The contribution of physicochemical properties to multiple in vitro cytotoxicity endpoints

Attrition due to safety reasons remains a serious problem for the pharmaceutical industry. This has prompted efforts to develop early predictive in vitro screens that can assist in selecting compounds with a more desirable safety profile early on in the drug discovery process. Here we examined the relationship between physicochemical properties, such as partition coefficient (clogP), topological polar surface area (TPSA), acid dissociation constant (pKa), and in vitro mechanistic endpoints generated using a high content imaging approach. We demonstrate in our initial analysis that compounds with clogP > 2 and pKa > 5.5 flagged more endpoints than compounds with clogP ⩽ 2 and pKa ⩽ 5.5. In contrast, TPSA did not stand on its own in predicting cytotoxicity. When this knowledge was applied to eight different mechanistic cytotoxicity endpoints (cell loss, apoptosis, ER stress, DNA fragmentation, mitochondrial potential, nuclear size, neutral lipids/steatosis and lysosomal mass), we found that compounds with such properties preferentially flagged in the lysosomal endpoint. We also saw a slight enrichment of such compounds in the endpoints cell loss, DNA fragmentation and nuclear size. We demonstrate that lysosomal compound accumulation is a potential contributor to cell death and possibly organ toxicity.

► Large scale evaluation of physicochemical properties and eight mechanistic endpoints. ► Compounds with clogP > 2 and pKa > 5.5 flagged more endpoints. ► TPSA did not stand on its own in predicting cytotoxicity. ► Compounds with such properties preferentially flagged the lysosomal endpoint.