RESUMEN
We describe our efforts to identify structurally diverse leads in the triazole-containing N1-carboline series of bromodomain and extra-terminal inhibitors. Replacement of the N5 "cap" phenyl moiety with various heteroaryls, coupled with additional modifications to the carboline core, provided analogs with similar potency, improved pharmacokinetic properties, and increased solubility compared to our backup lead, BMS-986225 (2). Rapid SAR exploration was enabled by a convergent, synthetic route. These efforts provided a potent BET inhibitor, 3-fluoropyridyl 12, that demonstrated robust efficacy in a multiple myeloma mouse tumor model at 1 mg/kg.
Asunto(s)
Antineoplásicos/farmacología , Carbolinas/farmacología , Desarrollo de Medicamentos , Mieloma Múltiple/dietoterapia , Proteínas/antagonistas & inhibidores , Triazoles/farmacología , Animales , Antineoplásicos/síntesis química , Antineoplásicos/química , Carbolinas/síntesis química , Carbolinas/química , Relación Dosis-Respuesta a Droga , Humanos , Ratones , Estructura Molecular , Mieloma Múltiple/metabolismo , Proteínas/metabolismo , Relación Estructura-Actividad , Triazoles/síntesis química , Triazoles/químicaRESUMEN
We describe our efforts to introduce structural diversity to a previously described triazole-containing N1-carboline series of bromodomain and extra-terminal (BET) inhibitors. N9 carbolines were designed to retain favorable binding interactions that the N1-carbolines possess. A convergent synthetic route enabled modifications to reduce clearance, enhance physicochemical properties, and improve the overall in vitro profile. This work led to the identification of a potent BET inhibitor, (S)-2-{8-fluoro-5-[(3-fluoropyridin-2-yl)(oxan-4-yl)methyl]-7-[4-(2H3)methyl-1-methyl-1H-1,2,3-triazol-5-yl]-5H-pyrido[3,2-b]indol-3-yl}propan-2-ol (10), a compound with enhanced oral exposure in mice. Subsequent evaluation in a mouse triple-negative breast cancer tumor model revealed efficacy at 4 mg/kg of N9-carboline 10.
Asunto(s)
Antineoplásicos/farmacología , Carbolinas/farmacología , Desarrollo de Medicamentos , Proteínas/antagonistas & inhibidores , Neoplasias de la Mama Triple Negativas/tratamiento farmacológico , Administración Oral , Animales , Antineoplásicos/administración & dosificación , Antineoplásicos/química , Carbolinas/administración & dosificación , Carbolinas/química , Supervivencia Celular/efectos de los fármacos , Relación Dosis-Respuesta a Droga , Ensayos de Selección de Medicamentos Antitumorales , Humanos , Neoplasias Mamarias Experimentales/tratamiento farmacológico , Neoplasias Mamarias Experimentales/patología , Ratones , Estructura Molecular , Proteínas/metabolismo , Relación Estructura-Actividad , Neoplasias de la Mama Triple Negativas/patologíaRESUMEN
The discovery of orally bioavailable FXIa inhibitors has been a challenge. Herein, we describe our efforts to address this challenge by optimization of our imidazole-based macrocyclic series. Our optimization strategy focused on modifications to the P2 prime, macrocyclic amide linker, and the imidazole scaffold. Replacing the amide of the macrocyclic linker with amide isosteres led to the discovery of substituted amine linkers which not only maintained FXIa binding affinity but also improved oral exposure in rats. Combining the optimized macrocyclic amine linker with a pyridine scaffold afforded compounds 23 and 24 that were orally bioavailable, single-digit nanomolar FXIa inhibitors with excellent selectivity against relevant blood coagulation enzymes.
Asunto(s)
Aminas/química , Factor XIa/antagonistas & inhibidores , Compuestos Macrocíclicos/química , Inhibidores de Serina Proteinasa/síntesis química , Administración Oral , Animales , Sitios de Unión , Diseño de Fármacos , Factor XIa/metabolismo , Semivida , Compuestos Macrocíclicos/metabolismo , Compuestos Macrocíclicos/farmacocinética , Simulación de Dinámica Molecular , Estructura Terciaria de Proteína , Piridinas/química , Ratas , Inhibidores de Serina Proteinasa/metabolismo , Inhibidores de Serina Proteinasa/farmacocinética , Relación Estructura-ActividadRESUMEN
This manuscript describes the discovery of a series of macrocyclic inhibitors of FXIa with oral bioavailability. Assisted by structure based drug design and ligand bound X-ray crystal structures, the group linking the P1 moiety to the macrocyclic core was modified with the goal of reducing H-bond donors to improve pharmacokinetic performance versus 9. This effort resulted in the discovery of several cyclic P1 linkers, exemplified by 10, that are constrained mimics of the bioactive conformation displayed by the acrylamide linker of 9. These cyclic P1 linkers demonstrated enhanced bioavailability and improved potency.
Asunto(s)
Diseño de Fármacos , Descubrimiento de Drogas , Factor XIa/antagonistas & inhibidores , Compuestos Macrocíclicos/administración & dosificación , Compuestos Macrocíclicos/química , Inhibidores de Serina Proteinasa/administración & dosificación , Inhibidores de Serina Proteinasa/química , Administración Oral , Disponibilidad Biológica , Humanos , Ligandos , Compuestos Macrocíclicos/farmacología , Modelos Moleculares , Estructura Molecular , Inhibidores de Serina Proteinasa/farmacología , Relación Estructura-ActividadRESUMEN
Pyridazine and pyridazinone derivatives were designed and synthesized as coagulation factor XIa inhibitors. Potent and selective inhibitors with single digit nanomolar affinity for factor XIa were discovered. Selected inhibitors demonstrated moderate oral bioavailability.
Asunto(s)
Factor XIa/antagonistas & inhibidores , Piridazinas/farmacología , Inhibidores de Serina Proteinasa/farmacología , Cristalografía por Rayos X , Relación Dosis-Respuesta a Droga , Factor XIa/metabolismo , Humanos , Microsomas Hepáticos/efectos de los fármacos , Microsomas Hepáticos/metabolismo , Modelos Moleculares , Estructura Molecular , Piridazinas/síntesis química , Piridazinas/química , Inhibidores de Serina Proteinasa/síntesis química , Inhibidores de Serina Proteinasa/química , Relación Estructura-ActividadRESUMEN
The TGFß-TGFßR signaling pathway has been reported to play a protective role in the later stages of tumorigenesis via increasing immunosuppressive Treg cells and facilitating the epithelial to mesenchymal transition (EMT). Therefore, inhibition of TGFßR has the potential to enhance antitumor immunity. Herein we disclose the identification and optimization of novel heterobicyclic inhibitors of TGFßRI that demonstrate potent inhibition of SMAD phosphorylation. Application of structure-based drug design to the novel pyrrolotriazine chemotype resulted in improved binding affinity (Ki apparentâ¯=â¯0.14â¯nM), long residence time (T1/2â¯>â¯120â¯min) and significantly improved potency in the PSMAD cellular assay (IC50â¯=â¯24â¯nM). Several analogs inhibited phosphorylation of SMAD both in vitro and in vivo. Additionally, inhibition of TGFß-stimulated phospho-SMAD was observed in primary human T cells.
Asunto(s)
Compuestos Bicíclicos con Puentes/química , Proteínas Serina-Treonina Quinasas/antagonistas & inhibidores , Receptores de Factores de Crecimiento Transformadores beta/antagonistas & inhibidores , Sitios de Unión , Compuestos Bicíclicos con Puentes/síntesis química , Compuestos Bicíclicos con Puentes/farmacología , Células Cultivadas , Cristalografía por Rayos X , Diseño de Fármacos , Transición Epitelial-Mesenquimal/efectos de los fármacos , Humanos , Simulación de Dinámica Molecular , Fosforilación , Unión Proteica , Proteínas Serina-Treonina Quinasas/metabolismo , Estructura Terciaria de Proteína , Pirroles/síntesis química , Pirroles/química , Pirroles/metabolismo , Receptor Tipo I de Factor de Crecimiento Transformador beta , Receptores de Factores de Crecimiento Transformadores beta/metabolismo , Proteínas Smad/metabolismo , Relación Estructura-Actividad , Linfocitos T/citología , Linfocitos T/metabolismo , Tiazinas/síntesis química , Tiazinas/química , Tiazinas/metabolismoRESUMEN
Alkoxyanthranilic acid derivatives have been identified to inhibit HCV NS5B polymerase, binding in an allosteric site located at the convergence of the palm and thumb regions. Information from co-crystal structures guided the structural design strategy. Ultimately, two independent structural modifications led to a similar shift in binding mode that when combined led to a synergistic improvement in potency and the identification of inhibitors with sub-micromolar HCV NS5B binding potency.
Asunto(s)
Descubrimiento de Drogas , Inhibidores Enzimáticos/farmacología , Proteínas no Estructurales Virales/antagonistas & inhibidores , ortoaminobenzoatos/farmacología , Cristalografía por Rayos X , Relación Dosis-Respuesta a Droga , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/química , Modelos Moleculares , Estructura Molecular , Relación Estructura-Actividad , Proteínas no Estructurales Virales/metabolismo , ortoaminobenzoatos/síntesis química , ortoaminobenzoatos/químicaRESUMEN
A series of macrocyclic factor XIa (FXIa) inhibitors was designed based on an analysis of the crystal structures of the acyclic phenylimidazole compounds. Further optimization using structure-based design led to inhibitors with pM affinity for FXIa, excellent selectivity against a panel of relevant serine proteases, and good potency in the activated partial thromboplastin time (aPTT) clotting assay.
Asunto(s)
Factor XIa/antagonistas & inhibidores , Imidazoles/farmacología , Compuestos Macrocíclicos/farmacología , Inhibidores de Serina Proteinasa/farmacología , Relación Dosis-Respuesta a Droga , Factor XIa/metabolismo , Humanos , Imidazoles/síntesis química , Imidazoles/química , Compuestos Macrocíclicos/síntesis química , Compuestos Macrocíclicos/química , Estructura Molecular , Inhibidores de Serina Proteinasa/síntesis química , Inhibidores de Serina Proteinasa/química , Relación Estructura-ActividadRESUMEN
Optimization of macrocyclic inhibitors of FXIa is described which focused on modifications to both the macrocyclic linker and the P1 group. Increases in potency were discovered through interactions with a key hydrophobic region near the S1 prime pocket by substitution of the macrocyclic linker with small alkyl groups. Both the position of substitution and the absolute stereochemistry of the alkyl groups on the macrocyclic linker which led to improved potency varied depending on the ring size of the macrocycle. Replacement of the chlorophenyltetrazole cinnamide P1 in these optimized macrocycles reduced the polar surface area and improved the oral bioavailability for the series, albeit at the cost of a decrease in potency.
Asunto(s)
Amidas/farmacología , Descubrimiento de Drogas , Factor XIa/antagonistas & inhibidores , Compuestos Macrocíclicos/farmacología , Inhibidores de Serina Proteinasa/farmacología , Amidas/síntesis química , Amidas/química , Cristalografía por Rayos X , Relación Dosis-Respuesta a Droga , Factor XIa/metabolismo , Humanos , Compuestos Macrocíclicos/síntesis química , Compuestos Macrocíclicos/química , Modelos Moleculares , Estructura Molecular , Inhibidores de Serina Proteinasa/síntesis química , Inhibidores de Serina Proteinasa/química , Relación Estructura-ActividadRESUMEN
Pyridine-based Factor XIa (FXIa) inhibitor (S)-2 was optimized by modifying the P2 prime, P1, and scaffold regions. This work resulted in the discovery of the methyl N-phenyl carbamate P2 prime group which maintained FXIa activity, reduced the number of H-bond donors, and improved the physicochemical properties compared to the amino indazole P2 prime moiety. Compound (S)-17 was identified as a potent and selective FXIa inhibitor that was orally bioavailable. Replacement of the basic cyclohexyl methyl amine P1 in (S)-17 with the neutral p-chlorophenyltetrazole P1 resulted in the discovery of (S)-24 which showed a significant improvement in oral bioavailability compared to the previously reported imidazole (S)-23. Additional improvements in FXIa binding affinity, while maintaining oral bioavailability, was achieved by replacing the pyridine scaffold with either a regioisomeric pyridine or pyrimidine ring system.
Asunto(s)
Anticoagulantes/química , Anticoagulantes/farmacología , Factor XIa/antagonistas & inhibidores , Piridinas/química , Piridinas/farmacología , Pirimidinas/química , Pirimidinas/farmacología , Administración Oral , Animales , Anticoagulantes/administración & dosificación , Anticoagulantes/farmacocinética , Coagulación Sanguínea/efectos de los fármacos , Cristalografía por Rayos X , Perros , Factor XIa/metabolismo , Humanos , Modelos Moleculares , Fenilcarbamatos/administración & dosificación , Fenilcarbamatos/química , Fenilcarbamatos/farmacocinética , Fenilcarbamatos/farmacología , Piridinas/administración & dosificación , Piridinas/farmacocinética , Pirimidinas/administración & dosificación , Pirimidinas/farmacocinéticaRESUMEN
Compound 2 was previously identified as a potent inhibitor of factor XIa lacking oral bioavailability. A structure-based approach was used to design analogs of 2 with novel P1 moieties with good selectivity profiles and oral bioavailability. Further optimization of the P1 group led to the identification of a 4-chlorophenyltetrazole P1 analog, which when combined with further modifications to the linker and P2' group provided compound 32 with FXIa Ki=6.7 nM and modest oral exposure in dogs.
Asunto(s)
Diseño de Fármacos , Inhibidores Enzimáticos/farmacología , Factor XIa/antagonistas & inhibidores , Indazoles/farmacología , Administración Oral , Animales , Disponibilidad Biológica , Perros , Relación Dosis-Respuesta a Droga , Inhibidores Enzimáticos/administración & dosificación , Inhibidores Enzimáticos/química , Factor XIa/efectos de los fármacos , Humanos , Indazoles/administración & dosificación , Indazoles/química , Modelos Moleculares , Estructura Molecular , Relación Estructura-ActividadRESUMEN
In this Letter, we describe the synthesis of several nonamidine analogs of biaryl acid factor VIIa inhibitor 1 containing weakly basic or nonbasic P1 groups. 2-Aminoisoquinoline was found to be an excellent surrogate for the benzamidine group (compound 2) wherein potent inhibition of factor VIIa is maintained relative to most other related serine proteases. In an unanticipated result, the m-benzamide P1 (compounds 21a and 21b) proved to be a viable benzamidine replacement, albeit with a 20-40 fold loss in potency against factor VIIa.
Asunto(s)
Ácidos Carboxílicos/química , Descubrimiento de Drogas , Factor VIIa/antagonistas & inhibidores , Inhibidores de Serina Proteinasa/química , Inhibidores de Serina Proteinasa/farmacología , Benzamidinas , Cristalografía por Rayos X , Relación Dosis-Respuesta a Droga , Factor VIIa/metabolismo , Humanos , Modelos Moleculares , Estructura Molecular , Inhibidores de Serina Proteinasa/síntesis química , Relación Estructura-ActividadRESUMEN
We describe the synthesis of triazole-containing carboline derivatives and their utility as bromodomain and extra-terminal (BET) inhibitors. A convergent synthetic route permitted the detailed investigation of deuteration and fluorination strategies to reduce clearance while maintaining a favorable in vitro profile. This work led to the identification of a potent BET inhibitor, 2-{8-fluoro-3-[4-(2H3)methyl-1-methyl-1H-1,2,3-triazol-5-yl]-5-[(S)-(oxan-4-yl)(phenyl)methyl]-5H-pyrido[3,2-b]indol-7-yl}propan-2-ol (15), which demonstrated reduced clearance and an improved pharmacokinetic (PK) profile across preclinical species. Importantly, no major metabolite was observed when 15 was incubated with human hepatocytes (hHEP) for 2 h. This study culminated with the evaluation of 15 in a mouse triple-negative breast cancer (TNBC) tumor model where it demonstrated robust efficacy at low doses.
RESUMEN
Factor XIa (FXIa) is an enzyme in the coagulation cascade thought to amplify thrombin generation but has a limited role in hemostasis. From preclinical models and human genetics, an inhibitor of FXIa has the potential to be an antithrombotic agent with superior efficacy and safety. Reversible and irreversible inhibitors of FXIa have demonstrated excellent antithrombotic efficacy without increased bleeding time in animal models (Weitz, J. I., Chan, N. C. Arterioscler. Thromb. Vasc. Biol. 2019, 39 (1), 7-12). Herein, we report the discovery of a novel series of macrocyclic FXIa inhibitors containing a pyrazole P2' moiety. Optimization of the series for (pharmacokinetic) PK properties, free fraction, and solubility resulted in the identification of milvexian (BMS-986177/JNJ-70033093, 17, FXIa Ki = 0.11 nM) as a clinical candidate for the prevention and treatment of thromboembolic disorders, suitable for oral administration.
Asunto(s)
Trombosis de las Arterias Carótidas , Factor XIa , Fibrinolíticos , Pirimidinas , Triazoles , Animales , Ratones , Conejos , Administración Oral , Trombosis de las Arterias Carótidas/tratamiento farmacológico , Factor XIa/antagonistas & inhibidores , Fibrinolíticos/administración & dosificación , Fibrinolíticos/síntesis química , Fibrinolíticos/farmacocinética , Fibrinolíticos/uso terapéutico , Macaca fascicularis , Estructura Molecular , Pirazoles/administración & dosificación , Pirazoles/síntesis química , Pirazoles/farmacocinética , Pirazoles/uso terapéutico , Pirimidinas/administración & dosificación , Pirimidinas/síntesis química , Pirimidinas/farmacocinética , Pirimidinas/uso terapéutico , Ratas Sprague-Dawley , Relación Estructura-Actividad , Triazoles/administración & dosificación , Triazoles/síntesis química , Triazoles/farmacocinética , Triazoles/uso terapéuticoRESUMEN
Structure based rationales for the activities of potent N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamide inhibitors of the hepatitis C viral polymerase are described herein. These compounds bind to the hepatitis C virus non-structural protein 5B (NS5B), and co-crystal structures of select examples from this series with NS5B are reported. Comparison of co-crystal structures of a potent analog with both NS5B genotype 1a and genotype 1b provides a possible explanation for the genotype-selectivity observed with this compound class and suggests opportunities for the further optimization of the series.
Asunto(s)
Amidas/química , Antivirales/química , Inhibidores Enzimáticos/química , Hepacivirus/enzimología , Proteínas no Estructurales Virales/antagonistas & inhibidores , Amidas/síntesis química , Amidas/farmacología , Antivirales/síntesis química , Antivirales/farmacología , Sitios de Unión , Simulación por Computador , Cristalografía por Rayos X , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/farmacología , Hepacivirus/efectos de los fármacos , Proteínas no Estructurales Virales/metabolismoRESUMEN
Herein, we present initial SAR studies on a series of bridged 2-arylindole-based NS5B inhibitors. The introduction of bridging elements between the indole N1 and the ortho-position of the 2-aryl moiety resulted in conformationally constrained heterocycles that possess multiple additional vectors for further exploration. The binding mode and pharmacokinetic (PK) properties of select examples, including: 13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[2,1-d][1,4]benzodiazepine-10-carboxylic acid (7) (IC(50)=0.07 µM, %F=18), are reported.
Asunto(s)
Activación Enzimática/efectos de los fármacos , Hepacivirus/enzimología , Compuestos Heterocíclicos/síntesis química , Compuestos Heterocíclicos/farmacología , Indoles/química , Proteínas no Estructurales Virales/antagonistas & inhibidores , Diseño de Fármacos , Compuestos Heterocíclicos/química , Concentración 50 Inhibidora , Modelos Moleculares , Estructura Molecular , Relación Estructura-ActividadRESUMEN
Derived from the HTS hit 1, a series of hydroxyisoquinolines was discovered as potent and selective 11ß-HSD1 inhibitors with good cross species activity. Optimization of substituents at the 1 and 4 positions of the isoquinoline group in addition to the core modifications, with a special focus on enhancing metabolic stability and aqueous solubility, resulted in the identification of several compounds as potent advanced leads.
Asunto(s)
11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/antagonistas & inhibidores , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/metabolismo , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Isoquinolinas/química , Isoquinolinas/farmacología , Animales , Línea Celular , Diabetes Mellitus Tipo 2/tratamiento farmacológico , Inhibidores Enzimáticos/farmacocinética , Humanos , Isoquinolinas/farmacocinética , Ratones , Ratones Endogámicos BALB C , Relación Estructura-ActividadRESUMEN
The method of conserved core substructure matching (CSM) for the overlay of protein-ligand complexes is described. The method relies upon distance geometry to align structurally similar substructures without regard to sequence similarity onto substructures from a reference protein empirically selected to include key determinants of binding site location and geometry. The error in ligand position is reduced in reoriented ensembles generated with CSM when compared to other overlay methods. Since CSM can only succeed when the selected core substructure is geometrically conserved, misalignments only rarely occur. The method may be applied to reliably overlay large numbers of protein-ligand complexes in a way that optimizes ligand position at a specific binding site or subsite or to align structures from large and diverse protein families where the conserved binding site is localized to only a small portion of either protein. Core substructures may be complex and must be chosen with care. We have created a database of empirically selected core substructures to demonstrate the utility of CSM alignment of ligand binding sites in important drug targets. A Web-based interface can be used to apply CSM to align large collections of protein-ligand complexes for use in drug design using these substructures or to evaluate the use of alternative core substructures that may then be shared with the larger user community. Examples show the benefit of CSM in the practice of structure-based drug design.
Asunto(s)
Química Farmacéutica/métodos , Descubrimiento de Drogas/métodos , Preparaciones Farmacéuticas/análisis , Proteínas Quinasas/análisis , Programas Informáticos , Estaurosporina/análisis , Sitios de Unión , Dominio Catalítico , Simulación por Computador , Minería de Datos , Bases de Datos de Proteínas , Diseño de Fármacos , Humanos , Ligandos , Modelos Moleculares , Preparaciones Farmacéuticas/química , Preparaciones Farmacéuticas/metabolismo , Unión Proteica , Proteínas Quinasas/química , Proteínas Quinasas/metabolismo , Alineación de Secuencia , Bibliotecas de Moléculas Pequeñas , Estaurosporina/química , Estaurosporina/metabolismo , Relación Estructura-Actividad , Especificidad por SustratoRESUMEN
Protein tyrosine phosphatase γ is a membrane-bound receptor and is designated RPTPγ. RPTPγ and two mutants, RPTPγ(V948I, S970T) and RPTPγ(C858S, S970T), were recombinantly expressed and purified for X-ray crystallographic studies. The purified enzymes were crystallized using the hanging-drop vapor-diffusion method. Crystallographic data were obtained from several different crystal forms in the absence and the presence of inhibitor. In this paper, a description is given of how three different crystal forms were obtained that were used with various ligands. An orthorhombic crystal form and a trigonal crystal form were obtained both with and without ligand, and a monoclinic crystal form was only obtained in the presence of a particularly elaborated inhibitor.
Asunto(s)
Dominio Catalítico , Proteínas Tirosina Fosfatasas Similares a Receptores/química , Secuencia de Aminoácidos , Clonación Molecular , Cristalización , Cristalografía por Rayos X , Humanos , Datos de Secuencia Molecular , Proteínas Tirosina Fosfatasas Similares a Receptores/genética , Proteínas Tirosina Fosfatasas Similares a Receptores/aislamiento & purificaciónRESUMEN
Hematopoietic progenitor kinase 1 (HPK1) is an intracellular kinase that plays an important role in modulating tumor immune response and thus is an attractive target for drug discovery. Crystallization of the wild-type HPK1 kinase domain has been hampered by poor expression in recombinant systems and poor solubility. In this study, yeast surface display was applied to a library of HPK1 kinase-domain variants in order to select variants with an improved expression level and solubility. The HPK1 variant with the most improved properties contained two mutations, crystallized readily in complex with several small-molecule inhibitors and provided valuable insight to guide structure-based drug design. This work exemplifies the benefit of yeast surface display towards engineering crystallizable proteins and thus enabling structure-based drug discovery.