RESUMO
Using fragment-based screening techniques, 5-methyl-4-phenyl-1H-pyrazole (IC50 80 microM) was identified as a novel, low molecular weight inhibitor of protein kinase B (PKB). Herein we describe the rapid elaboration of highly potent and ligand efficient analogues using a fragment growing approach. Iterative structure-based design was supported by protein-ligand structure determinations using a PKA-PKB "chimera" and a final protein-ligand structure of a lead compound in PKBbeta itself.
Assuntos
Antineoplásicos/síntese química , Modelos Moleculares , Proteínas Proto-Oncogênicas c-akt/antagonistas & inibidores , Proteínas Proto-Oncogênicas c-akt/química , Pirazóis/síntese química , Trifosfato de Adenosina/metabolismo , Antineoplásicos/química , Sítios de Ligação , Cristalografia por Raios X , Proteínas Quinases Dependentes de AMP Cíclico/genética , Ligantes , Proteínas Proto-Oncogênicas c-akt/genética , Pirazóis/química , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/genética , Estereoisomerismo , Relação Estrutura-AtividadeRESUMO
Fragment-based lead discovery has been successfully applied to the aspartyl protease enzyme beta-secretase (BACE-1). Fragment hits that contained an aminopyridine motif binding to the two catalytic aspartic acid residues in the active site of the enzyme were the chemical starting points. Structure-based design approaches have led to identification of low micromolar lead compounds that retain these interactions and additionally occupy adjacent hydrophobic pockets of the active site. These leads form two subseries, for which compounds 4 (IC50 = 25 microM) and 6c (IC50 = 24 microM) are representative. In the latter series, further optimization has led to 8a (IC50 = 690 nM).
Assuntos
Aminoquinolinas/química , Secretases da Proteína Precursora do Amiloide/antagonistas & inibidores , Secretases da Proteína Precursora do Amiloide/química , Ácido Aspártico Endopeptidases/antagonistas & inibidores , Ácido Aspártico Endopeptidases/química , Modelos Moleculares , Relação Quantitativa Estrutura-Atividade , Aminoquinolinas/síntese química , Sítios de Ligação , Cristalografia por Raios X , Humanos , Indóis/síntese química , Indóis/química , Ligantes , Ligação Proteica , Proteínas Recombinantes/antagonistas & inibidores , Proteínas Recombinantes/químicaRESUMO
Fragment-based lead generation has led to the discovery of a novel series of cyclic amidine-based inhibitors of beta-secretase (BACE-1). Initial fragment hits with an isocytosine core having millimolar potency were identified via NMR affinity screening. Structure-guided evolution of these fragments using X-ray crystallography together with potency determination using surface plasmon resonance and functional enzyme inhibition assays afforded micromolar inhibitors. Similarity searching around the isocytosine core led to the identification of a related series of inhibitors, the dihydroisocytosines. By leveraging the knowledge of the ligand-BACE-1 recognition features generated from the isocytosines, the dihydroisocytosines were efficiently optimized to submicromolar potency. Compound 29, with an IC50 of 80 nM, a ligand efficiency of 0.37, and cellular activity of 470 nM, emerged as the lead structure for future optimization.
Assuntos
Amidinas/síntese química , Secretases da Proteína Precursora do Amiloide/antagonistas & inibidores , Ácido Aspártico Endopeptidases/antagonistas & inibidores , Citosina/análogos & derivados , Modelos Moleculares , Pirimidinas/síntese química , Amidinas/química , Amidinas/farmacologia , Secretases da Proteína Precursora do Amiloide/química , Secretases da Proteína Precursora do Amiloide/genética , Ácido Aspártico Endopeptidases/química , Ácido Aspártico Endopeptidases/genética , Linhagem Celular , Cristalografia por Raios X , Citosina/síntese química , Citosina/química , Citosina/farmacologia , Transferência Ressonante de Energia de Fluorescência , Humanos , Ligantes , Espectroscopia de Ressonância Magnética , Pirimidinas/química , Pirimidinas/farmacologia , Estereoisomerismo , Relação Estrutura-AtividadeRESUMO
Fragment-based lead discovery (also referred to as needles, shapes, binding elements, seed templates or scaffolds) is a new lead discovery approach in which much lower molecular weight (120-250 Da) compounds are screened relative to HTS campaigns. Fragment-based hits are typically weak inhibitors (10 microM-mM), and therefore need to be screened at higher concentration using very sensitive biophysical detection techniques such as protein crystallography and NMR as the primary screening techniques, rather than bioassays. Compared with HTS hits, these fragments are simpler, less functionalized compounds with correspondingly lower affinity. However, fragment hits typically possess high 'ligand efficiency' (binding affinity per heavy atom) and so are highly suitable for optimization into clinical candidates with good drug-like properties.
Assuntos
Desenho de Fármacos , Tecnologia Farmacêutica/métodos , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Peso Molecular , Tecnologia Farmacêutica/tendênciasRESUMO
We describe the structure-guided optimization of the molecular fragments 2-amino-3-benzyloxypyridine 1 (IC(50) 1.3 mM) and 3-(2-(4-pyridyl)ethyl)indole 2 (IC(50) 35 microM) identified using X-ray crystallographic screening of p38alpha MAP kinase. Using two separate case studies, the article focuses on the key compounds synthesized, the structure-activity relationships and the binding mode observations made during this optimization process, resulting in two potent lead series that demonstrate significant increases in activity. We describe the process of compound elaboration either through the growing out from fragments into adjacent pockets or through the conjoining of overlapping fragments and demonstrate that we have exploited the mobile conserved activation loop, consisting in part of Asp168-Phe169-Gly170 (DFG), to generate significant improvements in potency and kinase selectivity.