Abstract
•We determined the crystal structures of JNK3 and p38α in complex with four indazole scaffold compounds, revealing key determinants of selectivity within both kinases.•In the JNK3:21J crystal structure, a stable water molecule bridges between Asn152 and the methoxymethyl oxygen of 21J, providing an enthalpic advantage and enhancing binding affinity.•Methyl substitution at the thiophene ring is favored in p38α due to surrounding hydrophobic residues, while the opposite is true for JNK3.•Ligand binding shifts differently affect affinity in JNK3 and p38α.•JNK3 prefers the DFG-in conformation, whereas p38α exhibits a conformational equilibrium between DFG-in and DFG-out states.
Selectivity is a primary focus in medicinal chemistry for ATP-competitive kinase inhibitors due to the highly conserved ATP binding pockets in the kinome. A decade of medicinal chemistry efforts has been carried out to develop selective inhibitors for JNKs, resulting in the identification of numerous promising scaffolds that even exhibit isoform selectivity. Thiophene-indazole is one of the scaffolds explored for isoform selectivity. Some iterations of this scaffold have also shown selectivity for p38α. In this study, we utilized four compounds derived from thiophene-indazole to investigate the mechanisms of selectivity for JNK3 and p38α. We determined crystal structures of the inhibitors bound to either JNK3 or p38α and subjected them to molecular dynamics (MD) simulations to understand the binding mechanism and critical interactions that govern affinity and selectivity for these two important kinases. The findings from this study provides valuable information for improving current lead inhibitors and developing a new generation of JNK3 isoform inhibitors.
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