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Data-Driven and Structure-Based Modelling for the Discovery of Human DNMT1 Inhibitors: A Pathway to Structure–Activity Relationships

Paris Christodoulou,Ellie Chytiri,M. Zervou,Igor Manushin,Charalampos Kolvatzis,V. Sinanoglou,Dionisis Cavouras,E. Kritsi

Published 2025 in Applied Sciences

ABSTRACT

Nowadays, the explosive growth of knowledge in the epigenetics field has highlighted DNA methyltransferase 1 (DNMT1) as a key regulator of genomic methylation patterns and a promising therapeutic target in several diseases. In light of the increasing clinical interest in epigenetic enzymes, the present study aimed to develop a robust computational framework for the discovery of novel DNMT1 inhibitors, merging both structure and data-driven strategies. Particularly, the study compiled a dataset of established DNMT1 inhibitors and calculated a series of molecular properties, thus enabling the training of a machine learning model to capture critical structure–activity relationships (SARs). When benchmarked against known active compounds, the model effectively discriminated between putative inhibitors and non-inhibitors with high accuracy. In parallel, molecular docking was conducted to screen additional uncharacterized compounds, estimating their binding affinity to human DNMT1. Their respective properties were then extracted and fed into the aforementioned model to predict their inhibitory potential. Our comparative evaluation against known human DNMT1 inhibitors demonstrated high predictive accuracy, confirming the reliability of the proposed integrated approach. By uniting molecular docking with data-driven SAR modelling, this workflow offers an expedited fast-track avenue for identifying promising human DNMT1 inhibitors while reducing experimental overhead. The results highlight the effectiveness of combining cheminformatics, machine learning, and in silico techniques to guide rational drug design, and accelerate the discovery of novel epigenetic inhibitors.

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