Structure-based design of oxygen-linked macrocyclic kinase inhibitors: discovery of SB1518 and SB1578, potent inhibitors of Janus kinase 2 (JAK2) and Fms-like tyrosine kinase-3 (FLT3)

Abstract

Macrocycles from our Aurora project were screened in a kinase panel and were found to be active on other kinase targets, mainly JAKs, FLT3 and CDKs. Subsequently these compounds became leads in our JAK2 project. Macrocycles with a basic nitrogen in the linker form a salt bridge with Asp86 in CDK2 and Asp698 in FLT3. This residue is conserved in most CDKs resulting in potent pan CDK inhibition. One of the main project objectives was to achieve JAK2 potency with 100-fold selectivity against CDKs. Macrocycles with an ether linker have potent JAK2 activity with the ether oxygen forming a hydrogen bond to Ser936. A hydrogen bond to the equivalent residues of JAK3 and most CDKs cannot be formed resulting in good selectivity for JAK2 over JAK3 and CDKs. Further optimization of the macrocyclic linker and side chain increased JAK2 and FLT3 activity as well as improving DMPK properties. The selective JAK2/FLT3 inhibitor 11 (Pacritinib, SB1518) has successfully finished phase 2 clinical trials for myelofibrosis and lymphoma. Another selective JAK2/FLT3 inhibitor, 33 (SB1578), has entered phase 1 clinical development for the non-oncology indication rheumatoid arthritis.

Robust patient-derived xenografts of MDS/MPN overlap syndromes capture the unique characteristics of CMML and JMML

“…Given promising results from our recent phase 1 clinical trial of the JAK1/2 inhibitor ruxolitinib in CMML, 40 we decided to test the utility of the CMML preclinical models for evaluation of the JAK2/FLT3 inhibitor pacritinib. 41,42 In addition to its capacity to potently inhibit JAK2 and FLT3, pacritinib is an attractive therapeutic because of its inhibitory effects on other deregulated pathways in CMML, such as those associated with CSF1R and IRAK1, both targets of pacritinib. [43][44][45] Short-term culture of BM MNCs from CMML patients ( Figure 4A; supplemental Table 1) in vehicle or increasing doses of pacritinib revealed effective CMML cell killing upon 48 hours of pacritinib exposure with a median half maximal inhibitory concentration of 339 nM (range 2.4-1363 nM) across 10 individual CMML patients ( Figure 4B).…”

The Synthesis of Macrocycles for Drug Discovery

“…Specifically, this strategy has been successfully applied to macrocyclic BACE inhibitors (47), 62,106-113 calpain inhibitors (48), 114,115 checkpoint kinase 1 (Chk1) inhibitors (49), [116][117][118] G-quadruplex stabilizing agents, 119 Grb2 SH2 domain inhibitors (50), 39,120-122 non-natural product inspired pan-HDAC inhibitors (51), 123 HIV inhibitors, [124][125][126][127] Hsp90 inhibitors (52), 128,129 insulin-regulated aminopeptidase (IRAP) inhibitors, 130 However, the most significant impact of this approach has been in the discovery and development of the plethora of macrocyclic HCV NS3/4A protease inhibitors, which relied almost exclusively on RCM to assemble the macrocyclic framework. [141][142][143] This includes several compounds that have progressed to advanced clinical evaluation, such as ITMN-191 (danoprevir, 55, Figure 11.7, site of cyclization indicated along with the catalyst employed using the designations in Figure 11.5), 144 Another series of clinical stage compounds prepared utilizing RCM are the multi-kinase inhibitors SB1317 (TG02, 62, Figure 11.8), an inhibitor of CDKs, Janus kinase 2 (JAK2) and Fms-like tyrosine kinase-3 (FLT3) for the treatment of cancers, including multiple myeloma and acute leukaemia, 154,155 SB1518 (pacritnib, 63), a JAK2, FLT3 and tyrosine kinase 2 (TYK2) inhibitor for the treatment of myelofibrosis and lymphoma, 156,157 and SB1578 (64), an inhibitor of JAK2, FLT3 and colony stimulating factor-1 receptor kinase (c-Fms) for the treatment of rheumatoid arthritis. 158 As is evident from the structures, these all originated from the same diaminopyridine-based core template.…”

Designed Macrocyclic Kinase Inhibitors

“…This residue is highlighted in green in the alignment in Figure 5.12. 7 When the basic nitrogen is exchanged for an oxygen the FLT3 and CDK2 activity was expected to drop significantly but this was only observed for CDK2 while FLT3 activity remained as for 1. When docked into CDK2, poses of 1 were either high energy conformations or had repulsive electrostatic interactions with the Asp86 side chain ( Figure 5.13a).…”

“…Thus the nature of the residue highlighted in green in Figure 5.12 explains the overall selectivity profile of both the nitrogen and the oxygen linked macrocycles. 7 Amine-linked compounds also tolerated substitution larger than a methyl group on the basic nitrogen. Comparing analogs 51-54 to 3 (Table 5.6) it is apparent that the optimal substituent for CDK2 activity is a methyl group as in 3.…”

“…Restricting the conformation of acyclic multi-kinase inhibitor scaffolds generates novel molecular scaffolds and could increase selectivity. [7][8][9][10][11] This focused rational approach opens up relatively under-explored chemical space. Macrocycles can possess high selectivity, attributable to their well defined threedimensional shape, allowing them to fit into the DFG-in conformation of the ATP-binding site of target kinases.…”