Aug 2026· International Journal of Biological Macromolecules· pp.
154141
· 0 citations· 73 references
Medicine
TL;DR
This work highlights how distinct inhibitors exploit different conformational states of cKIT and demonstrates the value of integrating structural analyses, biophysical measurements, calculations and molecular simulations to define the mechanism of kinase inhibition.
Abstract
The receptor tyrosine kinase cKIT plays a pivotal role in a variety of physiological processes and is implicated in a broad spectrum of pathological conditions. Its activity is controlled by phosphorylation-dependent conformational changes, which also influence the binding mode of small-molecule inhibitors. We employed an integrated experimental and computational strategy to characterize the conformational landscape of cKIT and to elucidate the binding mechanisms of four inhibitors, Avapritinib, Olverembatinib, Labuxtinib and Cenisertib. A combination of Surface Plasmon Resonance (SPR), enzymatic assay, Molecular Dynamics (MD) simulations, stability energy evaluation, Limited Proteolysis coupled to Mass Spectrometry (LiP-MS) and X-Ray crystallography was used to investigate both active and inactive kinase states. Avapritinib preferentially binds the active form of cKIT, as supported by SPR kinetics, LiP-MS patterns, and MD results. Structural data further confirm that this compound occupies the ATP-binding pocket, consistent with a Type I inhibitor. Olverembatinib and Labuxtinib exhibit high affinity for the inactive kinase, showing stronger binding to the inactive form by SPR and inducing extensive protection of residues spanning the ATP-binding pocket in LiP-MS experiment. MD analysis reveals the burial of key pocket residues, supporting a Type II inhibition mode. Cenisertib exhibits a more complex behavior. While SPR indicates binding to both kinase states, LiP-MS, MD and X-Ray crystallography analyses reveal distinct interaction patterns depending on phosphorylation. Overall, this work highlights how distinct inhibitors exploit different conformational states of cKIT and demonstrates the value of integrating structural analyses, biophysical measurements, calculations and molecular simulations to define the mechanism of kinase inhibition.
CK2 is a constitutively active serine/threonine kinase implicated in cancer, viral infection, and neurodegeneration, but its conserved ATP-binding site and complex holoenzyme assembly have long made selective inhibition challenging. This Perspective discusses three complementary strategies for selective CK2 inhibition: targeting the CK2α/β interface with small molecules, disrupting the same interface with conformationally constrained peptides, and exploiting the cryptic αD pocket for dual-site inhibitor design. CK2α/β-interface inhibitors, including CAM187, CAM7117 and P8C9, established structurally validated routes to modulate holoenzyme assembly and β-dependent substrate phosphorylation. Validation of the αD pocket as a ligandable cryptosteric site enabled dual-site ligands such as CAM4066 and αD-directed inhibitors such as CAM4712, followed by related advances including AB668, KDX1381 and Biv5. These efforts culminated in APL-5125, a highly selective, subnanomolar dual-site inhibitor now in Phase 1/2 clinical evaluation.
A. Sokhal, S. Krajcovicova, J. Iegre et al.· Journal of Medicinal Chemist...· 0 citations
Kinases are major drug targets especially in cancer therapy. However, the high degree of conservation of their active sites hinders the development of selective inhibitors, motivating a deeper understanding of kinase conformational ensembles and allosteric communication pathways. Here, we use dynamical network analysis to identify key residues involved in a dynamic allostery between the N- and C-lobes that connects the major functional units of the MAP kinase p38α. By combining NMR spectroscopy, activity assays, and in silico analysis of wildtype protein and mutants in the presence or absence of an active-site inhibitor, we experimentally validate the obtained architecture with respect to global protein motion and long-range allosteric modulation. Notably, the identified network highlights communication pathways across several functional sites, prominently involving the allosteric site, the activation loop, and even the lipid-binding domain with its embedded cryptic pocket in the C-lobe. These findings provide mechanistic insight into p38α allostery and suggest viable opportunities for the rational design of allosteric modulators of MAP kinases.
Suchandra Roy Acharyya, J. Weisner, Rafael C. Bernardi et al.· Nature Communications· 0 citations
p21-activated kinase 4 (PAK4), a Group II PAK family member, is a therapeutically relevant candidate target in cancer, metabolic disease, and tissue injury. However, translation of PAK4 biology into drug candidates has been constrained by the conserved ATP-binding architecture of PAK isoforms, unfavorable pharmacokinetic profiles, and suboptimal clinical efficacy. We summarize the evolution of ATP-competitive Type I inhibitors, Type I½ back-pocket inhibitors, allosteric modulators, and PROTAC degraders, and compare representative compounds using potency, isoform selectivity, cellular activity, oral bioavailability, and development status. Particular emphasis is placed on structural determinants of selectivity, including the αC-helix-dependent hydrophobic back pocket, the inward Asp444/Asp458 floor pocket arrangement, and peripheral microenvironment differences that distinguish PAK4 from Group I PAKs. We also summarize the potential ADMET liabilities-such as pronounced efflux, metabolic instability, and poor oral bioavailability-that may arise from structural modifications aimed at enhancing PAK4 selectivity, and discuss rational optimization strategies to navigate these inherent barriers. Finally, we discuss clinical lessons from PF-3758309 and KPT-9274/padnarsertib and highlight how allosteric inhibitors and PROTAC degraders may help address limitations of conventional ATP-site inhibitors.
Ruiqing Shi, Xue Feng, Zixu Wang et al.· European journal of medicina...· 0 citations
INTRODUCTION
Protein Kinase C alpha (PKCα), a key regulator of cellular signaling, is frequently dysregulated in breast cancer. Despite its clinical relevance, there is a dearth of selective and safe PKCα inhibitors. This study aims to identify and characterize novel PKCα inhibitors using computational and experimental methodologies.
METHODS
A structure-based virtual screening of the Enamine Hinge Binders Library against the PKCα receptor (PDB ID: 3IW4) was performed using the Glide module of Schrödinger Suite. Analysis of docking scores, protein-ligand interactions, binding free energies, and ADMET profiles helped identify lead candidates. The stability of protein-ligand complexes was confirmed using MD simulations. The functional activity of identified candidates was validated using a kinase assay, and cell death was analyzed using an MTT assay on breast cancer cell lines.
RESULTS
Compounds Z3077775938 (P1) and Z22177390 (P2) exhibited strong binding and stability within the hinge-binding region of PKCα and showed favorable drug-likeness profiles. Structural analysis revealed P1 and P2 as novel scaffolds. The kinase assay revealed dosedependent inhibition of PKCα's ATP-binding activity with IC50 values of P1 and P2 as 0.92 nM and 15.27 nM, respectively. Both compounds induced dose-dependent cytotoxicity in breast cancer cells.
DISCUSSION
This study identified two novel, structurally diverse PKCα inhibitors. Their low IC50 values and dose-dependent cytotoxicity, as observed in both ER+ and triple-negative breast cancer cell lines, validate their functional efficacy and highlight therapeutic potential for breast cancer treatment.
CONCLUSION
Overall, this study identified two PKCα inhibitors that provide a foundation for further optimization as selective therapeutic agents in PKCα-driven malignancies.
Shiven Das, Devika S. Kumar, Arunasree M. Kalle· Current Computer - Aided Dru...· 0 citations
Homeodomain-interacting protein kinase 4 (HIPK4) remains an understudied member of the dark kinome. While genetic knockout studies suggest its involvement in spermiogenesis and cutaneous squamous cell carcinoma, whether these cellular functions can be recapitulated by pharmacological inhibition remains to be determined. These investigations are currently hampered by a lack of high-quality chemical tools. To address this, we employed a rational design strategy utilizing macrocyclization of a bosutinib-based scaffold. Systematic optimization led to the discovery of AZ137 (28e), a potent and selective HIPK4 inhibitor (IC50: 11 nM; cellular EC50: 76 nM). AZ137 exhibits exceptional selectivity across three comprehensive orthogonal panels, high solubility, and no detectable cytotoxicity. Its cellular activity was confirmed in cell-based assays of HIPK4-dependent F-actin remodeling. Together with a negative control compound, this probe set provides a foundational framework for validating HIPK4 as a therapeutic target and a high-quality resource to elucidate its roles in normal physiology and disease.
Athina Zerva, Nicolai D. Raig, Zaile Zhuang et al.· Journal of Medicinal Chemist...· 0 citations
Alzheimer's disease (AD) remains a formidable global health challenge, driving the urgent need for potent and selective therapeutics targeting β-site amyloid precursor protein cleaving enzyme 1 (BACE1), a key enzyme involved in the generation of amyloid-β (Aβ) peptide and a promising target for disease-modifying interventions. In this work, approximately 16 million small molecules from diverse databases were subjected to ligand-based virtual screening (LBVS), using LY3202626 as a reference compound, to identify new potent inhibitors of BACE1. LY3202626 is a highly potent, central nervous system (CNS) penetrant BACE1 inhibitor (IC50 = 0.615 nM) that has progressed to clinical trials, demonstrating efficacy at low doses against BACE1 activity. The lead candidates identified using ensemble molecular docking displayed stronger binding affinities (-11.2 to -9.6 kcal mol-1) to BACE1 as compared to LY3202626. Notably, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis revealed high-affinity binding of ChEMBL3667410 (C1), ChEMBL3667414 (C2), and ChEMBL3976114 (C5) with binding affinities of -32.9 ± 0.8, -33.6 ± 1.8, and -36.1 ± 1.7 kcal mol-1, respectively, to BACE1 as compared to LY3202626 (-29.9 ± 1.8 kcal mol-1). Furthermore, MD simulations demonstrated enhanced structural stability and reduced residual fluctuations in BACE1 on the incorporation of C1, C2, and C5, as compared to apo-BACE1 and BACE1-LY3202626. Interestingly, the conformational snapshots, flap distances, and free energy landscape (FEL) analyses highlighted a closed flap, Val67-Glu77 (non-active) conformation in BACE1-C5 in comparison to an open flap (active) conformation in apo-BACE1, and partial restriction in the access to the active site of BACE1 due to the flap movement noticed in the presence of LY3202626, C1, and C2. Notably, conformational microstate analysis revealed key hydrogen bond interactions of C5 with the 10s loop (Gly11, Gly13), flap residues (Trp76), the catalytic residue (Asp228), Gly230, and Thr231 of BACE1, depicting its high-affinity binding to key residues of BACE1 and its potential as an effective inhibitor of BACE1 activity. The comprehensive in silico methodology in this work illuminated the inhibitory mechanism of LY3202626 and top hit compounds against BACE1 activity for the first time, which, in turn, will be highly valuable in further optimization and structural refinement using various functional group modifications to yield more potent next-generation therapeutic candidates against BACE1 in AD.
