HDAC inhibitors improve CRISPR-mediated HDR editing efficiency in iPSCs

Genome-edited human induced pluripotent stem cells(iPSCs)hold great promise for therapeutic applications.However,low editing efficiency has hampered the applications of CRISPR-Cas9 technology in creating knockout and homology-directed repair(HDR)-edited iPSC lines,particularly for silent genes.This is partially due to chromatin compaction,inevitably limiting Cas9 access to the target DNA.Among the six HDAC inhibitors we examined,vorinostat,or suberoylanilide hydroxamic acid(SAHA),led to the highest HDR efficiency at both open and closed loci,with acceptable toxicity.HDAC inhibitors equally increased non-homologous end joining(NHEJ)editing efficiencies(~50%)at both open and closed loci,due to the considerable HDAC inhibitor-mediated increase in Cas9 and sgRNA expression.However,we observed more substantial HDR efficiency improvement at closed loci relative to open chromatin(2.8 vs.1.7-fold change).These studies provide a new strategy for HDRediting of silent genes in iPSCs.

HDAC inhibitors with potential to overcome drug resistance in castration-resistant prostate cancer

Epigenetic mechanisms play an important role in the development and persistence of cancer,and histone deacetylase(HDAC)inhibitors are promising anticancer drugs targeting epigenetic modes.Efficient anticancer drugs for the treatment of castration-resistant prostate cancer(CRPC)are sought,and approved HDAC inhibitors have shown promising results on the one hand and severe drawbacks on the other hand.Hence,ways to break the drug resistance mechanisms of existing HDAC inhibitors as well as the design of new promising HDAC inhibitors which can overcome the disadvantages of the classic HDAC inhibitors are of great importance.In this work,HDAC inhibitors with the potential to become a mainstay for the treatment of CRPC in the future as well as suitable combination treatments of HDAC inhibitors with other anticancer drugs leading to considerable synergistic effects in treated CRPCs are discussed.

The Molecular Mechanism of HDAC Inhibitors in Anticancer Effects

HDACs and HATs are two kinds of enzymes which catalyse deacetylation and acetylation of histone in eukaryotes, whose dynamic balance has accurate regulation for gene transcription and gene expression of eukaryotes at DNA level. Disbalance of them can bring the disorder of proliferation and differentiation in normal cells, and then lead to the initiation of tumor. Their aberrant functions were directly related to the initiation and progression of various tumors, such as promyelocytic leukemia, Hodgkin lymphoma, colonic cancer and gastral cancer. The inhibitors of HDACs are used for treatment of tumor. They can restrain the activity of HDACs and block the inhibition of gene expression caused by the disorder of deacetylation. Its major biological effects lie in inducing differentiation of tumor cells, arresting cell circle at G0/G1, activating cell apoptosis gene, enhancing the sensitivity of chemical therapy and radioactive therapy. So far HDAC has been an important target enzyme in anticancer drug research.

HDAC Inhibitors:A Potential New Category of Anti-Tumor Agents

Over the past years, it has been found that the epigenetic silence of tumor suppressor genes induced by overexpression of histone deacetylases （HDACs） plays an important role in carcinogenesis. Thus, HDAC inhibitors have emerged as the accessory therapeutic agents for multiple human cancers, since they can block the activity of specific HDACs, restore the expression of some tumor suppressor genes and induce cell differentiation, growth arrest and apoptosis. To date, the precise mechanisms by which HDAC inhibitors induce cell death have not yet been fully elucidated and the roles of individual HDAC inhibitors have not been identified. Moreover, the practical uses of HDAC inhibitors in cancer therapy, as well as their synergistic effects with other therapeutic strategies are yet to be evaluated. In this review article, we discuss briefly the recent advances in studies of the developments of anti-cancer HDAC inhibitors and their potential clinical value.

HDAC inhibitors overcome immunotherapy resistance in B-cell lymphoma

Immunotherapy has been applied successully to treat B-cell lymphomas in preclinical models or clinical settings.However,immunotherapy resistance is a major challenge for B-cell lymphoma treatment.To overcome this issue,combinatorlal therapeutic strategies have been pursued to achieve a better efficacy for treating B-cell lymphomas.One of such strategies is to combine immunotherapy with histone deacetylase(HDAC)inhi-bitors.HDAC inhibitors can potentially increase tumor immunogenicity,promote antitumor immune respon-ses,or reverse immunosuppressive tumor environments.Thus,the combination of HDAC inhibitors and immunotherapy has drawn much attention in current cancer treatment.However,not all HDAC inhibitors are created equal and their net effects are highly dependent on the specific inhibitors used and the HDACs they target.Hence,we suggest that optimal treatment effh-cacy requires personalized design and rational combination based on prognostic biomarkers and unique profiles of HDAC inhibitors.Here,we discuss the possible mechanisms by which B-cell lymphomas acquire immunotherapy resistance and the effects of HDAC inhibitors on tumor cells and immune cells that could help overcome immunotherapy resistance.

Histone deacetylase inhibitors as a novel therapeutic approach for pheochromocytomas and paragangliomas

Epigenetic mechanisms,such as DNA methylation and histone modifications(e.g.,acetylation and deacetylation),are strongly implicated in the carcinogenesis of various malignancies.During transcription,the expression and functionality of coding gene products are altered following the histone acetylation and deacetylation.These processes are regulated by histone acetyltransferases(HATs)and histone deacetylases(HDACs),respectively.HDAC inhibitors(HDACis)have been developed as promising therapeutic agents,to limit exposure to traditional and toxic chemotherapies and offer more alternatives for some specific malignant diseases with limited options.Mechanistically,these agents affect many intracellular pathways,including cell cycle arrest,apoptosis and differentiation,and their mechanism of action mainly depends on the type of cancer.Currently,five HDACis have been approved for the treatment of several hematological malignancies(e.g.,T-cell lymphoma subtypes and multiple myeloma);while,many of them are tested for further therapeutic indications in solid tumors(e.g.,colorectal,thyroid,breast,lung and pancreatic cancer).Herein,we review the literature and gather all available evidence,from in vitro and in vivo data to clinical trial results,that recognizes the antitumor activity of HDACis on pheochromocytomas and paragangliomas;and supports their clinical implementation in the treatment of these rare neuroendocrine tumors at metastatic setting.

The HDAC inhibitor GCJ-490A suppresses c-Met expression through IKKα and overcomes gefitinib resistance in non-small cell lung cancer

Objective:The novel compound GCJ-490A has been discovered as a pan-histone deacetylase(HDAC)inhibitor that exerts potent inhibitory activity against HDAC1,HDAC3,and HDAC6.Because of the important roles of HDACs in lung cancer development and the high distribution of GCJ-490A in lung tissue,we explored the anti-tumor potency of GCJ-490A against non-small cell lung cancer(NSCLC)in vitro and in vivo in this study.Methods:The in vitro effects of GCJ-490A alone or combined with the EGFR inhibitor gefitinib against NSCLC were measured with proliferation,apoptosis,and colony formation assays.NSCLC xenograft models were used to investigate the efficacy of GCJ-490A combined with gefitinib for the treatment of NSCLC in vivo.Western blot assays,luciferase reporter assays,chromatin immunoprecipitation assays,quantitative real time-PCR,immunohistochemistry,and transcription factor activity assays were used to elucidate possible mechanisms.Results:GCJ-490A effectively inhibited NSCLC cell proliferation and induced apoptosis in vitro and in vivo.Interestingly,inhibition of HDAC1 and HDAC6 by GCJ-490A increased histone acetylation at the IKKαpromoter and enhanced IKKαtranscription,thus decreasing c-Met.Moreover,this c-Met downregulation was found to be essential for the synergistic anti-tumor activity of GCJ-490A and gefitinib.Conclusions:These findings highlight the promising potential of HDAC inhibitors in NSCLC treatment and provide a rational basis for the application of HDAC inhibitors in combination with EGFR inhibitors in clinical trials.

Histone deacetylase inhibitor pracinostat suppresses colorectal cancer by inducing CDK5-Drp1 signaling-mediated peripheral mitofission

Divisions at the periphery and midzone of mitochondria are two fission signatures that determine the fate of mitochondria and cells.Pharmacological induction of excessively asymmetric mitofissionassociated cell death(MFAD)by switching the scission position from the mitochondrial midzone to the periphery represents a promising strategy for anticancer therapy.By screening a series of paninhibitors,we identified pracinostat,a pan-histone deacetylase(HDAC)inhibitor,as a novel MFAD inducer,that exhibited a significant anticancer effect on colorectal cancer(CRC)in vivo and in vitro.Pracinostat increased the expression of cyclin-dependent kinase 5(CDK5)and induced its acetylation at residue lysine 33,accelerating the formation of complex CDK5/CDK5 regulatory subunit 1 and dynaminrelated protein 1(Drp1)-mediated mitochondrial peripheral fission.CRC cells with high level of CDK5(CDK5-high)displayed midzone mitochondrial division that was associated with oncogenic phenotype,but treatment with pracinostat led to a lethal increase in the already-elevated level of CDK5 in the CRC cells.Mechanistically,pracinostat switched the scission position from the mitochondrial midzone to the periphery by improving the binding of Drp1 from mitochondrial fission factor(MFF)to mitochondrial fission 1 protein(FIS1).Thus,our results revealed the anticancer mechanism of HDACi pracinostat in CRC via activating CDK5-Drp1 signaling to cause selective MFAD of those CDK5-high tumor cells,which implicates a new paradigm to develop potential therapeutic strategies for CRC treatment.

A phaseⅠtrial of an oral subtype-selective histone deacetylase inhibitor,chidamide,in combination with paclitaxel and carboplatin in patients with advanced non-small cell lung cancer

Objective： This phase I study was to evaluate safety, maximum tolerated dose, pharmacokinetics and preliminary antitumor activity of chidamide, a novel subtype-selective histone deacetylase （HDAC） inhibitor, in combination with paclitaxel and carboplatin in patients with advanced non-small cell lung cancer （NSCLC）. Methods： Ten patients received oral chidamide 20, 25, or 30 mg twice per week continuously with paclitaxel （175 mg/m2） and carboplatin [area under the curve （AUC） 5 mg/mL/min] administered in a 3-week cycle. Patients with response and stable disease after four cycles maintained chidamide monotherapy until disease progression or unacceptable toxicity. Blood samples were collected for pharmacoldnetic analysis after the first single oral of chidamide and first combination treatment in cycle 1 from all patients. Results： Two dose-limiting toxicities were recorded in the 30 mg cohort, including thrombocytopenia and prolonged neutropenia in the first cycle. Grade 3/4 neutropenia in any cycle was observed in all patients, but was not associated with significant complications. Other grade 3/4 hematologic toxicities included thrombocytopenia and leucopenia. No significant changes were observed in pharmacokinetic parameters for both chidamide and paclitaxel. One patient in the 20 mg cohort had confirmed partial response （PR）. Two out of 5 patients with brain metastases had intracranial complete remission after 4-cycle treatment. Conclusions： Chidamide combined with paclitaxel and carboplatin was generally tolerated without unanticipated toxicities or clinically relevant pharmacokinetic interactions. The recommended dose for chidamide in this combination was established at 20 mg, and a phase II trial is ongoing with this regimen in patients with advanced NSCLC.

Regulating regulatory T cells to achieve transplant tolerance

BACKGROUND:Regulatory T cells(Tregs) play crucial roles in both induction and maintenance of tolerance. This active immune regulation may contribute not only to the control of immune responses to self-antigens and thereby prevent autoimmune diseases,but also the control of responses to non-self molecules in adaptive immunity. Numerous experimental and clinical studies indicate that manipulating the balance between regulatory and responder T cells is an effective strategy to control immune responsiveness after transplantation. DATA SOURCES:Literature search was conducted using PubMed on the related subjects. Part of the material was based on the most recent work in the authors’ laboratory. RESULTS:We propose some new strategies to achieve transplant tolerance in rodent animals via manipulating Treg function,including using histone deacetylase(HDAC) inhibitor to regulate Foxp3 transcription and enhance Treg suppression,induction of Treg-sparing apoptosis via Nur77,and identification of the co-inhibitory molecule herpes virus entry mediator(HVEM) as an effector molecule for Treg function. CONCLUSION:Regulation of Treg function will definitely provide us very promising tools to achieve clinical tolerance in the future.

HDAC I/IIb selective inhibitor Purinostat Mesylate combined with GLS1 inhibition effectively eliminates CML stem cells

Purinostat Mesylate(PM)is a novel highly selective and active HDAC I/IIb inhibitor,and the injectable formulation of PM(PMF)based on the compound prescription containing cyclodextrin completely can overcome PM’s poor solubility and improves its stability and pharmacokinetic properties.Here,we showed that PM effectively repressed the survival of Ph+leukemia cells and CD34+leukemia cells from CML patients in vitro.In vivo studies demonstrated that PMF significantly prevented BCR-ABL(T315I)induced CML progression by restraining leukemia stem cells(LSCs),which are insensitive to chemotherapy and responsible for CML relapse.Mechanism studies revealed that targeting HDAC I/IIb repressed several important factors for LSCs survival including c-Myc,β-Catenin,E2f,Ezh2,Alox5,and mTOR,as well as interrupted some critical biologic processes.Additionally,PMF increased glutamate metabolism in LSCs by increasing GLS1.The combination of PMF and glutaminase inhibitor BPTES synergistically eradicated LSCs by altering multiple key proteins and signaling pathways which are critical for LSC survival and self-renewal.Overall,our findings represent a new therapeutic strategy for eliminating LSCs by targeting HDAC I/IIb and glutaminolysis,which potentially provides a guidance for PMF clinical trials in the future for TKI resistance CML patients.

Design, Synthesis and Biological Evaluation of Novel Selective Thiol-based Histone Deacetylase（HDAC） Ⅵ Inhibitors Bearing Indeno[1,2-c]pyrazole or Benzoindazole Scaffold

A series of thiol-based mdeno[1,2-c]pyrazoles and benzoindazole compounds was designed and synthesized according to the structural specificity of his-tone deacetylase VI（HDAC6） and the structural characteristics of HDAC inhibitors. The inhibitory activities of the target compounds against HDAC6 and HDAC1 were screened by fluorescence analysis. Most of the target compounds showed moderate inhibitory activity against HDAC6（IC50=44-598 nmol/L）. Among them, compound A-4 displayed the highest selectivity against HDAC6 and similar inhibitory activity（IC50=44 nmol/L） to that of the positive drug SAHA（IC50=41 nmol/L） against HDAC6.

Valproic Acid,a Drug with Multiple Molecular Targets Related to Its Potential Neuroprotective Action

Valproic acid (VA) is used worldwide as an antiepileptic drug and a mood stabilizer. Recently, VA was shown to act on cell growth, differentiation and apoptosis, by regulating gene expression at the molecular level, through epigenetic mechanisms. Thus, VA was demonstrated to act on the chromatin remodeling what is a consequence of the drug inhibition of histone deacetylases (HDACs) activity. Other studies uncovered the potential of VA to interfere with multiple regulatory mechanisms besides HDACs, as the GSK3 alpha and beta, Akt, ERK and phosphoinositol pathways, tricarboxylic acid cycle, GABA and OXPHOS system. The review focuses on the mechanisms of action of VA, showing that HDAC inhibitors, as VA, can be successfully used in the treatment of neurodegenerative disorders. This molecule, whose biological activities range from interactions with receptors and ion channels to the regulation of many catalytic reactions, has a central role in cellular cascades that regulate gene expression. Thus, inhibitors of HDACs, by positively affecting both neuronal degeneration and cognitive deficits, appear as promising drugs against various pathological conditions and neurodegenerative diseases. VA is known to present anti-inflammatory and antioxidative properties. And, since inflammation and oxidative stress are common links in neurodegeneration, VA is a drug that, from a clinical point of view, shows a great potential as a candidate for the treatment of neurodegenerative diseases related to excitotoxic events.

Histone deacetylases and their inhibitors:molecular mechanisms and therapeutic implications in diabetes mellitus

Epigenetic mechanisms such as DNA methylation,histone modification and microRNA changes have been shown to be important for the regulation of cellular functions.Among them,histone deacetylases(HDACs)are enzymes that balance the acetylation activities of histone acetyltransferases in chromatin remodeling and play essential roles in gene transcription to regulate cell proliferation,migration and death.Recent studies indicate that HDACs are promising drug targets for a wide range of diseases including cancer,neurodegenerative and psychiatric disorders,cardiovascular dysfunction,autoimmunity and diabetes mellitus.This review highlights the role of HDACs in diabetes mellitus and outlines several important cellular and molecular mechanisms by which HDACs regulate glucose homeostasis and can be targeted for the treatment of dia betic microvascular complications.It is hoped that our understanding of the role of HDACs in diabetes.mellitus will lead to the development of better diagnostic tools and the design of more potent and specific drugs targeting selective HDAC proteins for the treatment of the disease.

HDAC4 inhibits the transcriptional activation of mda-7/IL-24 induced by Sp1

Melanoma differentiation-associated gene/interleukin-24(mda-7/IL-24)is a cytokine that can activate monocytes and T helper 2 cells.The expression of mda-7/IL-24 gradually fades with the progression of melanoma,and it is undetectable at the metastatic stage.Ectopic expression of mda-7/IL-24 selectively suppresses growth and induces apoptosis in cancer cells with little harm to normal cells.However,the transcriptional regulation of the mda-7/IL-24 gene has not been extensively studied.In this study,we show that the expression of mda-7/IL-24 was upregulated by the histone deacetylase(HDAC)inhibitors trichostatin A(TSA)and sodium butyrate(NaBu),whereas it was downregulated by HDAC4.We also found that the histone acetylation level and the binding of the transcriptional factor Sp1 to the mad-7 promoter were reduced upon HDAC4 treatment.Moreover,the HDAC inhibitor TSA induced histone hyperacetylation and stimulated Sp1 binding to the mda-7/IL-24 promoter,which in turn enhanced the expression of mda-7/IL-24.Therefore,we conclude that histone acetylation modification plays an important role in the regulation of mda-7/IL-24 and that the transcription factor Sp1 participates in this process.

Improvement of histone deacetylase inhibitor efficacy by SN38 through TWIST1 suppression in synovial sarcoma

Background:Synovial sarcoma(SS)is an SS18-SSX fusion gene-driven soft tissue sarcoma with mesenchymal characteristics,associated with a poor prognosis due to frequent metastasis to a distant organ,such as the lung.Histone deacetylase(HDAC)inhibitors(HDACis)are arising as potent molecular targeted drugs,as HDACi treatment disrupts the SS oncoprotein complex,which includes HDACs,in addition to general HDACi effects.To provide further molecular evidence for the advantages of HDACi treatment and its limitations due to drug resistance induced by the microenvironment in SS cells,we examined cellular responses to HDACi treatment in combination with two-dimensional(2D)and 3D culture conditions.Methods:Using several SS cell lines,biochemical and cell biological assays were performed with romidepsin,an HDAC1/2 selective inhibitor.SN38 was concomitantly used as an ameliorant drug with romidepsin treatment.Cytostasis,apoptosis induction,and MHC class I polypeptide-related sequence A/B(MICA/B)induction were monitored to evaluate the drug efficacy.In addition to the conventional 2D culture condition,spheroid culture was adopted to evaluate the influence of cell-mass microenvironment on chemoresistance.Results:By monitoring the cellular behavior with romidepsin and/or SN38 in SS cells,we observed that responsiveness is diverse in each cell line.In the apoptotic inducible cells,co-treatment with SN38 enhanced cell death.In nonapoptotic inducible cells,cytostasis and MICA/B induction were observed,and SN38 improved MICA/B induction further.As a novel efficacy of SN38,we revealed TWIST1 suppression in SS cells.In the spheroid(3D)condition,romidepsin efficacy was severely restricted in TWIST1-positive cells.We demonstrated that TWIST1 downregulation restored romidepsin efficacy even in spheroid form,and concomitant SN38 treatment along with romidepsin reproduced the reaction.Conclusions:The current study demonstrated the benefits and concerns of using HDACi for SS treatment in 2D and 3D culture conditions and provided molecular evidence that concomitant treatment with SN38 can overcome drug resistance to HDACi by suppressing TWIST1 expression.

Expression of histone deacetylase (HDAC) family members in bortezomib-refractory multiple myeloma and modulation by panobinostat

Aim:Multiple myeloma(MM)is a hematological malignancy of antibody-producing mature B cells or plasma cells.The proteasome inhibitor,bortezomib,was the first-in-class compound to be FDA approved for MM and is frequently utilized in induction therapy.However,bortezomib refractory disease is a major clinical concern,and the efficacy of the pan-histone deacetylase inhibitor(HDACi),panobinostat,in bortezomib refractory disease indicates that HDAC targeting is a viable strategy.Here,we utilized isogenic bortezomib resistant models to profile HDAC expression and define baseline and HDACi-induced expression patterns of individual HDAC family members in sensitive vs.resistant cells to better understanding the potential for targeting these enzymes.Methods:Gene expression of HDAC family members in two sets of isogenic bortezomib sensitive or resistant myeloma cell lines was examined.These cell lines were subsequently treated with HDAC inhibitors:panobinostat or vorinostat,and HDAC expression was evaluated.CRISPR/Cas9 knockdown and pharmacological inhibition of specific HDAC family members were conducted.Results:Interestingly,HDAC6 and HDAC7 were significantly upregulated and downregulated,respectively,in bortezomib-resistant cells.Panobinostat was effective at inducing cell death in these lines and modulated HDAC expression in cell lines and patient samples.Knockdown of HDAC7 inhibited cell growth while pharmacologically inhibiting HDAC6 augmented cell death by panobinostat.Conclusion:Our data revealed heterogeneous expression of individual HDACs in bortezomib sensitive vs.resistant isogenic cell lines and patient samples treated with panobinostat.Cumulatively our findings highlight distinct roles for HDAC6 and HDAC7 in regulating cell death in the context of bortezomib resistance.

HDAC inhibitor chidamide synergizes with venetoclax to inhibit the growth of diffuse large B-cell lymphoma via down-regulation of MYC, BCL2, and TP53 expression

Diffuse large B-cell lymphoma(DLBCL) is an aggressive type of non-Hodgkin’s lymphoma. A total of 10%-15% of DLBCL cases are associated with myelocytomatosis viral oncogene homolog(MYC) and/or B-cell lymphoma-2(BCL2) translocation or amplification. BCL2 inhibitors have potent anti-tumor effects in DLBCL;however, resistance can be acquired through up-regulation of alternative anti-apoptotic proteins. The histone deacetylase(HDAC) inhibitor chidamide can induce BIM expression, leading to apoptosis of lymphoma cells with good efficacy in refractory recurrent DLBCL. In this study, the synergistic mechanism of chidamide and venetoclax in DLBCL was determined through in vitro and in vivo models. We found that combination therapy significantly reduced the protein levels of MYC, TP53, and BCL2 in activated apoptotic-related pathways in DLBCL cells by increasing BIM levels and inducing cell apoptosis. Moreover, combination therapy regulated expression of multiple transcriptomes in DLBCL cells, involving apoptosis, cell cycle, phosphorylation, and other biological processes, and significantly inhibited tumor growth in DLBCL-bearing xenograft mice. Taken together, these findings verify the in vivo therapeutic potential of chidamide and venetoclax combination therapy in DLBCL, warranting pre-clinical trials for patients with DLBCL.

SAHA, an HDAC inhibitor, synergizes with tacrolimus to Prevent murine cardiac allograft rejection

Suberoylanilide hydroxamic acid （SAHA）, as a histone deacetylase （HDAC） inhibitor （HDACi）, was recently found to exhibit an immunosuppressive effect. However, whether SAHA can synergize with calcineurin inhibitors （CNIs） to inhibit allograft rejection and its underlying mechanism remain elusive. In this study, we demonstrated the synergistic effects of SAHA and non-therapeutic dose of tacrolimus （FK506） in prolonging the allograft survival in a murine cardiac transplant model. Concomitant intragraft examination revealed that allografts from SAHA-treated recipients showed significantly lower levels of IL-17 expression, and no discernable difference for IL-17 expressions was detected between SAHA- and SAHA/FK506-treated allograft as compared with allografts from FK506-treated animals. In contrast, administration of FK506 significantly suppressed interferon （IFN）-y but increased IL-IO expression as compared with that of SAHA-treated animals, and this effect was independent of SAHA. Interestingly, SAHA synergizes with FK506 to promote Foxp3 and CTLA4 expression. In vitro, SAHA reduced the proportion of Th17 cells in isolated CD4＋ T-cell population and decreased expressions of IL-17A, IL-17F, STAT3 and RORyt in these cells. Moreover, SAHA enhances suppressive function of regulatory T （Treg） cells by upregulating the expression of CTLA-4 without affecting T effector cell proliferation, and increased the proportion of Treg by selectively promoting apoptosis of T effector cells. Therefore, SAHA, a HDACi, may be a promising immunosuppressive agent with potential benefit in conjunction with CNI drugs.

Studies on the Molecular Mechanism between HDAC8 and Inhibitory in Different Bioactivities by Molecular Docking and MD Simulations

HDAC8 is an important target for the treatment of many cancers and other diseases. To develop potent and selective HDAC8 inhibitors, molecular docking and molecular dynamics(MD) simulations were employed for investigation of the mechanism of HDAC8 inhibitions containing hydroxamic acid group. Compound 1 with high activity and compound 2 with low activity were selected for comparative study. Compound 1 formed a stronger chelation with Zn ion and was more stable in the HDAC8 pocket than compound 2. Residues HIS-180, ASP-178, ASP-267, and GLY-140 played a critical role in securing the position of compound 1. Both the head and tail of compound 1 formed strong hydrogen bonds with ASP-178, facilitating the ZBG of compound 1 close to the Zn ion so that they formed permanent chelation during the simulation period. The Cap group of the compounds with branch and long chains was advantageous to form interaction with active pocket opening. What’s more, based on the results of this study, three innovative recommendations for the design of highly active HDAC8 inhibitors were presented, which will be useful for the development of new HDAC8 inhibitors.