Discovery of a Brain-Penetrant ATP-Competitive Inhibitor of the Mechanistic Target of Rapamycin (mTOR) for CNS Disorders

Abstract

Recent clinical evaluation of everolimus for seizure reduction in patients with tuberous sclerosis complex (TSC), a disease with overactivated mechanistic target of rapamycin (mTOR) signaling, has demonstrated the therapeutic value of mTOR inhibitors for central nervous system (CNS) indications. Given that everolimus is an incomplete inhibitor of the mTOR function, we sought to develop a new mTOR inhibitor that has improved properties and is suitable for CNS disorders. Starting from an in-house purine-based compound, optimization of the physicochemical properties of a thiazolopyrimidine series led to the discovery of the small molecule 7, a potent and selective brain-penetrant ATP-competitive mTOR inhibitor. In neuronal cell-based models of mTOR hyperactivity, 7 corrected the mTOR pathway activity and the resulting neuronal overgrowth phenotype. The new mTOR inhibitor 7 showed good brain exposure and significantly improved the survival rate of mice with neuronal-specific ablation of the Tsc1 gene. These results demonstrate the potential utility of this tool compound to test therapeutic hypotheses that depend on mTOR hyperactivity in the CNS.

Second-generation tricyclic pyrimido-pyrrolo-oxazine mTOR inhibitor with predicted blood–brain barrier permeability

“…The (R)-3-methylmorpholine has been previously reported as a crucial feature to achieve selectivity for mTOR kinase over PI3Ks. 12,14 The orientation of the amino group on the 1,3,4-thiadiazole in 4 and on thiazole in 6 resembles that of the 2-amino substituted pyrimidine (1), pyrazine (3) and pyridine (5, Fig. 2b for 3-4), leading to the establishment of an H-bond network with Asp2195 and Glu2190.…”

“… 11 ) and a thiazolopyrimidine derivative. 12 Recently, we have disclosed a conformational restriction strategy to identify highly selective TORKi. 13 A systematic structure–activity relationship (SAR) study pinpointed the pyrazine derivative 12b as potent inhibitor of mTOR kinase ( K i = 8.0 nM), showing a 212-fold selectivity over the structurally related PI3Kα (see Table 1 for chemical structure).…”

Chemical and Structural Strategies to Selectively Target mTOR Kinase

“…The purine core of 20 was converted into a thiazolo[5,4‐ d ]pyrimidine and the physicochemical space investigated. Compound 21 showed an improved potency as compared to 20 , and optimized physicochemical properties [27] . For the ( R )‐configured tricyclic pyrimido‐pyrrolo‐oxazine scaffold, a ( S )‐3‐methylmorpholine slightly increased the potency and selectivity for mTOR as opposed to unsubstituted hinge region morpholines [28a] .…”

“…While DS‐7423 presents an unsubstituted morpholine, compound 20 has a ( R )‐3‐methylmorpholine pointing towards the hinge Valine. The ( R )‐3‐methylmorpholine has been described as an optimal moiety to establish a H‐bond with the backbone of Val2240 in mTOR and to provide selectivity over the closely related PI3K family [27] . This substituted morpholine has been exploited as mTOR selector in different chemotypes, including triazines ( 8 , 11 , Figure 3b), thiazolo[5,4‐ d ]pyrimidine and tricyclic pyrimido‐pyrrolo‐oxazines.…”

“…Similarly, the thieno[3,2‐ d ] pyrimidines 13 and 15 showed a PSA higher than 135 Å 2 leading to a lack in brain penetration [69] . The only sulphur‐containing TORKi able to access the brain was the thiazolo[5,4‐ d ]pyrimidine 21 , displaying a PSA of 121 Å 2 [27] . Among the brain penetrant TORKi, only compound 25 showed a PSA <90 Å 2 .…”