# Repositioning HDAC Inhibitors for Glioma Treatment: Synthesis and Biological Evaluation

**Authors:** Luciana Costa Furtado, Karoline de Barros Waitman, Nuno A. T. F. Silva, Leticia Marcelino Gouvea, Thales Kronenberger, Mônica Franco Zannini Junqueira Toledo, Elthon Gois Ferreira, João Agostinho Machado-Neto, Frank A. E. Kruyt, Roberto Parise Filho, Letícia V. Costa-Lotufo

PMC · DOI: 10.1021/acsomega.5c11083 · ACS Omega · 2026-02-03

## TL;DR

This study explores new HDAC inhibitors as potential treatments for gliomas, showing promising anti-cancer effects in laboratory tests.

## Contribution

The paper introduces novel hydroxamate- and benzamide-based HDAC inhibitors with selective enzyme inhibition and favorable drug profiles for glioma therapy.

## Key findings

- Compound 3a and 6a induced cell cycle arrest and apoptosis in glioma cells.
- Compound 6a showed higher potency in glioblastoma stem cells.
- Molecular simulations confirmed selective HDAC inhibition and favorable pharmacokinetics.

## Abstract

Gliomas are a type of brain tumor associated with poor
patient
prognosis, with current treatment, surgical resection when feasible,
followed by radiotherapy and chemotherapy (Temozolomide), yielding
a median survival of approximately 15 months. In light of the urgent
need for more effective therapies, histone deacetylases (HDACs) have
emerged as promising targets, given their differential expression
across tumor types and disease grades. Although HDAC inhibitors are
well established in the treatment of hematological malignancies, their
potential is now being explored in solid tumors, including glioblastoma
(GBM). In this study, hydroxamate-based (3a) and benzamide-based
(6a) HDAC inhibitors were synthesized and evaluated in
glioma cell lines and glioblastoma stem cells (GSC). Treatment with
these inhibitors resulted in cell cycle alterations, increased SubG1
populations, and enhanced apoptosis, particularly with compound 3a. Notably, 6a demonstrated greater potency
in GSCs. The observed cytotoxic effects were linked to selective inhibition
of HDAC6 by 3a and HDAC1/3 by 6a, as confirmed
through enzymatic assays and further supported by molecular docking
and molecular dynamics (MD) simulations. In silico analyses suggest that both compounds possess favorable pharmacokinetic
profiles, underscoring their potential as promising candidates for
glioma therapy and paving the way for future drug development in this
field.

## Linked entities

- **Proteins:** HDAC6 (histone deacetylase 6), HDAC1 (histone deacetylase 1), HDAC3 (histone deacetylase 3)
- **Chemicals:** Temozolomide (PubChem CID 5394), 3a (PubChem CID 5283820), 6a (PubChem CID 522079)
- **Diseases:** glioma (MONDO:0021042), glioblastoma (MONDO:0018177)

## Full-text entities

- **Genes:** CCND1 (cyclin D1) [NCBI Gene 595] {aka BCL1, D11S287E, PRAD1, U21B31}, IDH1 (isocitrate dehydrogenase (NADP(+)) 1) [NCBI Gene 3417] {aka HEL-216, HEL-S-26, IDCD, IDH, IDP, IDPC}, HDAC4 (histone deacetylase 4) [NCBI Gene 9759] {aka AHO3, BDMR, HA6116, HD4, HDAC-4, HDAC-A}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, HDAC2 (histone deacetylase 2) [NCBI Gene 3066] {aka HD2, KDAC2, RPD3, YAF1}, TUBA1B (tubulin alpha 1b) [NCBI Gene 10376] {aka K-ALPHA-1}, HDAC3 (histone deacetylase 3) [NCBI Gene 8841] {aka HD3, KDAC3, RPD3, RPD3-2}, HDAC6 (histone deacetylase 6) [NCBI Gene 10013] {aka CPBHM, HD6, JM21, KDAC6, PPP1R90}, CDKN1A (cyclin dependent kinase inhibitor 1A) [NCBI Gene 1026] {aka CAP20, CDKN1, CIP1, MDA-6, P21, SDI1}, HDAC1 (histone deacetylase 1) [NCBI Gene 3065] {aka GON-10, HD1, KDAC1, RPD3, RPD3L1}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, HDAC8 (histone deacetylase 8) [NCBI Gene 55869] {aka CDA07, CDLS5, HD8, HDACL1, KDAC8, MRXS6}, ANXA5 (annexin A5) [NCBI Gene 308] {aka ANX5, CPB-I, ENX2, HEL-S-7, PP4, RPRGL3}, POTEF (POTE ankyrin domain family member F) [NCBI Gene 728378] {aka A26C1B, POTE2alpha, POTEACTIN}, BHLHE41 (basic helix-loop-helix family member e41) [NCBI Gene 79365] {aka BHLHB3, DEC2, FNSS1, SHARP1, hDEC2}, APC (APC regulator of Wnt signaling pathway) [NCBI Gene 324] {aka BTPS2, DESMD, DP2, DP2.5, DP3, GS}, HDAC10 (histone deacetylase 10) [NCBI Gene 83933] {aka HD10}, RNASE1 (ribonuclease A family member 1, pancreatic) [NCBI Gene 6035] {aka RAC1, RIB1, RNS1}
- **Diseases:** necrosis (MESH:D009336), GBM (MESH:D005909), brain cancer (MESH:D001932), breast cancer (MESH:D001943), Cytotoxic (MESH:D064420), cardiotoxic (MESH:D066126), hematological malignancies (MESH:D019337), oligodendroglioma (MESH:D009837), neuropsychiatric disorders (MESH:D001523), cancer (MESH:D009369), neurodegenerative (MESH:D019636), Glioma (MESH:D005910)
- **Chemicals:** NAD+ (MESH:D009243), NaHSO3 (MESH:C569244), KCl (MESH:D011189), H (MESH:D006859), Benzamide (MESH:C037689), DMSO (MESH:D004121), EDC (MESH:C024565), ninhydrin (MESH:D009555), SRB (MESH:C022027), triazoles (MESH:D014230), 3-amino-1,2,4-triazole (MESH:D000640), Glutamine (MESH:D005973), CO2 (MESH:D002245), Na4P2O7 (MESH:C107241), THF (MESH:C018674), Na2CO3 (MESH:C005686), iodine (MESH:D007455), KOH (MESH:C029943), NH2OH (MESH:D019811), Tris (MESH:D014325), aspartate (MESH:D001224), 1,2,4-triazoles (MESH:C045575), amino acids (MESH:D000596), MTT (MESH:C070243), MgSO4 (MESH:D008278), Temozolomide (MESH:D000077204), TFA (MESH:D014269), 1,2-diaminobenzene (MESH:C034193), trichloroacetic acid (MESH:D014238), propidium iodide (MESH:D011419), 4-(Phenylsulfonamido)-N-(4H-1,2,4-triazol-3-yl)benzamide (-), 2H (MESH:D003903), hexane (MESH:D006586), Na+ (MESH:D012964), Penicillin (MESH:D010406), Ac)-AMC (MESH:C042319), SAHA (MESH:D000077337), methyl 4-aminobenzoate (MESH:C067182), Salicylic aldehyde (MESH:C013243), TSA (MESH:C481298), HCl (MESH:D006851), acetic (MESH:D019342), SDS (MESH:D012967), brine (MESH:C017082), EtOH (MESH:D000431), b (MESH:D001895), salicyl acyl-hydrazones (MESH:C000613208), 13C (MESH:C000615229), NaOH (MESH:D012972), glycine (MESH:D005998), H2O (MESH:D014867), amides (MESH:D000577), panobinostat (MESH:D000077767), benzenesulfonyl chloride (MESH:C010544), NaF (MESH:D012969), Trichostatin A (MESH:C012589), carboxylic acid (MESH:D002264), Sulfonamides (MESH:D013449), histidine (MESH:D006639), bromocresol green (MESH:D001961)
- **Species:** Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932]
- **Cell lines:** GSC23 — Homo sapiens (Human), Glioblastoma, Cancer cell line (CVCL_DR59), MES — Cricetulus griseus (Chinese hamster), Hamster chondrosarcoma, Cancer cell line (CVCL_JX17), T98G — Homo sapiens (Human), Glioblastoma, Cancer cell line (CVCL_0556), U251 — Homo sapiens (Human), Astrocytoma, Cancer cell line (CVCL_0021), U87MG — Homo sapiens (Human), Glioblastoma, Cancer cell line (CVCL_0022), HOG — Homo sapiens (Human), Oligodendroglioma, Cancer cell line (CVCL_D354), Caco-2 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0025), GG16 — Homo sapiens (Human), Ovarian serous cystadenocarcinoma, Cancer cell line (CVCL_A1IB), Sf9 — Spodoptera frugiperda (Fall armyworm), Spontaneously immortalized cell line (CVCL_0549), S2 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z232)

## Full text

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## Figures

10 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12917657/full.md

## References

81 references — full list in the complete paper: https://tomesphere.com/paper/PMC12917657/full.md

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Source: https://tomesphere.com/paper/PMC12917657