Histone deacetylases (HDACs) are essential epigenetic regulators, with HDAC6 overexpression linked to estrogen receptor (ER) activity and breast cancer progression. While several HDAC6 inhibitors have been investigated, their clinical success remains limited due to toxicity and off-target effects, necessitating the discovery of novel, selective inhibitors. This study employs a multi-stage computational approach to identify potent HDAC6 inhibitors for breast cancer therapy. A large-scale virtual screening of 264 834 compounds was conducted, followed by molecular docking, molecular dynamics (MD) simulations (100 ns), molecular mechanics/generalized born surface area (MM/GBSA) binding free energy calculations, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) predictions. The HDI-3 emerged as the most promising candidate among replicate simulations, exhibiting a substantially favorable MM/GBSA binding free energy of −130.67 kcal/mol—indicative of strong thermodynamic stability and stronger binding affinity compared to reference inhibitors Trichostatin A and Ricolinostat. Molecular dynamics simulations revealed that HDI-3 maintained structural stability, persistent key interactions with active site residues (ASP649, HIS651, ASP742), and low conformational fluctuations. The ADMET evaluation confirmed HDI-3’s favorable pharmacokinetic properties, including optimal bioavailability, non-mutagenicity, and low hepatotoxicity. Essential dynamics and principal component analysis further validated its stable binding profile. While these findings highlight HDI-3 as a selective and pharmacologically viable HDAC6 inhibitor, it is important to acknowledge that the results are entirely computational. Therefore, experimental validation is essential to confirm the compound’s efficacy and safety. This integrated computational pipeline provides an efficient strategy to accelerate targeted drug discovery, laying the groundwork for future experimental investigations.

2025-07-24·JOURNAL OF MEDICINAL CHEMISTRY

Discovery of TNI-97 as a Highly Selective, Orally Bioavailable HDAC6 Inhibitor for the Treatment of Triple-Negative Breast Cancer

Article

作者: Yu, Xintian ; Cui, Yifei ; Qin, Han ; Liu, Dan ; Zhao, Linxiang ; Wei, Leyan ; Luo, Meidi ; Sha, Jinyu ; Xu, Qihao ; Guo, Rongxian ; Wang, Siyuan ; Wen, Jiachen ; Li, Bo ; Bai, Changjun ; Shao, Shanshan ; Sun, Pinghua ; Zhang, Wenchao

Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by limited treatment options. PANoptosis, a newly identified programmed cell death pathway, offers therapeutic strategies for TNBC. ACY-1215 has demonstrated preliminary efficacy in patients with TNBC and HR⁺/HER2^- metastatic breast cancer. However, its moderate target engagement and suboptimal selectivity may limit its clinical efficacy. In this study, a series of potent HDAC6-selective inhibitors bearing a 5-pyrazolyl-benzotriazole scaffold has been developed. Compound TNI-97 demonstrated potent HDAC6 inhibitory activity and great isoform selectivity. TNI-97 elicited PANoptotic cell death in MDA-MB-453 cell models in vitro and in vivo. TNI-97 exhibited a TGI of 91% in MDA-MB-453 CDX as monotherapy and a TGI of 92% in 4T1 CDA when combined with paclitaxel. The discovery of TNI-97 holds promise for the development of more potent HDAC6 inhibitors as PANoptotic inducers and TNBC drug candidates.

2025-06-01·BIOORGANIC CHEMISTRY

Discovery of novel selective HDAC6 inhibitors via a scaffold hopping approach for the treatment of idiopathic pulmonary fibrosis (IPF) in vitro and in vivo

Article

作者: Ma, Chao ; Zhou, Xinru ; Guo, Yuxi ; Ma, Enlong ; Xu, Yongnan ; Zhao, Xianchen ; Quan, Jishun ; Qu, Wenhui

Idiopathic pulmonary fibrosis (IPF) is a progressive, irreversible, and fatal pulmonary disease. Owing to its complex pathogenesis and lack of effective treatment, patients have a short survival time after diagnosis. Although pirfenidone and nintedanib can mitigate declines in lung function, neither has stopped the progression of IPF nor significantly improved long-term survival in patients. HDAC6 inhibitors have been reported to inhibit TGF-β1-induced collagen expression to protect mice from pulmonary fibrosis, and this pharmacological mechanism has been supported by immunohistochemical studies of HDAC6 overexpression in IPF lung tissue. In this study, a series of novel derivatives were obtained based on the reported active compounds through the ring closure strategy in scaffold hopping theory. Compound W28 was selected from in vitro screening for better HDAC6 selectivity, and it was used for in-depth pharmacokinetic and pharmacodynamic studies. Detailed molecular docking studies, molecular dynamics (MD) simulations and the structure-activity relationship (SAR) discussion will contribute to guiding the design of new molecules. In further studies, the ability of W28 to inhibit the IPF phenotype was confirmed, and the corresponding pharmacological mechanism was also demonstrated. Moreover, the pharmacokinetic characteristics of W28 were also tested to guide pharmacodynamic studies in vivo, and the therapeutic effect of W28 on bleomycin-induced pulmonary fibrosis in mice was found to be satisfactory. The results reported in this paper may provide a reference for promoting the discovery of new selective HDAC6 inhibitors as drug molecules for the treatment of IPF.

100 项与 HDAC6 inhibitors(Anhui Medical University/China Pharmaceutical University) 相关的药物交易

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