RESUMEN
Bruton's tyrosine kinase (BTK) is a Tec family kinase with a well-defined role in the B cell receptor (BCR) pathway. It has become an attractive kinase target for selective B cell inhibition, and for the treatment of B cell related diseases. Many BTK inhibitors have been discovered for the treatment of cancer and rheumatoid arthritis, including a series of BTK inhibitors based on 8-amino-imidazo[1,5-a]pyrazine we recently reported. The X-ray crystal structures of BTK with inhibitors were also published, which provided great help for the SAR design. Here we report our SAR work introducing ring constraints for the 3-position piperidine amides on the BTK inhibitors based on 8-amino-imidazo[1,5-a]pyrazine. This modification improved the potency in BTK inhibitions, as well as the PK profile and the off-target selectivity. The dose-dependent efficacy of two BTK inhibitors was observed in the rat collagen induced arthritis (CIA) model.
Asunto(s)
Agammaglobulinemia Tirosina Quinasa/antagonistas & inhibidores , Imidazoles/química , Inhibidores de Proteínas Quinasas/química , Pirazinas/química , Agammaglobulinemia Tirosina Quinasa/metabolismo , Animales , Artritis Experimental/tratamiento farmacológico , Sitios de Unión , Compuestos Bicíclicos con Puentes/química , Cristalografía por Rayos X , Modelos Animales de Enfermedad , Perros , Relación Dosis-Respuesta a Droga , Semivida , Humanos , Imidazoles/metabolismo , Imidazoles/uso terapéutico , Simulación de Dinámica Molecular , Inhibidores de Proteínas Quinasas/metabolismo , Inhibidores de Proteínas Quinasas/uso terapéutico , Pirazinas/metabolismo , Pirazinas/uso terapéutico , Ratas , Ratas Wistar , Relación Estructura-Actividad , Familia-src Quinasas/antagonistas & inhibidores , Familia-src Quinasas/metabolismoRESUMEN
Two orthogonal approaches for hit identification in drug discovery are large-scale in vitro and in silico screening. In recent years, due to the emergence of new targets and a rapid increase in the size of the readily synthesizable chemical space, there is a growing emphasis on the integration of the two techniques to improve the hit finding efficiency. Here, we highlight three examples of drug discovery projects at Merck & Co., Inc., Kenilworth, NJ, USA in which different virtual screening (VS) techniques, each specifically tailored to leverage knowledge available for the target, were utilized to augment the selection of high-quality chemical matter for in vitro assays and to enhance the diversity and tractability of hits. Central to success is a fully integrated workflow combining in silico and experimental expertise at every stage of the hit identification process. We advocate that workflows encompassing VS as part of an integrated hit finding plan should be widely adopted to accelerate hit identification and foster cross-functional collaborations in modern drug discovery.
Asunto(s)
Descubrimiento de Drogas , Ensayos Analíticos de Alto Rendimiento , Simulación por Computador , Bibliotecas de Moléculas PequeñasRESUMEN
The 2016 D3R Grand Challenge 2 includes both pose and affinity or ranking predictions. This article is focused exclusively on affinity predictions submitted to the D3R challenge from a collaborative effort of the modeling and informatics group. Our submissions include ranking of 102 ligands covering 4 different chemotypes against the FXR ligand binding domain structure, and the relative binding affinity predictions of the two designated free energy subsets of 15 and 18 compounds. Using all the complex structures prepared in the same way allowed us to cover many types of workflows and compare their performances effectively. We evaluated typical workflows used in our daily structure-based design modeling support, which include docking scores, force field-based scores, QM/MM, MMGBSA, MD-MMGBSA, and MacroModel interaction energy estimations. The best performing methods for the two free energy subsets are discussed. Our results suggest that affinity ranking still remains very challenging; that the knowledge of more structural information does not necessarily yield more accurate predictions; and that visual inspection and human intervention are considerably important for ranking. Knowledge of the mode of action and protein flexibility along with visualization tools that depict polar and hydrophobic maps are very useful for visual inspection. QM/MM-based workflows were found to be powerful in affinity ranking and are encouraged to be applied more often. The standardized input and output enable systematic analysis and support methodology development and improvement for high level blinded predictions.
Asunto(s)
Descubrimiento de Drogas , Simulación del Acoplamiento Molecular , Receptores Citoplasmáticos y Nucleares/metabolismo , Termodinámica , Flujo de Trabajo , Sitios de Unión , Diseño Asistido por Computadora , Bases de Datos de Proteínas , Diseño de Fármacos , Humanos , Ligandos , Unión Proteica , Conformación Proteica , Receptores Citoplasmáticos y Nucleares/agonistas , Receptores Citoplasmáticos y Nucleares/antagonistas & inhibidores , Receptores Citoplasmáticos y Nucleares/química , Compuestos de Espiro/química , Compuestos de Espiro/farmacología , Sulfonamidas/química , Sulfonamidas/farmacologíaRESUMEN
We describe the performance of multiple pose prediction methods for the D3R 2016 Grand Challenge. The pose prediction challenge includes 36 ligands, which represent 4 chemotypes and some miscellaneous structures against the FXR ligand binding domain. In this study we use a mix of fully automated methods as well as human-guided methods with considerations of both the challenge data and publicly available data. The methods include ensemble docking, colony entropy pose prediction, target selection by molecular similarity, molecular dynamics guided pose refinement, and pose selection by visual inspection. We evaluated the success of our predictions by method, chemotype, and relevance of publicly available data. For the overall data set, ensemble docking, visual inspection, and molecular dynamics guided pose prediction performed the best with overall mean RMSDs of 2.4, 2.2, and 2.2 Å respectively. For several individual challenge molecules, the best performing method is evaluated in light of that particular ligand. We also describe the protein, ligand, and public information data preparations that are typical of our binding mode prediction workflow.
Asunto(s)
Diseño Asistido por Computadora , Diseño de Fármacos , Descubrimiento de Drogas , Simulación del Acoplamiento Molecular , Receptores Citoplasmáticos y Nucleares/metabolismo , Sitios de Unión , Cristalografía por Rayos X , Bases de Datos de Proteínas , Humanos , Ligandos , Simulación de Dinámica Molecular , Unión Proteica , Conformación Proteica , Receptores Citoplasmáticos y Nucleares/química , TermodinámicaRESUMEN
8-Amino-imidazo[1,5-a]pyrazine-based Bruton's tyrosine kinase (BTK) inhibitors, such as 6, exhibited potent inhibition of BTK but required improvements in both kinase and hERG selectivity (Liu et al., 2016; Gao et al., 2017). In an effort to maintain the inhibitory activity of these analogs and improve their selectivity profiles, we carried out SAR exploration of groups at the 3-position of pyrazine compound 6. This effort led to the discovery of the morpholine group as an optimized pharmacophore. Compounds 13, 23 and 38 displayed excellent BTK potencies, kinase and hERG selectivities, and pharmacokinetic profiles.
Asunto(s)
Artritis Reumatoide/tratamiento farmacológico , Descubrimiento de Drogas , Imidazoles/farmacología , Morfolinas/farmacología , Inhibidores de Proteínas Quinasas/farmacología , Proteínas Tirosina Quinasas/antagonistas & inhibidores , Artritis Reumatoide/metabolismo , Relación Dosis-Respuesta a Droga , Humanos , Imidazoles/síntesis química , Imidazoles/química , Leucocitos Mononucleares/efectos de los fármacos , Leucocitos Mononucleares/metabolismo , Modelos Moleculares , Estructura Molecular , Morfolinas/síntesis química , Morfolinas/química , Inhibidores de Proteínas Quinasas/síntesis química , Inhibidores de Proteínas Quinasas/química , Proteínas Tirosina Quinasas/metabolismo , Relación Estructura-Actividad , Regulador Transcripcional ERG/antagonistas & inhibidores , Regulador Transcripcional ERG/metabolismoRESUMEN
We report the design and synthesis of a series of novel Bruton's Tyrosine Kinase (BTK) inhibitors with a carboxylic acid moiety in the ribose pocket. This series of compounds has demonstrated much improved off-target selectivities including adenosine uptake (AdU) inhibition compared to the piperidine amide series. Optimization of the initial lead compound 4 based on BTK enzyme inhibition, and human peripheral blood mononuclear cell (hPBMC) and human whole blood (hWB) activity led to the discovery of compound 40, with potent BTK inhibition, reduced off target activities, as well as favorable pharmacokinetic profile in both rat and dog.
Asunto(s)
Ácidos Carboxílicos/farmacología , Descubrimiento de Drogas , Inhibidores de Proteínas Quinasas/farmacología , Proteínas Tirosina Quinasas/antagonistas & inhibidores , Agammaglobulinemia Tirosina Quinasa , Animales , Humanos , RatasRESUMEN
Novel potent and selective 5,6,5- and 5,5,6-tricyclic pyrrolidine dipeptidyl peptidase IV (DPP-4) inhibitors were identified. Structure-activity relationship (SAR) efforts focused on improving the intrinsic DPP-4 inhibition potency, increasing protease selectivity, and demonstrating clean ion channel and cytochrome P450 profiles while trying to achieve a pharmacokinetic profile suitable for once weekly dosing in humans.
Asunto(s)
Dipeptidil Peptidasa 4/metabolismo , Inhibidores de la Dipeptidil-Peptidasa IV/farmacología , Descubrimiento de Drogas , Pirrolidinas/farmacología , Animales , Cristalografía por Rayos X , Inhibidores de la Dipeptidil-Peptidasa IV/síntesis química , Inhibidores de la Dipeptidil-Peptidasa IV/química , Perros , Relación Dosis-Respuesta a Droga , Humanos , Modelos Moleculares , Estructura Molecular , Pirrolidinas/síntesis química , Pirrolidinas/química , Ratas , Relación Estructura-ActividadRESUMEN
A series of novel substituted-[(3R)-amino-2-(2,5-difluorophenyl)]tetrahydro-2H-pyran analogs have been prepared and evaluated as potent, selective and orally active DPP-4 inhibitors. These efforts lead to the discovery of a long acting DPP-4 inhibitor, omarigliptin (MK-3102), which recently completed phase III clinical development and has been approved in Japan.
Asunto(s)
Amidas/química , Inhibidores de la Dipeptidil-Peptidasa IV/química , Compuestos Heterocíclicos con 2 Anillos/química , Piranos/química , Sulfonamidas/química , Animales , Sitios de Unión , Dipeptidil Peptidasa 4/química , Dipeptidil Peptidasa 4/metabolismo , Inhibidores de la Dipeptidil-Peptidasa IV/síntesis química , Inhibidores de la Dipeptidil-Peptidasa IV/farmacocinética , Perros , Semivida , Compuestos Heterocíclicos con 2 Anillos/síntesis química , Compuestos Heterocíclicos con 2 Anillos/farmacocinética , Simulación del Acoplamiento Molecular , Estructura Terciaria de Proteína , Piranos/síntesis química , Piranos/farmacocinética , Ratas , Relación Estructura-ActividadRESUMEN
A series of novel tri-2,3,5-substituted tetrahydropyran analogs were synthesized and evaluated as inhibitors of dipeptidyl peptidase IV (DPP-4) for the treatment of type 2 diabetes. Optimization of the series provided inhibitors with good DPP-4 potency and selectivity over other peptidases (QPP, DPP8, and FAP). Compound 23, which is very potent, selective, efficacious in the diabetes PD model, and has an excellent pharmacokinetic profile, is selected as a clinical candidate.
Asunto(s)
Inhibidores de la Dipeptidil-Peptidasa IV/síntesis química , Compuestos Heterocíclicos con 2 Anillos/síntesis química , Piranos/síntesis química , Animales , Diabetes Mellitus Tipo 2/tratamiento farmacológico , Inhibidores de la Dipeptidil-Peptidasa IV/química , Inhibidores de la Dipeptidil-Peptidasa IV/farmacología , Perros , Activación Enzimática/efectos de los fármacos , Prueba de Tolerancia a la Glucosa , Haplorrinos , Humanos , Concentración 50 Inhibidora , Piranos/química , Piranos/farmacología , Ratas , EstereoisomerismoRESUMEN
Bombesin receptor subtype 3 (BRS-3) is an orphan G-protein coupled receptor expressed primarily in the hypothalamus which plays a role in the onset of both diabetes and obesity. We report herein our progress made towards identifying a potent, selective bombesin receptor subtype-3 (BRS-3) agonist related to the previously described MK-7725(1) Chobanian et al. (2012) that would prevent atropisomerization through the increase of steric bulk at the C-2 position. This would thereby make clinical development of this class of compounds more cost effective by inhibiting racemization which can occur over long periods of time at room/elevated temperature.
Asunto(s)
Benzodiazepinas/química , Diseño de Fármacos , Receptores de Bombesina/agonistas , Sulfonamidas/química , Sulfonamidas/síntesis química , Animales , Humanos , Ratones , Unión Proteica , Ratas , Receptores de Bombesina/metabolismo , Estereoisomerismo , Sulfonamidas/farmacocinética , TemperaturaRESUMEN
One approach to estimating the "chemical tractability" of a candidate protein target where we know the atomic resolution structure is to examine the physical properties of potential binding sites. A number of other workers have addressed this issue. We characterize ~290,000 "pockets" from ~42,000 protein crystal structures in terms of a three parameter "pocket space": volume, buriedness, and hydrophobicity. A metric DLID (drug-like density) measures how likely a pocket is to bind a drug-like molecule. This is calculated from the count of other pockets in its local neighborhood in pocket space that contain drug-like cocrystallized ligands and the count of total pockets in the neighborhood. Surprisingly, despite being defined locally, a global trend in DLID can be predicted by a simple linear regression on log(volume), buriedness, and hydrophobicity. Two levels of simplification are necessary to relate the DLID of individual pockets to "targets": taking the best DLID per Protein Data Bank (PDB) entry (because any given crystal structure can have many pockets), and taking the median DLID over all PDB entries for the same target (because different crystal structures of the same protein can vary because of artifacts and real conformational changes). We can show that median DLIDs for targets that are detectably homologous in sequence are reasonably similar and that median DLIDs correlate with the "druggability" estimate of Cheng et al. (Nature Biotechnology 2007, 25, 71-75).
Asunto(s)
Bases de Datos de Proteínas , Descubrimiento de Drogas/métodos , Preparaciones Farmacéuticas/química , Preparaciones Farmacéuticas/metabolismo , Proteínas/química , Proteínas/metabolismo , Animales , Bovinos , Humanos , Interacciones Hidrofóbicas e Hidrofílicas , Ligandos , Ratones , Modelos Moleculares , Unión Proteica , Conformación ProteicaRESUMEN
A series of spiroindoline-3,4'-piperidine derivatives were synthesized and evaluated for their binding affinities and antagonistic activities at Y5 receptors. Potent Y5 antagonists were tested for their oral bioavailabilities and brain penetration in rats. Some of the antagonists showed good oral bioavailability and/or good brain penetration. In particular, compound 6e was orally bioavailable and brain penetrant, and oral administration of 6e inhibited bPP-induced food intake in rats with a minimum effective dose of 10mg/kg.
Asunto(s)
Química Farmacéutica/métodos , Indoles/administración & dosificación , Indoles/farmacología , Receptores de Neuropéptido Y/antagonistas & inhibidores , Receptores de Neuropéptido Y/química , Administración Oral , Aminas/química , Animales , Disponibilidad Biológica , Encéfalo/efectos de los fármacos , Diseño de Fármacos , Concentración 50 Inhibidora , Isocianatos/química , Modelos Químicos , Biblioteca de Péptidos , Ratas , Urea/químicaRESUMEN
Analogs of the previously reported voltage gated sodium channel blocker CDA54 were prepared in which one of the amide functions was replaced with aromatic and non-aromatic heterocycles. Replacement of the amide with an aromatic heterocycle resulted in significant loss of sodium channel blocking activity, while non-aromatic heterocycle replacements were well tolerated.
Asunto(s)
Isoxazoles/química , Isoxazoles/farmacología , Bloqueadores de los Canales de Sodio/química , Bloqueadores de los Canales de Sodio/farmacología , Animales , Isoxazoles/uso terapéutico , Modelos Moleculares , Estructura Molecular , Dolor/tratamiento farmacológico , Ratas , Ratas Sprague-Dawley , Bloqueadores de los Canales de Sodio/uso terapéutico , Nervios Espinales/efectos de los fármacos , Relación Estructura-ActividadRESUMEN
A series of novel isoxazole voltage gated sodium channel blockers have been synthesized and evaluated. Substitutions on the benzylic position of benzamide were investigated to determine their effect on Na(v)1.7 inhibitory potency. The spirocyclobutyl substitution had the most significant enhancement on Na(v)1.7 inhibitory activity.
Asunto(s)
Isoxazoles/uso terapéutico , Dolor/tratamiento farmacológico , Bloqueadores de los Canales de Sodio/uso terapéutico , Canales de Sodio/metabolismo , Animales , Línea Celular , Enfermedad Crónica , Humanos , Isoxazoles/química , Isoxazoles/farmacología , Dolor/inmunología , Ratas , Bloqueadores de los Canales de Sodio/química , Bloqueadores de los Canales de Sodio/farmacología , Nervios Espinales/efectos de los fármacos , Relación Estructura-ActividadRESUMEN
Probing with tool molecules, and by modeling and X-ray crystallography the binding modes of two structurally distinct series of DPP-4 inhibitors led to the discovery of a rare aromatic fluorine H-bond and the spatial requirement for better biaryl binding in the DPP-4 enzyme active site. These newly found binding elements were successfully incorporated into novel DPP-4 inhibitors.
Asunto(s)
Dipeptidil Peptidasa 4/química , Sitios de Unión , Química Farmacéutica/métodos , Cristalografía por Rayos X/métodos , Inhibidores de la Dipeptidil-Peptidasa IV , Diseño de Fármacos , Flúor/química , Glicina/química , Humanos , Enlace de Hidrógeno , Concentración 50 Inhibidora , Modelos Químicos , Modelos Teóricos , Conformación Molecular , Programas Informáticos , beta-Alanina/químicaRESUMEN
AIMS: Since 2006, DPP-4 inhibitors have become established therapy for the treatment of type 2 diabetes. Despite sharing a common mechanism of action, considerable chemical diversity exists amongst members of the DPP-4 inhibitor class, raising the question as to whether structural differences may result in differentiated enzyme inhibition and antihyperglycaemic activity. METHODS: We have compared the binding properties of the most commonly used inhibitors and have investigated the relationship between their inhibitory potency at the level of the enzyme and their acute glucose-lowering efficacy. RESULTS: Firstly, using a combination of published crystal structures and in-house data, we demonstrated that the binding site utilized by all of the DPP-4 inhibitors assessed was the same as that used by neuropeptide Y, supporting the hypothesis that DPP-4 inhibitors are able to competitively inhibit endogenous substrates for the enzyme. Secondly, we ascertained that the enzymatic cleft of DPP-4 is a relatively large cavity which displays conformational flexibility to accommodate structurally diverse inhibitor molecules. Finally, we found that for all inhibitors, irrespective of their chemical structure, the inhibition of plasma DPP-4 enzyme activity correlates directly with acute plasma glucose lowering in mice. CONCLUSION: The common binding site utilized by different DPP-4 inhibitors enables similar competitive inhibition of the cleavage of the endogenous DPP-4 substrates. Furthermore, despite chemical diversity and a range of binding potencies observed amongst the DPP-4 inhibitors, a direct relationship between enzyme inhibition in the plasma and glucose lowering is evident in mice for each member of the classes studied.
RESUMEN
In our efforts to develop second generation DPP-4 inhibitors, we endeavored to identify distinct structures with long-acting (once weekly) potential. Taking advantage of X-ray cocrystal structures of sitagliptin and other DPP-4 inhibitors, such as alogliptin and linagliptin bound to DPP-4, and aided by molecular modeling, we designed several series of heterocyclic compounds as initial targets. During their synthesis, an unexpected chemical transformation provided a novel tricyclic scaffold that was beyond our original design. Capitalizing on this serendipitous discovery, we have elaborated this scaffold into a very potent and selective DPP-4 inhibitor lead series, as highlighted by compound 17c.
RESUMEN
Bruton's tyrosine kinase (BTK) is a Tec family kinase with a well-defined role in the B cell receptor (BCR) pathway. It has become an attractive kinase target for selective B cell inhibition and for the treatment of B cell related diseases. We report a series of compounds based on 8-amino-imidazo[1,5-a]pyrazine that are potent reversible BTK inhibitors with excellent kinase selectivity. Selectivity is achieved through specific interactions of the ligand with the kinase hinge and driven by aminopyridine hydrogen bondings with Ser538 and Asp539, and by hydrophobic interaction of trifluoropyridine in the back pocket. These interactions are evident in the X-ray crystal structure of the lead compounds 1 and 3 in the complex with the BTK enzyme. Our lead compounds show desirable PK profiles and efficacy in the preclinical rat collagen induced arthritis model.
RESUMEN
To gain insight into the molecular determinants that define the specificity of interaction of pore-blocking peptides, such as agitoxin 2 (AgTX2), charybdotoxin (ChTX), and iberiotoxin (IbTX) with the Shaker-type voltage-gated potassium channel Kv1.3, or the large-conductance Ca(2+)-activated K(+) (Maxi-K) channel, homology models of these channels were generated based on the crystal structure of the bacterial, KcsA, potassium channel. Peptide-channel complexes were analyzed to evaluate the predicted interaction interfaces between the peptides and the channels' outer vestibules. The docking model, for either AgTX2 or ChTX with the Kv1.3 channel, predicts a novel hydrogen bonding interaction between the Asn30 side-chain of the peptide and the Asp381 side-chain of the channel. This interaction is consistent with the >500-fold decreased potency of both AgTX2 and ChTX mutants at position 30 for the Shaker channel [(Ranganathan et al., Neuron 1996;16:131-139); (Goldstein et al., Neuron 1994;12:1377-1388)]. This hydrogen bonding interaction also suggests that Gly30 in IbTX may be the critical determinant for its lack of activity against Shaker Kv channels. The model of the Maxi-K channel reveals a narrower and more structurally restrained outer vestibule in which the aromatic residues Phe266 and Tyr294 may stabilize binding of IbTX and ChTX by pi-pi stacking with the aromatic residues Trp14 and Tyr36 of the peptides. This study also suggests that the extra net negative charge of IbTX is not related to the selectivity of this peptide for the Maxi-K channel.
Asunto(s)
Bloqueadores de los Canales de Potasio/química , Canales de Potasio Calcio-Activados/química , Canales de Potasio con Entrada de Voltaje/química , Canales de Potasio/química , Venenos de Escorpión/química , Toxinas Biológicas/química , Secuencia de Aminoácidos , Animales , Sitios de Unión , Caribdotoxina/química , Caribdotoxina/metabolismo , Enlace de Hidrógeno , Canal de Potasio Kv1.3 , Canales de Potasio de Gran Conductancia Activados por el Calcio , Modelos Moleculares , Datos de Secuencia Molecular , Péptidos/química , Péptidos/metabolismo , Péptidos/farmacología , Bloqueadores de los Canales de Potasio/metabolismo , Canales de Potasio/metabolismo , Canales de Potasio Calcio-Activados/metabolismo , Canales de Potasio con Entrada de Voltaje/metabolismo , Unión Proteica , Subunidades de Proteína , Venenos de Escorpión/metabolismo , Alineación de SecuenciaRESUMEN
Iberiotoxin (IbTX) is a remarkably selective alpha-K toxin peptide (alpha-KTx) inhibitor of the maxi-K channel. In contrast, the highly homologous charybdotoxin inhibits both the maxi-K and K(V)1.3 channels with similar high affinity. The present study investigates the molecular basis for this specificity through mutagenesis of IbTX. The interactions of mutated peptides with maxi-K and K(V)1.3 channels were monitored through dose-dependent displacement of specifically bound iodinated alpha-KTx peptides from membranes expressing these channels. Results of these studies suggest that the presence of a glycine at position 30 in IbTX is a major determinant of its specificity while the presence of four unique acidic residues in IbTX is not.