Computational Approach for HDAC1 Predicting Protein-Ligand Interactions for Cancer through Homology Modelling, Virtual Screening and Molecular Docking

M. Bhargavi, Sri Gayathri Bhargavi and Esha Sripada

Chapter 2 in Convergence of Technology & Biology ─ Transforming Life Sciences, 2025, pp 8-21 from Shanlax Publications

Abstract: Histone Deacetylase 1 (HDAC1) is vital for controlling gene expression, chromatin remodelling, and biological functions like distinction and cellular proliferation by acetylation of histone tail residues. Its abnormal expression is of high significance in inflammatory diseases, cancers and allergic diseases. Thus, considering the structure and function of HDAC1 is very crucial because it may be used as a therapeutic target for cancer, neurologicalillnesses, and other disorders. In this study, the structure of HDAC1 was predicted using homology modelling. First, based on the known crystal structures of template proteins, a high-quality 3D model of HDAC1 was generated using the concepts of homology modelling by Modeller 10.6 software. The correctness and reliability of this model were enhanced using a GalaxyWEB refine tool and for energy minimization YASARA software was put to use.The model obtained after refinement and energy minimization was put for validation on the ProSA-WEB and SAVES server where the results of z-score, ERRAT, VERIFY-3D and Ramachandran plot were obtained and analysed. The analysed model was then employed to investigate the binding interactions with ligands that may inhibit HDAC1 activity, in molecular docking studies. The steps involved were performed using Schrodinger suites Maestro 13.5 included: protein preparation using protein preparation wizard, grid generation using GLIDE and virtual screening employing molecular docking using virtual screening workflow wizard. Therefore, through this study HDAC1's structure was predicted, validated and molecular docking studies were performed on it.

Date: 2025
ISBN: 978-93-6163-763-6
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