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ACS Medicinal Chemistry Letters
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Discovery of 3-Quinazolin-4(3H)-on-3-yl-2,N-dimethylpropanamides as
Orally Active and Selective PI3Kα Inhibitors
Jiaqiang Dong1, Jingjie Huang2*, Ji Zhou2, Ye Tan2, Jing Jin3, Xi Tan3, Bei Wang4, Tao Yu2, Chengde
Wu2, Shuhui Chen2, and Tie-Lin Wang1*
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1Luoxin Pharmaceutical (Shanghai) Co., Ltd., Building 1 and 1st-3rd Floors, Building 2, No.85 Faladi Road, China (Shanghai) Pilot Free
Trade Zone, Shanghai, 201203, China
2Domestic Discovery Service Unit, WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai
200131, China
3LTD, WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
4OIU, WuXi AppTec Co., Ltd., 1336 Wuzhong Avenue, Suzhou, 215104, China
ABSTRACT: PI3K kinases mediate a series of events related to cell growth, proliferation, survival and differentiation.
Overexpression of PI3Ks can lead to the dysregulation of cell homeostasis and cause tumorigenesis. In this study, rationally
designed compounds were investigated as PI3Kα selective inhibitors. Our efforts culminated to the discovery of a series of
quinazolin-4(3H)-one derivatives with 2-substitued-N-methylpropanamide substitutions as PI3Kα selective inhibitors. The best
compound, 10 has PI3Kα enzymatic and cellular IC50 of 1.8 and 12.1 nM. It has biochemical selectivity over PI3Kβ/δ/γ of
150/7.72/7.67 fold and cellular selectivity of 115/15.1/>826 fold, respectively. Compound 10 is 59% orally bioavailable with dose
normalized AUC of 3090 nM. These effects translated into in vivo, as 10 significantly time- and dose-dependently inhibited
phosphorylation of Akt in BT-474 subcutaneous xenograft mice and inhibited tumor growth.
KEYWORDS PI3Kα inhibitor, breast cancer, PIK3CA mutant, structure-based design, DMPK, PD study
The phosphatidylinositol 3-kinase (PI3K)/mammalian target
of rapamycin (mTOR) signaling pathway plays a key role in a
series of cellular functions related to cell growth, proliferation,
survival and differentiation1. PI3Ks are a class of lipid kinases
that catalyze the phosphorylation of phosphoinositides at the
3-hydroxyl position. PI3Ks are divided into three classes (I, II
and III) based on substrate specificity, sequence homology,
and structural features2. Class I PI3Ks are heterodimer formed
by a regulatory and a catalytic (p110) subunit, including
PI3Kα, PI3Kβ, PI3Kδ and PI3Kγ3.
The clinical development of pan-PI3K and dual
PI3K/mTOR inhibitors has been limited by off-target
toxicities such as GI toxicities, hepatotoxicity, and mood
alterations. Such toxicities have limited the dose escalation4.
Isoform specific inhibitors could allow administration at
higher, pharmacologically active doses, with fewer off-target
toxicities5.
Based on published binding interactions between PI3Kα
ATP binding pocket and small molecule such as BYL-71917,
residue Gln859 is unique for PI3Kα isoform and contributes to
its selectivity against other PI3K isoforms. The hydrogen bond
formation of PI3Kα selective inhibitors with Gln859 is
essential to selectivity. Our starting point came from the
design and synthesis of compound 1 through the hybridization
between our previously reported pyrido[1,2-a]pyrimidin
scaffold18 and L-prolinamide as seen in BYL-719, which was
essential to the selectivity (Figure 1). To our delight,
compound 1 showed very good PI3Kα activity in a
biochemical assay (IC50 = 0.5 nM) and the selectivity over
PI3Kβ/δ/γ was 130/3.4/7.4 fold, respectively. However, it
demonstrated modest cellular potency (IC50 = 188.0 nM in
MCF-7 cell, Table 1), which might be due to poor
permeability (A to B: 0.45*10-6cm/s, MDCK assay), and it
was speculated relating to high polar surface area19.
One of the most attracted isoforms is the PI3Kα subtype. It
is ubiquitously expressed, and associates with angiogenesis
and glucose homeostasis6. PI3K/mTOR pathway is frequently
dysregulated in cancers, often because of activating mutations
or amplification of PIK3CA. Gain of function mutations in
PIK3CA, the gene encoding the p110α catalytic subunit of
PI3K, are among the most common somatic alterations in solid
tumors7,8, such as 42% to 55% of endometrial9, 42% of
cervical10, 27%-36% of breast11,12, 18% of colorectal13, 13% of
head and neck14, and 12% of ovarian cancers15. BYL-719 is
the first and only PI3Kα inhibitor that was approved by FDA
in May, 2019 for the treatment of PIK3CA mutant HER2-
/ER+ metastasis advanced breast cancer16.
We envisioned that reducing polarity of 1 might improve its
cellular potency. With compound 1 as template, scaffold
hopping together20,21 with modification on L-prolinamide were
conducted and led to the generation of compound 2 (Figure
1). As shown in Table 1, although the biochemical potency
was maintained, the selectivity over PI3Kβ decreased
significantly (30 vs 130). The linker between hinge binding
region motif and solvent access region motif of 2 was too
flexible, which was unfavorable to the conformation needed to
form hydrogen bonds interactions with Gln859 in PI3Kα. Next,
different side chains which could help restrict conformation
were introduced to the linker to explore the optimal
conformation, such as methyl, germinal difluoro, amine, ethyl,
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