Proteochemometric Modeling of the Origin of Thymidylate Synthase Inhibition

Abstract

Due to its crucial role in DNA synthesis, thymidylate synthase (TS) has been considered as a potential therapeutic target. Inhibition of the enzyme is a promising strategy for the treatment of some hyper-proliferative diseases, including infections. Since TS species-specific inhibitors would be able to distinguish between the host and the pathogens, developing highly selective inhibitors is of great clinical importance. TS is among the most highly conserved enzymes over evolutionary history, making the design of its species-selective inhibitor significantly challenging. The chemical interaction space, governed by a set of non-selective TS inhibitors, has been explored for human TS and its homologous proteins in both T. gondii and E. coli using proteochemometrics modeling (PCM). Validity, robustness and prediction power of the PCM model have been assessed applying a diverse set of internal/external validation approaches. Our PCM model has provided major structural information, which is indeed of great help to design new TS species-specific inhibitors with the simultaneous inhibition ability towards both T. gondii and E. coli. To show applicability of the PCM model, new compounds have been designed based on structural information provided by the constructed model. Final results have been very promising with regard to selectivity ratios of the designed compounds for different TS isoforms, confirming the applicability of the PCM model.

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Proteochemometrics analysis has shed a light on major structural features, suggesting that implementation of specific dual moieties such as HBD/HBA in certain distances can affect the selectivity of a compound for different isoforms of thymidylate synthase.

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