Fig 1.
Binding modes of active site inhibitors and LiPoLis in p38α MAPK.
(A) Superposed kinase domains of p38α MAPK (cyan) in complex with active site inhibitor BIRB-796 (yellow) (PDB: 1KV2) and the quinazoline-based LiPoLi 3 (green) (PDB: 4DLJ). (B) Detailed binding mode of 3 (green) in the LP of p38α MAPK (cyan), highlighting key structural elements and main interactions formed between the protein and the ligand. (C) Chemical structure of 3 with systematic numbering of the quinazoline scaffold and highlighted moieties selected for derivatization.
Fig 2.
(A) Design of LiPoLis based on the alignment of the crystal structures of 3 (green) and 1 (yellow) in complex with p38α (PDB-codes: 4DLJ and 3HVC). Overlay of 1 and modeled structures of (B) 9c (cyan), (C) 9j (white) and (D) 9i (magenta) showcasing the proposed binding modes.
Fig 3.
a Synthesis and identity of 2-arylquinazolines.
a Reagents and conditions: (a) method A: benzamidine hydrochloride hydrate, AcOH, 2-methoxyethanol, 130°C, 18 h, 18–32%; method B: benzoic anhydride, formamide, 200°C, 5 min, MW, 31–37%; (b) method C: aldehyde, NaHSO3, pTSA, DMAc, 155°C, 18 h, 10–34%; (c) method A: 1) SOCl2, DMF, 80°C, 4 h, 2) amine, DIPEA, DCM/iPrOH (3:2), rt, 18 h, 66–95%; method B: 1) HCCP, DIPEA, MeCN, rt, 1 h, 2) amine, rt, 18 h, 68–87%; (d) method A: 10% Pd/C, ammonium formate, EtOH, 80°C, 1–3 h, 56–96%; method B: Fe, NH4Cl, MeOH:H2O (4:1), 80°C, 3–6 h, 81–87%; (e) acyl chloride, DIPEA, DCM, 0°C to rt or 50°C, 1–6 h, 69–80%.
Fig 4.
a Synthesis of amine building block 14.
a Reagents and conditions: (a) Ac2O, DCM, rt, 18 h, 88%; (b) AlCl3, cyclopropanecarbonyl chloride, DCM, rt, 30 min, 58%; (c) 1) HCl (conc.), rt, 18 h, 2) TFA, TES, rt, 18 h, 92%.
Fig 5.
a Synthesis of amine building block 16.
a Reagents and conditions: (a) ethane-1,2-diamine, K2CO3, I2, tBuOH, 70°C, 3.5 h, 54%.
Fig 6.
a Synthesis of aldehyde building blocks 17a and 17b.
a Reagents and conditions: (a) amine, Na2CO3, H2O, reflux, 18 h, 55–58%.
Fig 7.
a Reagents and conditions: (a) mCPBA, DCM, rt, 3 h, 87%.
Fig 8.
a Reagents and conditions: (a) hydrazine, EtOH, reflux, 21 h, 50%; (b) oxobutanoate, AcOH reflux, 19 h, 51–60%.
Fig 9.
Crystal structures of LiPoLis in complex with p38α.
Diagrams of the experimental electron densities of (A) 9c (yellow), (B) 9g (green), (C) 9h (cyan), (D) 9j (white), (E) 9l (magenta) and (F) 9m (orange). At resolutions ranging from 1.85 to 2.4 Å; 2mFo-DFc map (grey) contoured at 1.0σ. Water molecules are shown as red spheres. Hydrogen-bond interactions of the ligands with the protein and water molecules are illustrated by yellow dotted lines. All LiPoLis bind to the LP flanked by helices 1L14, 2L14 and the αEF/αF loop.
Fig 10.
Conformational changes of the LP upon LiPoLi binding.
(A) Alignment of the p38α-9c (cyan) and p38α-9h (yellow) complex crystal structures. Displacement of helix 2L14 and minor rearrangement of loop αEF/αF and helix 1L14 (trajectories are shown as red dots); (B) Opening of the LP (red arrows) when 9c is bound compared to the closed LP in presence of 9h.