RESUMEN
MAPKAPK5 has been proposed to play a role in regulation of matrix metalloprotease expression and so to be a potential target for intervention in rheumatoid arthritis. We present here the identification of a series of compounds against this target which are effective in both biochemical and cell assays. The expansion of the series is described, along with early SAR and pharmacokinetics for some representative compounds.
Asunto(s)
Antirreumáticos/síntesis química , Imidazoles/síntesis química , Péptidos y Proteínas de Señalización Intracelular/antagonistas & inhibidores , Inhibidores de Proteínas Quinasas/síntesis química , Proteínas Serina-Treonina Quinasas/antagonistas & inhibidores , Pirazoles/síntesis química , Animales , Antirreumáticos/farmacocinética , Antirreumáticos/farmacología , Artritis Reumatoide/tratamiento farmacológico , Artritis Reumatoide/enzimología , Sitios de Unión , Ensayos Analíticos de Alto Rendimiento , Humanos , Enlace de Hidrógeno , Imidazoles/farmacocinética , Imidazoles/farmacología , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Modelos Moleculares , Unión Proteica , Inhibidores de Proteínas Quinasas/farmacocinética , Inhibidores de Proteínas Quinasas/farmacología , Proteínas Serina-Treonina Quinasas/metabolismo , Pirazoles/farmacocinética , Pirazoles/farmacología , Ratas , Bibliotecas de Moléculas Pequeñas , Relación Estructura-ActividadRESUMEN
We describe a drug-design strategy termed REPLACE (REplacement with Partial Ligand Alternatives through Computational Enrichment) in which nonpeptidic surrogates for specific determinants of known peptide ligands are identified in silico by using a core peptide-bound protein structure as a design anchor. In the REPLACE application example, we present the effective replacement of two critical binding motifs in a lead protein-protein interaction inhibitor pentapeptide with more druglike phenyltriazole and diphenyl ether groups. These were identified through docking of fragment libraries into the volume of the cyclin-binding groove of CDK2/cyclin A vacated through truncation of the inhibitor peptide-binding determinants. Proof of concept for this strategy was obtained through the generation of potent peptide-small-molecule hybrids and by the confirmation of inhibitor-binding modes in X-ray crystal structures. This method therefore allows nonpeptide fragments to be identified without the requirement for a high-sensitivity binding assay and should be generally applicable in replacing amino acids as individual residues or groups in peptide inhibitors to generate pharmaceutically acceptable lead molecules.
Asunto(s)
Ciclina A/química , Inhibidor p21 de las Quinasas Dependientes de la Ciclina/química , Diseño de Fármacos , Biblioteca de Péptidos , Péptidos/química , Ingeniería de Proteínas/métodos , Sustitución de Aminoácidos , Sitios de Unión , Cristalografía por Rayos X , Ciclina A/antagonistas & inhibidores , Ciclina A/metabolismo , Estructura Molecular , Péptidos/metabolismo , Péptidos/farmacologíaRESUMEN
This article reviews the literature from January 2004 to January 2006 relating to the use of parallel chemistry compound libraries in drug discovery. Examples of libraries that have yielded active compounds across a range of biological targets are presented, together with synthetic details where relevant. The background of the biological target, and any structure-activity relationship that can be discerned from members of a library series, are also commented upon. A brief discussion of new technological developments in library design and synthesis, and likely future directions for parallel chemistry in the context of drug discovery, is also presented.
Asunto(s)
Química Farmacéutica/métodos , Preparaciones Farmacéuticas/química , Animales , Química Farmacéutica/tendencias , Inhibidores Enzimáticos/química , HumanosRESUMEN
Inhibition of cyclin A- and cyclin E-associated cyclin-dependent kinase-2 (CDK2) activities is an effective way of selective induction of apoptotic cell death via the E2F pathway in tumour cells. The cyclin groove recognition motif (CRM) in the natural CDK-inhibitory (CDKI) tumour suppressor protein p27KIP1 was used as the basis for the design and synthesis of a series of cyclic peptides whose biological activity and structural characterisation by NMR and X-ray crystallography is reported. Whereas linear p27KIP1 sequence peptides were comparatively ineffective, introduction of side chain-to-tail constraints was found to be productive. An optimal macrocyclic ring size for the conformational constraint was determined, mimicking the intramolecular H-bonding system of p27. Molecular dynamics calculations of various macrocycles suggested a close correlation between ring flexibility and biological activity. Truncated inhibitor peptide analogues also confirmed the hypothesis that introduction of a cyclic conformational constraint is favourable in terms of affinity and potency. The structural basis for the potency increase in cyclic versus linear peptides was demonstrated through the determination and interpretation of X-ray crystal structures of complexes between CDK2/cylin A (CDK2A) and a constrained pentapeptide.
Asunto(s)
Quinasa 2 Dependiente de la Ciclina/antagonistas & inhibidores , Complejos Multienzimáticos/antagonistas & inhibidores , Péptidos Cíclicos/farmacología , Sitios de Unión/efectos de los fármacos , Biología Computacional , Cristalografía por Rayos X , Ciclina A/química , Quinasa 2 Dependiente de la Ciclina/química , Inhibidor p27 de las Quinasas Dependientes de la Ciclina/química , Evaluación Preclínica de Medicamentos , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Complejos Multienzimáticos/química , Complejos Multienzimáticos/efectos de los fármacos , Biblioteca de Péptidos , Péptidos Cíclicos/química , Péptidos Cíclicos/metabolismo , Conformación ProteicaRESUMEN
Inhibition of CDK2/CA (cyclin-dependent kinase 2/cyclin A complex) activity through blocking of the substrate recognition site in the cyclin A subunit has been demonstrated to be an effective method for inducing apoptosis in tumor cells. We have used the cyclin binding motif (CBM) present in the tumor suppressor proteins p21(WAF1) and p27(KIP1) as a template to optimize the minimal sequence necessary for CDK2/CA inhibition. A series of peptides were prepared, containing nonnatural amino acids, which possess nano- to micromolar CDK2-inhibitory activity. Here we present X-ray structures of the protein complex CDK2/CA, together with the cyclin groove-bound peptides H-Ala-Ala-Abu-Arg-Ser-Leu-Ile-(p-F-Phe)-NH(2) (peptide 1), H-Arg-Arg-Leu-Ile-Phe-NH(2) (peptide 2), Ac-Arg-Arg-Leu-Asn-(m-Cl-Phe)-NH(2) (peptide 3), H-Arg-Arg-Leu-Asn-(p-F-Phe)-NH(2) (peptide 4), and H-Cit-Cit-Leu-Ile-(p-F-Phe)-NH(2) (peptide 5). Some of the peptide complexes presented here were obtained through the novel technique of ligand exchange within protein crystals. This method may find general application for obtaining complex structures of proteins with surface-bound ligands.
Asunto(s)
Ciclinas/química , Secuencias de Aminoácidos , Sitios de Unión , Quinasas CDC2-CDC28/antagonistas & inhibidores , Quinasas CDC2-CDC28/química , Cristalografía por Rayos X , Ciclina A/antagonistas & inhibidores , Ciclina A/química , Quinasa 2 Dependiente de la Ciclina , Inhibidor p21 de las Quinasas Dependientes de la Ciclina , Humanos , Ligandos , Modelos Moleculares , Péptidos/química , Unión Proteica , Conformación Proteica , Estructura Secundaria de Proteína , Relación Estructura-ActividadRESUMEN
The recognition of cyclin-dependent kinase (CDK)/cyclin complexes by various cell-cycle regulatory proteins, including certain tumour suppressors and transcription factors, occurs at least in part through a protein-protein interaction with a binding groove on the cyclin subunit. Since CDK function is generally deregulated in tumour cells, blocking of this recruitment site prevents recognition and subsequent phosphorylation of CDK substrates and offers a therapeutic approach towards restoration of checkpoint control in transformed cells. Here we discuss the finding that peptides derived from such cyclin-interacting proteins, and rendered permeable through conjugation to cellular delivery vectors, can apparently induce tumour cells to undergo apoptosis selectively. We review the current status of 3D-structural information available on cyclin-peptide interactions and we summarise our extensive peptide structure-activity relationship studies in light of this information. We also show how a combination of molecular modelling and introduction into synthetic peptides of peptidomimetic elements, such as non-natural amino acid residues and conformational constraints, is being used hopefully to arrive at drug candidates capable of modulating CDK function in a selective mechanism-based approach rather than through ATP antagonism.