In silico identification of 2-oxo-1,3-thiazolidine derivatives as novel inhibitor candidate of class II histone deacetylase (HDAC) in cervical cancer treatment

Abstract

Cervical cancer ranks third among the most prevalent deadly cancer in women worldwide and ranks first in developing countries. It is caused by human papilloma virus (HPV) infection. Thus HDACs have become prominent inhibition target for cervical cancer treatment. In order to discover the new alternative HDAC inhibitors (HDACIs), we conducted a computer-aided drug discovery and development (CADDD) based on de novo approach. The compound library is based on 4-[(2-oxo-1,3-thiazolidin-3-yl)carbonyl] aniline. Screening of the best drug leads was evaluated from several parameters, such as docking and interaction analysis, pharmacology, in silico preclinical trial and molecular dynamics analysis. The inhibitory activity of these new designed ligands against Homo sapiens class II HDAC was determined by molecular docking simulation. Docking analysis yielded eight best ligands which have better binding affinity than the standards. Therefore, interaction analysis indicated that all best ligands performed coordination with Zn2+ cofactor in HDAC charge-relay system which are essential for HDAC inhibitory activities of these inhibitors. Pharmacology analysis and preclinical trials of these compounds including pharmacology properties, bioactivity, mutagenicity–carcinogenicity, absorption, distribution, metabolism, excretion and toxicity (ADMET) properties were done through in silico methods. Through this analysis, the best ligands meet Lipinski's rule of five, have a better drug score than standards, and show good bioactivities, oral bioavailability and ADMET properties. All best ligands also have good synthetic accessibility and were proved to be new compounds that have never been synthesized before. Stability of HDAC–ligand complexes was also calculated through molecular dynamics (MD) simulation. Based on this simulation, complex of the best ligands with corresponding HDAC has a good stability based on RMSD (root mean square deviation) and interaction analysis. The study thus reveals eight best ligands (F, Ib14, O38, Kb17, Gd40, Aa50, Gc42 and Bb38) which have better binding affinity against human class II histone deacetylase (HDAC) through molecular docking, dynamics and interaction analysis. The best ligands were also found to have good bioactivities, oral bioavailability and ADMET properties through in silico pharmacology analysis and preclinical trial. These compounds were found to have a good synthetic accessibility; therefore they could be synthesized for further biological and clinical test.