IUPAC-induced computational approaches for identifying boosters of small biomolecule functionality: A case study of human tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors

This paper introduces several proof-of-concept (PoC) computational methods intended to offer biochemical researchers straightforward, time- and cost-effective strategies to accelerate their work. While Machine Learning (ML) models were developed, the study's central purpose was to explore approaches for the identification of desirable functional groups/fragments in small biomolecules regarding a specific functionality, which, in this case, was human tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibition. This was achieved primarily by tokenising IUPAC names to generate features. Additionally, the applicability of the CID_SID ML model for predicting TDP1 activity was developed and explored. Since these computational approaches were not experimentally validated due to a lack of appropriate laboratory facilities, they are presented as open proposals for further laboratory investigation.