Development of potent small molecule inhibitors of protein?protein interactions with optimized druglike properties represents a challenging task in lead optimization process. Here, we report synthesis and structure-based optimization of new thienopyrimidine class of compounds, which block the protein?protein interaction between menin and MLL fusion proteins that plays an important role in acute leukemias with <
i>
MLL<
/i>
translocations. We performed simultaneous optimization of both activity and druglike properties through systematic exploration of substituents introduced to the indole ring of lead compound <
b>
1<
/b>
(MI-136) to identify compounds suitable for in vivo studies in mice. We report this work resulted in the identification of compound <
b>
27<
/b>
(MI-538), which showed significantly increased activity, selectivity, polarity, and pharmacokinetic profile over <
b>
1<
/b>
and demonstrated a pronounced effect in a mouse model of MLL leukemia. This study, which reports detailed structure?activity and structure?property relationships for the menin?MLL inhibitors, demonstrates challenges in optimizing inhibitors of protein?protein interactions for potential therapeutic applications.