Discovery of novel 2-phenylamino-4-prolylpyrimidine derivatives as TRK/ALK dual inhibitors with promising antitumor effects

Highlights

• Twenty-one novel 2-phenylamino-4-prolylpyrimidine derivatives were designed and synthesized.

• Compound 21 displayed remarkable antitumor effects on NTRK1 and ALK positive cancer cells, respectively.

• Compound 21 showed superior potency against TRK, ALK^WT and ALK^L1196M.

• Molecular docking analysis was supplied to guide and explain the observed SARs.

Abstract

In order to explore novel TRK and ALK dual inhibitors, a series of 2-phenylamino-4-prolylpyrimidine derivatives were designed, synthesized and evaluated for their in vitro cytotoxicity and enzymatic activities. Delightfully, most compounds were detected moderated to excellent activities in cellular assay. Among them, compound 21 exhibited encouraging cytotoxicity on KM12, H2228 and KARPAS299 cells with IC₅₀ values of 0.86, 0.141 and 0.072 μM. Meanwhile, the performances of 21 in the enzymatic assays were in good accordance with anti-proliferative activity with IC₅₀ values of 2.2, 9.3 and 38 nM towards TRKA, ALK^WT and ALK^L1196M, respectively. Compared with Entrectinib, compound 21 not only ensured the inhibitory activity on TRKA, but also improved the affinity with ALK and ALK^L1196M to a certain extent. Ultimately, the binding model of 21 with TRKA and ALK were ideally established through molecular docking, which further confirmed the SARs analysis.

Introduction

Tropomyosin receptor kinases A, B and C (TRKA, TRKB and TRKC), encoded by the neurotrophic receptor tyrosine kinase 1, 2 and 3 (NTRK1, NTRK2 and NTRK3) genes, respectively, are members of cell surface receptor tyrosine kinase (RTK) family.¹ The TRK receptors express abundantly in the nervous system, regulating cell proliferation, differentiation, apoptosis and survival of neurons.2, 3 However, NTRK is observed as a fusion oncogene in cancer, e.g., tropomyosin 3-NTRK1 (TPM3-NTRK1) in colorectal cancer⁴ and ETS translocation variant 6-NTRK3 (ETV6-NTRK3) in secreted mesoblastic congenital fibrosarcoma,5, 6 which can mediate the same downstream pathway resulting in cancer progression.⁷ The growth of NTRK fusion-positive cancers depends on TRK tyrosine kinase activity, turning TRK inhibitors as viable therapeutic agents for cancer treatment.⁸

In recent years, a number of small molecular TRK inhibitors such as Larotrectinib,⁹ Entrectinib,10, 11 LOXO-195¹² and TPX-005¹³ have been developed (Fig. 1), which achieved significant clinical progress in the treatment of NTRK fusion positive cancers. Especially, Entrectinib, a multi-target inhibitor developed by Roche, has been approved for the treatment of patients with solid tumors bearing NTRK gene fusion, which demonstrated a durable overall response rate (ORR) of 57%.¹⁴ However, the emergence of drug resistance due to the TRK secondary point mutations such as G595R in the solvent front and G667C in the DFG motif limited the efficacy of TRK inhibitors in clinical cases.15, 16 Therefore, discovery of novel inhibitors with versatile chemical structures to overcome secondary mutations of TRK is of great value for NTRK-positive cancer therapy.

The anaplastic lymphoma kinase (ALK), a RTK from the insulin receptor superfamily,¹⁷ was identified as an oncogene driver for a variety of human cancers including anaplastic large cell lymphoma (ALCL), inflammatory myofibroblastic tumor (IMT), non-small cell lung cancer (NSCLC) and so on.¹⁸ To date, five ALK inhibitors have been approved by FDA, among which Ceritinib has demonstrated marked clinical therapeutic effect for ALK-rearranged cancers.19, 20, 21 It is worth noting that ALK and TRK harbor a high amino acid sequence homology within the kinase domain, providing a proof-of-concept for the research of TRK/ALK dual inhibitors.²² In addition, Entrectinib exhibited extremely low nanomolar inhibitory activity on both ALK and TRK kinases,²³ which promoted the treatment of TRK- and ALK- positive tumors and provided a superior lead for novel TRK/ALK dual inhibitors.

Based on co-crystal structures of Entrectinib with TRKA and ALK proteins (PDB: 5KVT and 5FTO),23, 24 a dedicated structure-guided design was conducted. As shown in Fig. 2A and 2B, it was suggested that the 3,5-difluorophenyl moiety created favorable contacts with the backbone carbonyls of Gly667 and Asp668 from the DFG motif (Asn1254 and Gly1269 in ALK). Thus, 3,5-difluorophenyl was retained firstly as a fundamental pharmacophore to guarantee the rudimentary activity. More importantly, Entrectinib was anchored to the hinge region through three hydrogen bonds between the aminoindazole moiety and the backbone of residues Glu590 and Met592 (Glu1197 and Met1199 in ALK). However, the rigid aminoindazole skeleton was sterically hindered by bulk groups resulting from secondary mutations (such as TRK^G667C and ALK^L1196M). Therefore, the flexibility of the molecular skeleton was improved by using aryl-prolinamide instead of aminoindazole moiety on the basis of scaffold hopping strategy. Subsequently, superposition of the co-crystal structure of Entrectinib and Ceritinib within ALK protein (Fig. 2C)²¹ indicated that the 2,4-diaminopyrimidine of Ceritinib was highly coincident with the aminoindazole moiety by forming pivotal hydrogen bonds with the hinge residue Met1199. Through molecular hybridization strategy, as a surrogate of aminoindazole, prolyl substituted pyrimidinyl group was introduced to enhance the affinity for target proteins. Moreover, it was notable that the substituents at R₂ moiety filled the adenosine triphosphate (ATP) sugar pocket, which obviously affected the inhibitory profile. Therefore, using the amide bond as a linker, various aliphatic amines were integrated to explore the structure–activity relationships (SARs). Finally, the hydrophilic R₁ moiety was extended to the solvent region, which was tolerated for further modification with hydrophilic aliphatic amines.

Herein, twenty-one new chemical entities characterized by 2-phenylamino-4-prolylpyrimidine scaffold were rationally designed and synthesized. These compounds were evaluated for their anti-proliferative activities against four cancer cell lines. Subsequently, several potent compounds were selected into further in vitro enzymatic inhibitory studies including TRKA, ALK, ALK^L1196M. Finally, the possible binding model of optimal compound 21 with TRKA and ALK were established according to the corresponding co-crystal structures.