6 is a specific regulator of CSEγ expression. Consistent with this finding, HDAC6 mRNA, protein expression, and activity were upregulated in OxLDL-exposed HAEC, but not in human aortic smooth muscle cells. HDAC6 protein levels in aortas from high-fat diet-fed ApoE−/− mice were comparable to those in controls, whereas HDAC6 activity was robustly upregulated. Together, our findings indicate that HDAC6 is upregulated by atherogenic stimuli via posttranslational modifications and is a critical regulator of CSEγ expression in vascular endothelium. Inhibition of HDAC6 activity may improve endothelial function and prevent or reverse the development of atherosclerosis. NEW & NOTEWORTHY Oxidative injury to endothelial cells by oxidized LDL reduced cystathionine γ-lyase (CSEγ) expression and H2S production, leading to endothelial dysfunction, which was prevented by histone deacetylase 6 (HDAC6) inhibition. Our data suggest HDAC6 as a novel therapeutic target to prevent the development of atherosclerosis.

scholarly journals Design and in silico screening of aryl allyl mercaptan analogs as potential histone deacetylases (HDAC) inhibitors

Heliyon ◽  
2020 ◽  
Vol 6 (5) ◽  
pp. e03517 ◽  
Author(s):  
Sugandha Singhal ◽  
Mallika Pathak ◽  
Paban K. Agrawala ◽  
Himanshu Ojha
Keyword(s):  
In Silico ◽  
Histone Deacetylases ◽  
Hdac Inhibitors ◽  
In Silico Screening ◽  
Allyl Mercaptan

scholarly journals In silico screening of W. salutaris bioactive constituents reveal betulinic acid, ursolic acid acetate and eucosterol as potential M. tuberculosis antagonists targeting FabF

2021 ◽  
Author(s):  
Nokukhanya Gumede ◽  
Kgothatso E. Machaba ◽  
Umar Ndagi ◽  
Hezekiel M. Kumalo ◽  
Ndumiso N. Mhlongo
Keyword(s):  
Ursolic Acid ◽  
Betulinic Acid ◽  
In Silico ◽  
Fatty Acid Biosynthesis ◽  
Binding Energies ◽  
Active Site Residues ◽  
Bioactive Constituents ◽  
Inhibitory Potential ◽  
Dynamics Simulations ◽  
Potential Inhibitors

Abstract Tuberculosis (TB) remains a long-standing burdening disease to control worldwide. The lengthy current TB treatment, which boasts with unbearable adverse effects, and frequent emergence of drug resistant strains of M. tuberculosis lays an increasing burden. This behests urgent discovery and development of alternative novel medicine to alleviate TB. In this report, in silico methods were applied to examine the propensity of W. salutaris active compounds as potential inhibitors of M. tuberculosis fatty acid biosynthesis protein (FabF). Thirteen compounds were virtually screened against FabF and subjected to molecular dynamics simulations and post-dynamics analyses to examine their inhibitory potential. Betulinic acid, ursolic acid and ursolic acid acetate had the best binding energies and hence the best inhibitory potential against FabF and desirable cytotoxicity profile. These compounds bind and interact with FabF active site residues to exert their inhibitory potential. Findings in this preliminary report warrant further experimental validation towards the development of these compounds as potential drugs targeting FabF in the treatment of tuberculosis.

scholarly journals Pathways and microRNAs bioinformatics analyses identifying possible existing therapeutics for COVID-19 treatment

2020 ◽  
Author(s):  
Laura Teodori ◽  
Piero Sestili ◽  
Valeria Madiai ◽  
Sofia Coppari ◽  
Daniele Fraternale ◽  
...  
Keyword(s):  
Angiotensin Converting Enzyme ◽  
In Silico ◽  
Molecular Mechanisms ◽  
Hdac Inhibitors ◽  
Converting Enzyme ◽  
Bioinformatics Analyses ◽  
Off Label ◽  
Host Virus Interactions ◽  
Virus Interactions ◽  
Ranked List

Abstract Over 180.000 SARS-COV-2 positive cases have been confirmed in Italy as April 20, with the number of deaths exceeding 23 thousand, making Italy the second Country for world COVID-19 deaths. Such enormous occurrence of infected and dead people raises the urgent demand of effective fast available treatments to control and diminish this pandemic. Discovering the cellular/molecular mechanisms of SARS-COV-2 pathogenicity is of paramount importance to understand how the infection becomes a disease and for therapeutically approaching it. From literature data, through a bioinformatics approach, an in silico analysis was performed, to predict the putative virus targets and evidence the already available therapeutics. Literature experimental results identified angiotensin-converting enzyme ACE and Spike proteins particularly involved in COVID-19. We thus investigate on the signaling pathways modulated by the two proteins through query miRNet, the platform linking miRNAs, targets and functions. We predicted microRNAs (miRs), miR-335-5p and miR-26b-5p, as being modulated by Spike and ACE together with deacetylate histones pathway HDAC. Our results matched with the available clinical data. We hypothesize the current and EMA-approved, SARS-COV-2 off-label, HDAC inhibitors (HDACis) drugs may be repurposed to limit or block host-virus interactions. A ranked list of compounds is given that can be tested.

scholarly journals Upregulation of ERK-EGR1-heparanase axis by HDAC inhibitors provides targets for rational therapeutic intervention in synovial sarcoma

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Cinzia Lanzi ◽  
Enrica Favini ◽  
Laura Dal Bo ◽  
Monica Tortoreto ◽  
Noemi Arrighetti ◽  
...  
Keyword(s):  
Synovial Sarcoma ◽  
Cell Response ◽  
Histone Deacetylases ◽  
Molecular Mechanisms ◽  
Combined Treatment ◽  
Single Agent ◽  
Hdac Inhibitors ◽  
Xenograft Model

Abstract Background Synovial sarcoma (SS) is an aggressive soft tissue tumor with limited therapeutic options in advanced stage. SS18-SSX fusion oncogenes, which are the hallmarks of SS, cause epigenetic rewiring involving histone deacetylases (HDACs). Promising preclinical studies supporting HDAC targeting for SS treatment were not reflected in clinical trials with HDAC inhibitor (HDACi) monotherapies. We investigated pathways implicated in SS cell response to HDACi to identify vulnerabilities exploitable in combination treatments and improve the therapeutic efficacy of HDACi-based regimens. Methods Antiproliferative and proapoptotic effects of the HDACi SAHA and FK228 were examined in SS cell lines in parallel with biochemical and molecular analyses to bring out cytoprotective pathways. Treatments combining HDACi with drugs targeting HDACi-activated prosurvival pathways were tested in functional assays in vitro and in a SS orthotopic xenograft model. Molecular mechanisms underlying synergisms were investigated in SS cells through pharmacological and gene silencing approaches and validated by qRT-PCR and Western blotting. Results SS cell response to HDACi was consistently characterized by activation of a cytoprotective and auto-sustaining axis involving ERKs, EGR1, and the β-endoglycosidase heparanase, a well recognized pleiotropic player in tumorigenesis and disease progression. HDAC inhibition was shown to upregulate heparanase by inducing expression of the positive regulator EGR1 and by hampering negative regulation by p53 through its acetylation. Interception of HDACi-induced ERK-EGR1-heparanase pathway by cell co-treatment with a MEK inhibitor (trametinib) or a heparanase inhibitor (SST0001/roneparstat) enhanced antiproliferative and pro-apoptotic effects. HDAC and heparanase inhibitors had opposite effects on histone acetylation and nuclear heparanase levels. The combination of SAHA with SST0001 prevented the upregulation of ERK-EGR1-heparanase induced by the HDACi and promoted caspase-dependent cell death. In vivo, the combined treatment with SAHA and SST0001 potentiated the antitumor efficacy against the CME-1 orthotopic SS model as compared to single agent administration. Conclusions The present study provides preclinical rationale and mechanistic insights into drug combinatory strategies based on the use of ERK pathway and heparanase inhibitors to improve the efficacy of HDACi-based antitumor therapies in SS. The involvement of classes of agents already clinically available, or under clinical evaluation, indicates the transferability potential of the proposed approaches.

scholarly journals In silico drug discovery strategies identified ADMET properties of decoquinate RMB041 and its potential drug targets against Mycobacterium Tuberculosis

2021 ◽  
Author(s):  
Kirsten Elke Knoll ◽  
Mietha M. van der Walt ◽  
Du toit Loots
Keyword(s):  
Mycobacterium Tuberculosis ◽  
In Silico ◽  
Drug Targets ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
Antimicrobial Agents ◽  
Screening Methods ◽  
Discovery Studio ◽  
Optimal Drug

The highly adaptive cellular response of Mycobacterium tuberculosis to various antibiotics and the high costs for clinical trials, hampers the development of novel antimicrobial agents with improved efficacy and safety. Subsequently, in silico drug screening methods are more commonly being used for the discovery and development of drugs, and have been proven useful for predicting the pharmacokinetics, toxicities, and targets, of prospective new antimicrobial agents. In this investigation, we used a reversed target fishing approach to determine potential hit targets and their possible interactions between M. tuberculosis and decoquinate RMB041, a propitious new antituberculosis compound. Two of the thirteen identified targets, Cyp130 and BlaI, were strongly proposed as optimal drug-targets for dormant M. tuberculosis, of which the first showed the highest comparative binding affinity to decoquinate RMB041. The metabolic pathways associated to the selected target proteins were compared to previously published molecular mechanisms of decoquinate RMB041 against M. tuberculosis, whereby we confirmed disrupted metabolism of proteins, cell wall components, and DNA. We also described the steps within these pathways that are inhibited and elaborated on decoquinate RMB041's activity against dormant M. tuberculosis. This compound has previously showed promising in vitro safety and good oral bioavailability, which were both supported by this in silico study. The pharmacokinetic properties and toxicity of this compound were predicted and investigated using the online tools pkCSM and SwissADME, and Discovery Studio software, which furthermore supports previous safety and bioavailability characteristics of decoquinate RMB041 for use as an antimycobacterial medication.

Suppression of monosodium urate crystal-induced cytokine production by butyrate is mediated by the inhibition of class I histone deacetylases

2015 ◽  
Vol 75 (3) ◽  
pp. 593-600 ◽  
Author(s):  
Maartje C P Cleophas ◽  
Tania O Crişan ◽  
Heidi Lemmers ◽  
Helga Toenhake-Dijkstra ◽  
Gianluca Fossati ◽  
...  
Keyword(s):  
Hdac Inhibitor ◽  
Histone Deacetylases ◽  
Mononuclear Cells ◽  
Cytokine Production ◽  
Hdac Inhibitors ◽  
Class I ◽  
Acute Gout ◽  
Monosodium Urate ◽  
Healthy Donors ◽  
Anti Inflammatory

ObjectivesAcute gouty arthritis is caused by endogenously formed monosodium urate (MSU) crystals, which are potent activators of the NLRP3 inflammasome. However, to induce the release of active interleukin (IL)-1β, an additional stimulus is needed. Saturated long-chain free fatty acids (FFAs) can provide such a signal and stimulate transcription of pro-IL-1β. In contrast, the short-chain fatty acid butyrate possesses anti-inflammatory effects. One of the mechanisms involved is inhibition of histone deacetylases (HDACs). Here, we explored the effects of butyrate on MSU+FFA-induced cytokine production and its inhibition of specific HDACs.MethodsFreshly isolated peripheral blood mononuclear cells (PBMCs) from healthy donors were stimulated with MSU and palmitic acid (C16.0) in the presence or absence of butyrate or a synthetic HDAC inhibitor. Cytokine responses were measured with ELISA and quantitative PCR. HDAC activity was measured with fluorimetric assays.ResultsButyrate decreased C16.0+MSU-induced production of IL-1β, IL-6, IL-8 and IL-1β mRNA in PBMCs from healthy donors. Similar results were obtained in PBMCs isolated from patients with gout. Butyrate specifically inhibited class I HDACs. The HDAC inhibitor, panobinostat and the potent HDAC inhibitor, ITF-B, also decreased ex vivo C16.0+MSU-induced IL-1β production.ConclusionsIn agreement with the reported low inhibitory potency of butyrate, a high concentration was needed for cytokine suppression, whereas synthetic HDAC inhibitors showed potent anti-inflammatory effects at nanomolar concentrations. These novel HDAC inhibitors could be effective in the treatment of acute gout. Moreover, the use of specific HDAC inhibitors could even improve the efficacy and reduce any potential adverse effects.

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