Structure-Based Drug Design-Pan-SIK Inhibitor GLPG3312

Background

At JMC, the drug company Galapagos published an important article reporting the discovery process of the pan-SIKs inhibitor GLPG3312. The researchers discovered Hit and identified the first X-ray crystal structure with SIK3 through high-throughput screening, revealing the binding mode of the inhibitor and taking a structure-based drug design approach to the optimization of Hit's kinase selectivity and pharmacokinetic properties.

SeeSAR, as a structure-based visualization 3D drug design tool, can show the combination of unoccupied space in the pocket to assist us in drug design, such as: 1) we can directly draw the structure in the unoccupied area according to the surrounding amino acid situation and then use HyDe to evaluate the results of our design; 2) we can also directly use FastGrow, ReCore, and MedChemisis in the inspirator mode to perform structural modification.

The pyrazole in compound 10 was plotted directly in the Molecule Editor module of SeeSAR. It can be seen that the introduction of a second methoxy group into the phenyl ring of compound 8 resulted in a 3-fold increase in the potency of 9 against SIK1, SIK2 and SIK3 (Table 1). More importantly, the partial replacement of bromine at the 5-position of the benzimidazole core with N-ethylpyrazole increased the potency by more than 50-fold, yielding a nanomolar pan-SIK inhibitor 10.

Table 1. Hit Identification and Preliminary SAR Optimization–Activity of Compounds 8, 9, and 10.

Optimization of compound 10 yielded compound 20 and a loss of its anti-AMPK activity was observed. One possible explanation is the difference in gatekeeper residues between the SIK family and AMPK. In the SIK family, the gatekeeper threonine (SIK3 Thr142) produces a pocket that can accommodate methoxy and difluoromethoxy (Fig. 1A, B). In contrast, the presence of gatekeeper methionine (Met95) in AMPK reduces the volume of the pocket, resulting in conflict with the larger difluoromethoxy. In addition, potential hydrogen bonding between the polarized hydrogen of the difluoromethoxy and the hydroxyl group of the gatekeeper threonine in the SIK family (SIK3 Thr142, Fig. 1A) can be speculated to account for the increased 20 potency.

After optimizing the potency and off-target selectivity of the SIKs, compound 28, also known as GLPG3312, with cyclopropyl formamide instead of ethyl formamide, showed IC50 values of 2.0 nM, 0.7 nM, and 0.6 nM for SIK1, SIK2, and SIK3, respectively.As shown in Table 2, GLPG3312 showed good metabolic stability in vitro, with 4.76 and <1.75 L/h/kg unbound clearance in mouse microsomes and hepatocytes, respectively. hepatocytes with unbound clearance of 4.76 and <1.75 L/h/kg, respectively.After intravenous administration of GLPG3312 at 1 mg/kg, total plasma clearance and unbound plasma clearance were observed to be 0.945 and 10.2 L/h/kg, respectively.Oral bioavailability was 60% after oral dosing at 5 mg/kg.

Table 2. Pharmacokinetics in Mice and the Structure–Property Relationship.

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