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Medicinal chemistry: an effect of a desolvation penalty of an amide group in the development of kinase inhibitors

Juraj Dobiaš, Marek Ondruš, Matúš Hlaváč, Miroslav Murár, Juraj Kóňa, Gabriela Addová, and Andrej Boháč

Comenius University in Bratislava, Bratislava, Slovakia



Abstract: An analysis of VEGFR-2 conformers from the PDB allowed us to identify an unused salt bridge containing pocket (SBCP) suitably positioned over an AAZ ligand (PDB: 1Y6A). The SBCP consists of Lys866, Glu883 and Phe1045. The closest distance (4.5 Å) between AAZ and the centre of the SBCP has para-carbon from the AAZ internal phenyl ring. This is a bit longer as required for a simple substitution on AAZ to interact with SBCP. To investigate ligand–SBCP interaction, we extended the structure of AAZ by an insertion of an amide group between an oxazole and its aromatic substituent. This allowed moving the internal Ph ring of the carboxamide ligand closer to the SBCP. Promising predictions (poses and scores) were determined for such novel ligands by the Glide (Schrödinger) and the Dock (UCSF) software. Fifteen novel carboxamides 4(a–j,l–p) were prepared and screened. Surprisingly, their enzymatic activities are much lower (IC50: 7.6–437 μM) as expected than the AAZ ligand (22 nM). To explain this discrepancy, we hypothesized that high solvation energy could be a main reason for the penalty that ligands have to pay by their binding to the target. Therefore, 11 additional AAZ analogues possessing modified or replaced amide group by less solvated substituents 4(q–r); 5(a–e), 7(a–b), 9, 10 were developed. A correlation between IC50 activities and calculated solvation energies clearly supported our hypothesis. The ligands possessing less solvated group (instead of the –CONH–) were more powerful VEGFR2 TK inhibitors and vice versa. This conclusion was supported also by a significance of hydrophobic enclosure descriptor in the identified QSAR models. We can conclude that the insertion of a highly solvated extension fragment (e.g. the amide group) in the ligand should be carefully considered especially when this group will act in a hydrophobic part of a protein without forming additional interaction(s). Otherwise, the desolvation penalty of an inserted group could be a limiting factor for a ligand activity.

Keywords: VEGFR-2 TK SBCP pocket ; Tyrosine kinase inhibitors ; Amide group insertion ; Energy of solvation ; Desolvation penalty ; 2-(Arylamino)oxazole-5-carboxamide ; N,5-Diaryloxazol-2-amine ; QSAR 

Full paper is available at

DOI: 10.1007/s11696-018-0576-6


Chemical Papers 73 (1) 71–84 (2019)

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