RESUMO
Apoptosis is regulated by the BCL-2 family of proteins, which is comprised of both pro-death and pro-survival members. Evasion of apoptosis is a hallmark of malignant cells. One way in which cancer cells achieve this evasion is thru overexpression of the pro-survival members of the BCL-2 family. Overexpression of MCL-1, a pro-survival protein, has been shown to be a resistance factor for Navitoclax, a potent inhibitor of BCL-2 and BCL-XL. Here we describe the use of fragment screening methods and structural biology to drive the discovery of novel MCL-1 inhibitors from two distinct structural classes. Specifically, cores derived from a biphenyl sulfonamide and salicylic acid were uncovered in an NMR-based fragment screen and elaborated using high throughput analog synthesis. This culminated in the discovery of selective and potent inhibitors of MCL-1 that may serve as promising leads for medicinal chemistry optimization efforts.
Assuntos
Desenho de Fármacos , Proteína de Sequência 1 de Leucemia de Células Mieloides/antagonistas & inibidores , Sítios de Ligação , Compostos de Bifenilo/química , Cristalografia por Raios X , Espectroscopia de Ressonância Magnética , Simulação de Dinâmica Molecular , Proteína de Sequência 1 de Leucemia de Células Mieloides/metabolismo , Ligação Proteica , Estrutura Terciária de Proteína , Ácido Salicílico/química , Ácido Salicílico/metabolismo , Sulfonamidas/química , Sulfonamidas/metabolismoRESUMO
Tumor necrosis factor α (TNFα) is a soluble cytokine that is directly involved in systemic inflammation through the regulation of the intracellular NF-κB and MAPK signaling pathways. The development of biologic drugs that inhibit TNFα has led to improved clinical outcomes for patients with rheumatoid arthritis and other chronic autoimmune diseases; however, TNFα has proven to be difficult to drug with small molecules. Herein, we present a two-phase, fragment-based drug discovery (FBDD) effort in which we first identified isoquinoline fragments that disrupt TNFα ligand-receptor binding through an allosteric desymmetrization mechanism as observed in high-resolution crystal structures. The second phase of discovery focused on the de novo design and optimization of fragments with improved binding efficiency and drug-like properties. The 3-indolinone-based lead presented here displays oral, in vivo efficacy in a mouse glucose-6-phosphate isomerase (GPI)-induced paw swelling model comparable to that seen with a TNFα antibody.
Assuntos
Produtos Biológicos/síntese química , Desenho de Fármacos , Fator de Necrose Tumoral alfa/antagonistas & inibidores , Administração Oral , Regulação Alostérica , Animais , Artrite Reumatoide/tratamento farmacológico , Doenças Autoimunes/tratamento farmacológico , Produtos Biológicos/farmacologia , Produtos Biológicos/uso terapêutico , Ligantes , Camundongos , Fator de Necrose Tumoral alfa/metabolismoRESUMO
Herein we describe the identification and characterization of a class of molecules that are believed to extend into a region of p38 known as the 'switch pocket'. Although these molecules lack a canonical hinge binding motif, they show K(i) values as low as 100 nM against p38. We show that molecules that interact with this region of the protein demonstrate different binding kinetics than a canonical ATP mimetic, as well as a wide range of kinome profiles. Thus, the switch pocket presents new opportunities for kinome selectivity which could result in unique biochemical responses and offer new opportunities in the field of kinase drug discovery.
Assuntos
Proteína Quinase 14 Ativada por Mitógeno/antagonistas & inibidores , Inibidores de Proteínas Quinases/química , Trifosfato de Adenosina/química , Sítios de Ligação , Simulação por Computador , Cristalografia por Raios X , Transferência Ressonante de Energia de Fluorescência , Cinética , Proteína Quinase 14 Ativada por Mitógeno/metabolismo , Ligação Proteica , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/farmacologia , Estrutura Terciária de Proteína , Relação Estrutura-AtividadeRESUMO
We present a probabilistic framework for interpreting structure-based virtual screening that returns a quantitative likelihood of observing bioactivity and can be quantitatively combined with ligand-based screening methods to yield a cumulative prediction that consistently outperforms any single screening metric. The approach has been developed and validated on more than 30 different protein targets. Transforming structure-based in silico screening results into robust probabilities of activity enables the general fusion of multiple structure- and ligand-based approaches and returns a quantitative expectation of success that can be used to prioritize (or deprioritize) further discovery activities. This unified probabilistic framework offers a paradigm shift in how docking and scoring results are interpreted, which can enhance early lead-finding efforts by maximizing the value of in silico computational tools.
Assuntos
Ligantes , Modelos Moleculares , Estrutura Molecular , Probabilidade , Proteínas/química , Relação Quantitativa Estrutura-Atividade , Bases de Dados FactuaisRESUMO
NMR spectroscopy has enjoyed widespread success as a method for screening protein targets, especially in the area of fragment-based drug discovery. However, current methods for NMR-based screening all suffer certain limitations. Two-dimensional methods like "SAR by NMR" require isotopically labeled protein and are limited to proteins less than about 50 kDa. For one-dimensional, ligand-based methods, results can be confounded by nonspecific compound binding, resonance overlap, or the need for a special NMR probe. We present here a ligand-based method that relies on the exchange broadening observed for a (13)C-labeled molecule upon binding to a protein target (labeled ligand displacement). This method can be used to screen both individual compounds and mixtures and is free of the artifacts inherent in other ligand-based methods.