RESUMEN
Inhibition of the Menin (MEN1) and MLL (MLL1, KMT2A) interaction is a potential therapeutic strategy for MLL-rearranged (MLL-r) leukemia. Structure-based design yielded the potent, highly selective, and orally bioavailable small-molecule inhibitor VTP50469. Cell lines carrying MLL rearrangements were selectively responsive to VTP50469. VTP50469 displaced Menin from protein complexes and inhibited chromatin occupancy of MLL at select genes. Loss of MLL binding led to changes in gene expression, differentiation, and apoptosis. Patient-derived xenograft (PDX) models derived from patients with either MLL-r acute myeloid leukemia or MLL-r acute lymphoblastic leukemia (ALL) showed dramatic reductions of leukemia burden when treated with VTP50469. Multiple mice engrafted with MLL-r ALL remained disease free for more than 1 year after treatment. These data support rapid translation of this approach to clinical trials.
Asunto(s)
Cromatina/efectos de los fármacos , Regulación Leucémica de la Expresión Génica/efectos de los fármacos , Leucemia Mieloide Aguda/tratamiento farmacológico , Proteínas Proto-Oncogénicas/efectos de los fármacos , Animales , Apoptosis/efectos de los fármacos , Apoptosis/genética , Diferenciación Celular/efectos de los fármacos , Diferenciación Celular/genética , Proliferación Celular/efectos de los fármacos , Proliferación Celular/genética , Cromatina/genética , Regulación Leucémica de la Expresión Génica/genética , Reordenamiento Génico/efectos de los fármacos , Reordenamiento Génico/genética , Humanos , Leucemia Mieloide Aguda/genética , Ratones , Proteínas Proto-Oncogénicas/genética , Factores de Transcripción/efectos de los fármacos , Factores de Transcripción/genéticaRESUMEN
With the continuous progress in ultralarge virtual libraries which are readily accessible, it is of great interest to explore this large chemical space for hit identification and lead optimization using reliable structure-based approaches. In this work, a novel growth-based screening protocol has been designed and implemented in the structure-based design platform CONTOUR. The protocol was used to screen the ZINC database in silico and optimize hits to discover 11ß-HSD1 inhibitors. In contrast to molecular docking, the virtual screening process makes significant improvements in computational efficiency without losing chemical equities through partitioning 1.8 million ZINC compounds into fragments, docking fragments to form key hydrogen bonds with anchor residues, reorganizing molecules into molecular fragment trees using matched fragments and common substructures, and then regrowing molecules with the help of developed intelligent growth features inside the protein binding site to find hits. The growth-base screening approach is validated by the high hit rate. A total of 50 compounds have been selected for testing; of these, 15 hits having diverse scaffolds are found to inhibit 11ß-HSD1 with IC50 values of less than 1 µM in a biochemical enzyme assay. The best hit which exhibits an enzyme IC50 of 33 nM is further developed to a novel series of bicyclic 11ß-HSD1 inhibitors with the best inhibition of enzyme IC50 of 3.1 nM. The final lead candidate exhibits IC50 values of 7.2 and 21 nM in enzyme and adipocyte assays, respectively, displayed greater than 1000-fold of selectivity over 11ß-HSD2 and two other related hydroxysteroid dehydrogenases, and can serve as good starting points for further optimization to develop clinical candidates.
Asunto(s)
11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/antagonistas & inhibidores , Simulación por Computador , Evaluación Preclínica de Medicamentos/métodos , Inhibidores Enzimáticos/farmacología , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/química , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/metabolismo , Dominio Catalítico , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/metabolismo , Simulación del Acoplamiento MolecularRESUMEN
A potent, in vivo efficacious 11ß hydroxysteroid dehydrogenase type 1 (11ß HSD1) inhibitor (11j) has been identified. Compound 11j inhibited 11ß HSD1 activity in human adipocytes with an IC50 of 4.3nM and in primary human adipose tissue with an IC80 of 53nM. Oral administration of 11j to cynomolgus monkey inhibited 11ß HSD1 activity in adipose tissue. Compound 11j exhibited >1000× selectivity over other hydroxysteroid dehydrogenases, displays desirable pharmacodynamic properties and entered human clinical trials in 2011.
Asunto(s)
11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/antagonistas & inhibidores , Oxazinas/química , Piridonas/química , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/metabolismo , Tejido Adiposo/citología , Tejido Adiposo/metabolismo , Administración Oral , Animales , Sitios de Unión , Células Cultivadas , Sistema Enzimático del Citocromo P-450/metabolismo , Evaluación Preclínica de Medicamentos , Semivida , Concentración 50 Inhibidora , Macaca fascicularis , Simulación del Acoplamiento Molecular , Oxazinas/administración & dosificación , Oxazinas/farmacocinética , Estructura Terciaria de Proteína , Piridonas/administración & dosificación , Piridonas/farmacocinética , Ratas , Relación Estructura-ActividadRESUMEN
Liver X receptor (LXR) agonists have been reported to lower brain amyloid beta (Aß) and thus to have potential for the treatment of Alzheimer's disease. Structure and property based design led to the discovery of a series of orally bioavailable, brain penetrant LXR agonists. Oral administration of compound 18 to rats resulted in significant upregulation of the expression of the LXR target gene ABCA1 in brain tissue, but no significant effect on Aß levels was detected.
Asunto(s)
Encéfalo/metabolismo , Receptores X del Hígado/efectos de los fármacos , Transportador 1 de Casete de Unión a ATP/genética , Transportador 1 de Casete de Unión a ATP/metabolismo , Animales , Masculino , ARN Mensajero/genética , Ratas , Ratas Sprague-Dawley , Relación Estructura-Actividad , Regulación hacia ArribaRESUMEN
Inhibition of local cortisol regeneration from circulating cortisone by blocking 11ß-hydroxysteroid dehydrogenase 1 (11ß-HSD1) has been shown to ameliorate the risk factors associated with the metabolic syndrome. Chronic modulation of glucocorticoid homeostasis may result in hypothalamic-pituitary-adrenal (HPA) axis stimulation. HPA axis over-activation leading androgen excess would be undesirable in a therapeutic intervention designed to treat a chronic condition such as the metabolic syndrome. To address whether 11ß-HSD1 inhibition would lead to excess androgens, we treated female cynomolgus monkeys with a selective inhibitor, BI 135558, for 4 weeks. Continual action of the compound over the dosing period was confirmed by constant plasma exposure, and a maintained change in urinary glucocorticoid metabolites consistent with 11ß-HSD1 inhibition. No significant changes in adrenal function, as evidenced by an adrenocorticotropic hormone (ATCH) challenge, were observed. An examination of androgenic hormones revealed a slight increase in dehydroepiandrosterone sulfate (DHEA-S), while other hormones such as testosterone remained within reference values. Overall, treatment with BI 135558 in monkeys did not result in obvious over-activation of the HPA axis.
Asunto(s)
11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/antagonistas & inhibidores , Inhibidores Enzimáticos/farmacología , Sistema Hipotálamo-Hipofisario/efectos de los fármacos , Oxazinas/farmacología , Sistema Hipófiso-Suprarrenal/efectos de los fármacos , Piridonas/farmacología , Animales , Inhibidores Enzimáticos/farmacocinética , Femenino , Sistema Hipotálamo-Hipofisario/fisiología , Macaca fascicularis , Oxazinas/farmacocinética , Sistema Hipófiso-Suprarrenal/fisiología , Piridonas/farmacocinética , Factores de TiempoRESUMEN
This article describes the application of Contour to the design and discovery of a novel, potent, orally efficacious liver X receptor ß (LXRß) agonist (17). Contour technology is a structure-based drug design platform that generates molecules using a context perceptive growth algorithm guided by a contact sensitive scoring function. The growth engine uses binding site perception and programmable growth capability to create drug-like molecules by assembling fragments that naturally complement hydrophilic and hydrophobic features of the protein binding site. Starting with a crystal structure of LXRß and a docked 2-(methylsulfonyl)benzyl alcohol fragment (6), Contour was used to design agonists containing a piperazine core. Compound 17 binds to LXRß with high affinity and to LXRα to a lesser extent, and induces the expression of LXR target genes in vitro and in vivo. This molecule served as a starting point for further optimization and generation of a candidate which is currently in human clinical trials for treating atopic dermatitis.
Asunto(s)
Bencilaminas/química , Diseño de Fármacos , Descubrimiento de Drogas , Receptores Nucleares Huérfanos/agonistas , Piperazinas/química , Pirimidinas/química , Pirimidinas/metabolismo , Sulfonas/química , Sulfonas/metabolismo , Sitios de Unión , Cristalografía por Rayos X , Humanos , Receptores X del Hígado , Relación Estructura-ActividadRESUMEN
To combat the increased morbidity and mortality associated with the developing diabetes epidemic new therapeutic interventions are desirable. Inhibition of intracellular cortisol generation from cortisone by blocking 11ß-hydroxysteroid dehydrogenase 1 (11ß-HSD1) has been shown to ameliorate the risk factors associated with the metabolic syndrome. A challenge in developing 11ß-HSD1 inhibitors has been the species selectivity of small molecules, as many compounds are primate specific. Here we describe our strategy to identify potent selective 11ß-HSD1 inhibitors while ensuring target engagement in key metabolic tissues, liver and fat. This strategy enabled the identification of the clinical candidate, BI 135585.
Asunto(s)
11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/antagonistas & inhibidores , Diabetes Mellitus Tipo 2/tratamiento farmacológico , Inhibidores Enzimáticos/farmacología , Oxazinas/farmacología , Piridonas/farmacología , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/química , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/metabolismo , Animales , Dominio Catalítico , Diabetes Mellitus Tipo 2/enzimología , Evaluación Preclínica de Medicamentos , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/uso terapéutico , Humanos , Macaca fascicularis , Masculino , Modelos Moleculares , Oxazinas/química , Oxazinas/uso terapéutico , Piridonas/química , Piridonas/uso terapéuticoRESUMEN
Contour(®) is a computational structure-based drug design technology that grows drug-like molecules by assembling context sensitive fragments in well-defined binding pockets. The grown molecules are scored by a novel empirical scoring function developed using high-resolution crystal structures of diverse classes of protein-ligand complexes and associated experimental binding affinities. An atomic model bearing features of the valence bond and VSEPR theories embodying their molecular electronic environment has been developed for non-covalent intermolecular interactions. On the basis of atomic hybridization and polarization states, each atom is modeled by features representing electron lone pairs, p-orbitals, and polar and non-polar hydrogens. A simple formal charge model was used to differentiate between polar and non-polar atoms. The interaction energy and the desolvation contribution of the protein-ligand association energy is computed as a linear sum of pair-wise interactions and desolvation terms. The pair-wise interaction energy captures short-range positive electrostatic interactions via hydrogen bonds, electrostatic repulsion of like charges, and non-bond contacts. The desolvation energy is estimated by calculating the energy required to desolvate interaction surfaces of the protein and the ligand in the complex. The scoring function predicts binding energies of a diverse set of protein-ligand complexes used for training with a correlation coefficient of 0.61. It also performs equally well in predicting association energies of a diverse validation set of protein-ligand complexes with a correlation coefficient of 0.57, which is equivalent to or better than 12 other scoring functions tested against this set including X-Score, GOLD, and DrugScore.
Asunto(s)
Proteínas/química , Programas Informáticos , Sitios de Unión , Enlace de Hidrógeno , Ligandos , Modelos Moleculares , Unión Proteica , Estructura Terciaria de Proteína , Teoría Cuántica , TermodinámicaRESUMEN
It is well-known that the structure-based design approach has had a measurable impact on the drug discovery process in identifying novel and efficacious therapeutic agents for a variety of disease targets. The de novo design approach has inherent potential to generate novel molecules that best fit into a protein binding site when compared to all of the computational methods applied to structure-based design. In its initial attempts, this approach did not achieve much success due to technical hurdles. More recently, the algorithmic advancements in the methodologies and clever strategies developed to design drug-like molecules have improved the success rate. We describe a state-of-the-art structure-based design technology called Contour and provide details of the algorithmic enhancements we have implemented. Contour was designed to create novel drug-like molecules by assembling synthetically viable fragments in the protein binding site using a high-resolution crystal structure of the protein. The technology consists of a sophisticated growth algorithm and a novel scoring function based on a directional model. The growth algorithm generates molecules by dynamically selecting only those fragments from the fragment library that are complementary to the binding site, and assembling them by sampling the conformational space for each attached fragment. The scoring function embodying the essential elements of the binding interactions aids in the rank ordering of grown molecules and helps identify those that have high probability of exhibiting activity against the protein target of interest. The application of Contour to identify inhibitors against human renin enzyme eventually leading to the clinical candidate VTP-27,999 will be discussed here.
Asunto(s)
Diseño de Fármacos , Inhibidores de Proteasas/química , Inhibidores de Proteasas/farmacología , Renina/antagonistas & inhibidores , Algoritmos , Sitios de Unión , Humanos , Modelos Moleculares , Conformación Proteica , Renina/química , Reproducibilidad de los ResultadosRESUMEN
Structure-based design led to the discovery of a novel class of renin inhibitors in which an unprecedented phenyl ring filling the S1 site is attached to the phenyl ring filling the S3 pocket. Optimization for several parameters including potency in the presence of human plasma, selectivity against CYP3A4 inhibition and improved rat oral bioavailability led to the identification of 8d which demonstrated antihypertensive efficacy in a transgenic rat model of human hypertension.
Asunto(s)
Antihipertensivos/farmacología , Inhibidores Enzimáticos/farmacología , Éteres Fenílicos/farmacología , Renina/antagonistas & inhibidores , Animales , Antihipertensivos/síntesis química , Antihipertensivos/química , Disponibilidad Biológica , Cristalografía por Rayos X , Citocromo P-450 CYP3A/sangre , Inhibidores del Citocromo P-450 CYP3A , Modelos Animales de Enfermedad , Relación Dosis-Respuesta a Droga , Descubrimiento de Drogas , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/química , Humanos , Hipertensión/tratamiento farmacológico , Modelos Moleculares , Conformación Molecular , Éteres Fenílicos/síntesis química , Éteres Fenílicos/química , Ratas , Ratas Transgénicas , Proteínas Recombinantes/antagonistas & inhibidores , Proteínas Recombinantes/aislamiento & purificación , Estereoisomerismo , Relación Estructura-ActividadRESUMEN
Structure based design led directly to 1,3-oxazinan-2-one 9a with an IC(50) of 42 nM against 11ß-HSD1 in vitro. Optimization of 9a for improved in vitro enzymatic and cellular potency afforded 25f with IC(50) values of 0.8 nM for the enzyme and 2.5 nM in adipocytes. In addition, 25f has 94% oral bioavailability in rat and >1000× selectivity over 11ß-HSD2. In mice, 25f was distributed to the target tissues, liver, and adipose, and in cynomolgus monkeys a 10 mg/kg oral dose reduced cortisol production by 85% following a cortisone challenge.
Asunto(s)
11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/antagonistas & inhibidores , Adipocitos/efectos de los fármacos , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/farmacología , Oxazinas/química , Adipocitos/citología , Adipocitos/enzimología , Administración Oral , Animales , Células CHO , Células Cultivadas , Cortisona/farmacología , Cricetinae , Cricetulus , Inhibidores Enzimáticos/farmacocinética , Humanos , Macaca fascicularis , Ratones , Ratas , Proteínas Recombinantes/antagonistas & inhibidores , Proteínas Recombinantes/metabolismo , Relación Estructura-Actividad , Distribución TisularRESUMEN
Structure guided optimization of a series of nonpeptidic alkyl amine renin inhibitors allowed the rational incorporation of additional polar functionality. Replacement of the cyclohexylmethyl group occupying the S1 pocket with a (R)-(tetrahydropyran-3-yl)methyl group and utilization of a different attachment point led to the identification of clinical candidate 9. This compound demonstrated excellent selectivity over related and unrelated off-targets, >15% oral bioavailability in three species, oral efficacy in a double transgenic rat model of hypertension, and good exposure in humans.
RESUMEN
Synthesis of 2-adamantyl carbamate derivatives of piperidines and pyrrolidines led to the discovery of 9a with an IC(50) of 15.2 nM against human 11ß-HSD1 in adipocytes. Optimization for increased adipocyte potency, metabolic stability and selectivity afforded 11k and 11l, both of which were >25% orally bioavailable in rat.
Asunto(s)
11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/antagonistas & inhibidores , Adamantano/farmacología , Inhibidores Enzimáticos/farmacología , Adamantano/química , Animales , Descubrimiento de Drogas , Inhibidores Enzimáticos/química , Modelos Moleculares , RatasRESUMEN
Structure-guided drug design led to the identification of a class of spirocyclic ureas which potently inhibit human 11beta-HSD1 in vitro. Lead compound 10j was shown to be orally bioavailable in three species, distributed into adipose tissue in the mouse, and its (R) isomer 10j2 was efficacious in a primate pharmacodynamic model.
Asunto(s)
11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/antagonistas & inhibidores , Diseño de Fármacos , Urea/administración & dosificación , Urea/farmacocinética , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/metabolismo , Administración Oral , Animales , Sitios de Unión/fisiología , Disponibilidad Biológica , Células CHO , Cricetinae , Cricetulus , Humanos , Macaca fascicularis , Ratones , Ratas , Relación Estructura-Actividad , Urea/análogos & derivadosRESUMEN
Structure-guided drug design led to new alkylamine renin inhibitors with improved in vitro and in vivo potency. Lead compound 21a, has an IC(50) of 0.83nM for the inhibition of human renin in plasma (PRA). Oral administration of 21a at 10mg/kg resulted in >20h reduction of blood pressure in a double transgenic rat model of hypertension.
Asunto(s)
Aminas/química , Carbamatos/química , Inhibidores Enzimáticos/química , Piperidinas/química , Renina/antagonistas & inhibidores , Administración Oral , Aminas/síntesis química , Aminas/farmacocinética , Animales , Sitios de Unión , Presión Sanguínea/efectos de los fármacos , Carbamatos/síntesis química , Carbamatos/farmacocinética , Cristalografía por Rayos X , Diseño de Fármacos , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/farmacocinética , Haplorrinos , Humanos , Piperidinas/síntesis química , Piperidinas/farmacocinética , Ratas , Ratas Transgénicas , Renina/sangre , Renina/metabolismo , Relación Estructura-ActividadRESUMEN
A novel series of annulated tricyclic compounds was synthesized and evaluated as NMDA/NR2B antagonists. Structure-activity development was directed towards in vitro optimization of NR2B activity and selectivity over the hERG K(+) channel. Preferred compounds were subsequently evaluated for selectivity in an alpha(1)-adrenergic receptor binding counter-screen and a cell-based assay of NR2B activity.
Asunto(s)
Benzocicloheptenos/síntesis química , Neurotransmisores/síntesis química , Piridinas/síntesis química , Receptores de N-Metil-D-Aspartato/antagonistas & inhibidores , Benzocicloheptenos/química , Benzocicloheptenos/farmacología , Línea Celular , Canales de Potasio Éter-A-Go-Go/metabolismo , Humanos , Neurotransmisores/química , Neurotransmisores/farmacología , Piridinas/química , Piridinas/farmacología , Receptores de N-Metil-D-Aspartato/metabolismo , Relación Estructura-ActividadRESUMEN
Structure-based drug design led to the identification of a novel class of potent, low MW alkylamine renin inhibitors. Oral administration of lead compound 21l, with MW of 508 and IC(50) of 0.47nM, caused a sustained reduction in mean arterial blood pressure in a double transgenic rat model of hypertension.
Asunto(s)
Antihipertensivos/química , Metilaminas/química , Renina/antagonistas & inhibidores , Administración Oral , Secuencia de Aminoácidos , Animales , Antihipertensivos/síntesis química , Antihipertensivos/farmacocinética , Presión Sanguínea , Simulación por Computador , Cristalografía por Rayos X , Diseño de Fármacos , Humanos , Metilaminas/síntesis química , Metilaminas/farmacocinética , Ratas , Ratas Transgénicas , Renina/metabolismo , Relación Estructura-ActividadRESUMEN
A novel series of cyclic benzamidines was synthesized and shown to exhibit NR2B-subtype selective NMDA antagonist activity. Compound 29 is orally active in a carrageenan-induced rat hyperalgesia model of pain.
Asunto(s)
Benzamidinas/farmacología , Antagonistas de Aminoácidos Excitadores/farmacología , Receptores de N-Metil-D-Aspartato/antagonistas & inhibidores , Administración Oral , Animales , Benzamidinas/administración & dosificación , Benzamidinas/uso terapéutico , Antagonistas de Aminoácidos Excitadores/administración & dosificación , Modelos Biológicos , Dolor/tratamiento farmacológico , RatasRESUMEN
The discovery of a novel series of NR2B subtype selective N-methyl-d-aspartate (NMDA) antagonists is reported. Initial optimization of a high-throughput screening lead afforded an aminopyridine derivative 13 with significant NR2B antagonist potency but limited selectivity over hERG-channel and other off-target activities. Further structure-activity studies on the aminoheterocycle moiety and optimization of the carbamate led to the highly potent 2-aminopyrimidine derivative 20j with a significantly improved off-target activity profile and oral bioavailability in multiple species coupled with good brain penetration. Compound 20j demonstrated efficacy in in vivo rodent models of antinociception, allodynia, and Parkinson's disease.
Asunto(s)
Analgésicos/síntesis química , Encéfalo/metabolismo , Pirimidinas/síntesis química , Receptores de N-Metil-D-Aspartato/antagonistas & inhibidores , Administración Oral , Analgésicos/farmacocinética , Analgésicos/farmacología , Animales , Antiparkinsonianos/síntesis química , Antiparkinsonianos/farmacocinética , Antiparkinsonianos/farmacología , Disponibilidad Biológica , Línea Celular , Perros , Femenino , Lóbulo Frontal/metabolismo , Humanos , Masculino , Dimensión del Dolor , Pirimidinas/farmacocinética , Pirimidinas/farmacología , Ensayo de Unión Radioligante , Ratas , Ratas Sprague-Dawley , Relación Estructura-ActividadRESUMEN
Two classes of 5-substituted benzimidazoles were identified as potent antagonists of the NR2B subtype of the N-methyl-d-aspartate (NMDA) receptor. Selected compounds show very good selectivity versus the NR2A, NR2C, and NR2D subtypes of the NMDA receptor as well as versus hERG-channel activity and alpha(1)-adrenergic binding. Benzimidazole 37a shows excellent activity in the carrageenan-induced mechanical hyperalgesia assay in rats as well as good pharmacokinetic behavior in dogs.