Computer-driven development of an in silico tool for finding selective histone deacetylase 1 inhibitors

Hajar Sirous (Lead / Corresponding author), Giuseppe Campiani, Simone Brogi, Vincenzo Calderone, Giulia Chemi

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)
55 Downloads (Pure)


Histone deacetylases (HDACs) are a class of epigenetic modulators overexpressed in numerous types of cancers. Consequently, HDAC inhibitors (HDACIs) have emerged as promising antineoplastic agents. Unfortunately, the most developed HDACIs suffer from poor selectivity towards a specific isoform, limiting their clinical applicability. Among the isoforms, HDAC1 represents a crucial target for designing selective HDACIs, being aberrantly expressed in several malignancies. Accordingly, the development of a predictive in silico tool employing a large set of HDACIs (aminophenylbenzamide derivatives) is herein presented for the first time. Software Phase was used to derive a 3D-QSAR model, employing as alignment rule a common-features pharmacophore built on 20 highly active/selective HDAC1 inhibitors. The 3D-QSAR model was generated using 370 benzamide-based HDACIs, which yielded an excellent correlation coefficient value (R2 = 0.958) and a satisfactory predictive power (Q2 = 0.822; Q2 F3 = 0.894). The model was validated (r2 ext_ts = 0.794) using an external test set (113 compounds not used for generating the model), and by employing a decoys set and the receiver-operating characteristic (ROC) curve analysis, evaluating the Güner–Henry score (GH) and the enrichment factor (EF). The results confirmed a satisfactory predictive power of the 3D-QSAR model. This latter represents a useful filtering tool for screening large chemical databases, finding novel derivatives with improved HDAC1 inhibitory activity.

Original languageEnglish
Article number1952
Pages (from-to)1-20
Number of pages20
Issue number8
Publication statusPublished - 22 Apr 2020


  • 3D-QSAR
  • Aminophenylbenzamide
  • HDACs
  • Isoform-selective histone deacetylase inhibitors
  • Ligand-based model
  • Pharmacophore modeling

ASJC Scopus subject areas

  • Analytical Chemistry
  • Chemistry (miscellaneous)
  • Molecular Medicine
  • Pharmaceutical Science
  • Drug Discovery
  • Physical and Theoretical Chemistry
  • Organic Chemistry


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