4‑Chlorothienopyridine Caps Yield Potent, Selective HDAC Inhibitors — Preclinical Report

Investigators report a series of hydroxamic-acid HDAC inhibitors built around substituted 4-chlorothieno[2,3-b]pyridine cap groups, spanning series 6a–c and 7a–c (aliphatic linkers) and 9a–c (cinnamic linkers). Each combines a cap, spacer, and hydroxamic acid zinc-binding motif in the final compounds described as 4-chlorothieno[2,3-b]pyridine-capped HDAC inhibitors. In enzymatic assays, the authors highlight compound 7a as their most potent tested example, reporting IC50 values of 0.37 µM against HDAC1, 0.58 µM against HDAC4, and 0.70 µM against HDAC6. The study also reports cellular screening, selectivity testing versus PBMCs, docking-based binding hypotheses, and in silico ADMET predictions summarized alongside reference compounds.

Across HDAC1, HDAC4, and HDAC6, the authors describe most screened compounds as showing single-digit micromolar inhibition, with 7a distinguished by submicromolar activity against each of the three enzymes tested. Trichostatin A was used as a positive control in the fluorogenic assay setup. For 7a, the reported isoform pattern showed HDAC1 as the lowest IC50, followed by HDAC4 and then HDAC6, based on the values presented. The authors use this enzymatic profile to frame the subsequent cellular and modeling analyses.

In the NCI-60 five-dose dataset, the authors summarize mean antiproliferative activity by reporting a mean GI50 of 2.15 µM for 7a and 1.89 µM for 9a (reported as 1.88 µM elsewhere in the manuscript), and they state that 9a had the lowest mean GI50 across the 60-cell-line panel in their tested set. In specific comparisons to SAHA described in the results tables and supplementary data for NCI-60 GI50 screening, the authors note examples where 7a or 9a/9b exceeded SAHA’s potency, including RPMI-8226 leukemia cells and the HCT-15 colon cancer line. Together, the panel-level summary and these named comparisons position 7a and 9a among the lead antiproliferative performers highlighted in the report.

To examine activity in a non-malignant cell context, the authors evaluated 7a in peripheral blood mononuclear cells using an MTT assay and report an IC50 of 15.03 µM on PBMCs. Using their RPMI-8226 readout as the comparator, they calculate a selectivity index of about 11 for RPMI-8226 cells over PBMCs. The paper presents this selectivity index as a quantitative adjunct to the NCI-60 screening narrative, without extending the calculation beyond the reported in vitro comparison. These biological readouts are then discussed alongside structural considerations and in silico analyses later in the manuscript.

For modeling, the authors report MOE-based docking of the final hydroxamic acids into the HDLP active site (PDB: 1ZZ1), describing a docking score range from −8.97 to −9.73 kJ/mol for the final compounds and noting that this range exceeded the reference docking scores they report for SAHA and panobinostat. In their interaction descriptions, they highlight contacts involving residues such as Gly151 and Cys153, as well as hydrophobic or other interactions described for residues including Phe208, His182, and Cys267, depending on the compound discussed. Alongside docking, SwissADME summaries in the paper report high predicted gastrointestinal absorption and no predicted blood–brain barrier penetration for the final compounds. The authors also report that ADMET prediction tools indicated 7a and 9b may have more favorable predicted pharmacokinetic properties than SAHA.

Key Takeaways:

• In the reported HDAC assay, 7a showed IC50 values of 0.37 µM (HDAC1), 0.58 µM (HDAC4), and 0.70 µM (HDAC6).
• In NCI-60 analyses, the reported mean GI50 pattern placed 9a (and 7a) among the strongest panel-wide antiproliferative performers described.
• SwissADME summaries reported high predicted GI absorption, no predicted BBB penetration, and a comparative note that 7a and 9b were flagged as more favorable than SAHA on the predicted pharmacokinetic properties reported.