RESUMEN
In the past few years, attempts have been made to use decision criteria beyond Lipinski's guidelines (Rule of five) to guide drug discovery projects more effectively. Several variables and formulations have been proposed and investigated within the framework of multiparameter optimization methods to guide drug discovery. In this context, the combination of Ligand Efficiency Indices (LEI) has been predominantly used to map and monitor the drug discovery process in a retrospective fashion. Here we provide an example of the use of a novel application of the LEI methodology for prospective lead optimization by using the transthyretin (TTR) fibrillogenesis inhibitor iododiflunisal (IDIF) as example. Using this approach, a number of compounds with theoretical efficiencies higher than the reference compound IDIF were identified. From this group, ten compounds were selected, synthesized and biologically tested. Half of the compounds (5, 6, 7, 8 and 10) showed potencies in terms of IC50 inhibition of TTR aggregation equal or higher than the lead compound. These optimized compounds mapped within the region of more efficient candidates in the corresponding experimental nBEI-NSEI plot, matching their position in the theoretical optimization plane that was used for the prediction. Due to their upstream (North-Eastern) position in the progression lines of NPOLâ¯=â¯3 or 4 of the nBEI-NSEI plot, three of them (5, 6 and 8) are more interesting candidates than iododiflunisal because they have been optimized in the three crucial LEI variables of potency, size and polarity at the same time. This is the first example of the effectiveness of using the combined LEIs within the decision process to validate the application of the LEI formulation for the prospective optimization of lead compounds.
Asunto(s)
Ligandos , Prealbúmina/metabolismo , Diflunisal/análogos & derivados , Diflunisal/farmacología , Humanos , Cinética , Mutagénesis Sitio-Dirigida , Prealbúmina/antagonistas & inhibidores , Prealbúmina/genética , Unión Proteica , Multimerización de Proteína/efectos de los fármacos , Relación Estructura-ActividadRESUMEN
This study represents a systematic chemical and biological study of the rufomycin (RUF) class of cyclic heptapeptides, which our anti-TB drug discovery efforts have identified as potentially promising anti-TB agents that newly target the caseinolytic protein C1, ClpC1. Eight new RUF analogues, rufomycins NBZ1-NBZ8 (1-8), as well as five known peptides (9-13) were isolated and characterized from the Streptomyces atratus strain MJM3502. Advanced Marfey's and X-ray crystallographic analysis led to the assignment of the absolute configuration of the RUFs. Several isolates exhibited potent activity against both pathogens M. tuberculosis H37Rv and M. abscessus, paired with favorable selectivity (selectivity index >60), which collectively underscores the promise of the rufomycins as potential anti-TB drug leads.
Asunto(s)
Antituberculosos/farmacología , Mycobacterium tuberculosis/efectos de los fármacos , Oligopéptidos/farmacología , Streptomyces/química , Cristalografía por Rayos X , Pruebas de Sensibilidad Microbiana , Estructura MolecularRESUMEN
The design and synthesis of indazolinone containing kinase inhibitors are reported. Regioisomers that showed profound potency variation in previously-reported isoindolinone and aminoindazole systems were surprisingly found to have similar potencies in the case of the indazolinone chemical series. An interpretation using differential hinge hydrogen bonding and tautomeric equilibrium of indazolinone ring system is supported by quantum mechanics calculations. The equipotent inhibition of a representative kinase (KDR) by regioisomeric indazolinones 4 and 5 is clear evidence that in case of the indazolinone hinge, both tautomers are equally favored, and should be considered in design of inhibitors.
Asunto(s)
Indazoles/síntesis química , Inhibidores de Proteínas Quinasas/síntesis química , Receptor 2 de Factores de Crecimiento Endotelial Vascular/antagonistas & inhibidores , Indazoles/farmacología , Isomerismo , Modelos Moleculares , Estructura Molecular , Inhibidores de Proteínas Quinasas/farmacología , Relación Estructura-ActividadRESUMEN
Four hinge-binding scaffolds have been explored for novel selective Aurora kinase inhibitors. The structure activity relationship, selectivity and pharmacokinetic profiles have been evaluated.
Asunto(s)
Inhibidores de Proteínas Quinasas/síntesis química , Proteínas Serina-Treonina Quinasas/antagonistas & inhibidores , Animales , Aurora Quinasas , Línea Celular , Ratones , Modelos Moleculares , Estructura Molecular , Inhibidores de Proteínas Quinasas/farmacología , Relación Estructura-ActividadRESUMEN
In an effort to discover Aurora kinase inhibitors, an HTS hit revealed an amide containing pyrrolopyrimidine compound. Replacement of the pyrrolopyrimidine residue with a thienopyrimidine moiety led to a series of potent and selective Aurora inhibitors.
Asunto(s)
Descubrimiento de Drogas , Inhibidores de Proteínas Quinasas/farmacología , Proteínas Serina-Treonina Quinasas/antagonistas & inhibidores , Pirimidinas/farmacología , Animales , Aurora Quinasas , Relación Dosis-Respuesta a Droga , Ensayos Analíticos de Alto Rendimiento , Enlace de Hidrógeno , Ratones , Modelos Moleculares , Estructura Molecular , Inhibidores de Proteínas Quinasas/síntesis química , Inhibidores de Proteínas Quinasas/química , Proteínas Serina-Treonina Quinasas/metabolismo , Pirimidinas/síntesis química , Pirimidinas/química , Estereoisomerismo , Relación Estructura-ActividadRESUMEN
Fructose-1,6-bisphosphatase (FBPase; EC 3.1.3.11), which is a key enzyme in gluconeogenesis, catalyzes the hydrolysis of fructose 1,6-bisphosphate to form fructose 6-phosphate and orthophosphate. The present investigation reports the crystallization and preliminary crystallographic studies of the glpX-encoded class II FBPase from Mycobacterium tuberculosis H37Rv. The recombinant protein, which was cloned using an Escherichia coli expression system, was purified and crystallized using the hanging-drop vapor-diffusion method. The crystals diffracted to a resolution of 2.7â Å and belonged to the hexagonal space group P6(1)22, with unit-cell parameters a = b = 131.3, c = 143.2â Å. The structure has been solved by molecular replacement and is currently undergoing refinement.
Asunto(s)
Fructosadifosfatos/química , Mycobacterium tuberculosis/enzimología , Cristalización , Cristalografía por Rayos X , Fructosadifosfatos/aislamiento & purificaciónRESUMEN
The true identity of the protein found in the crystals reported by Bondoc et al. [(2019), Acta Cryst. F75, 646-651] is given.
RESUMEN
OBJECTIVES: The secreted Mycobacterium tuberculosis protein tyrosine phosphatase (MptpB) is a virulence factor for M. tuberculosis and contributes to its survival within host macrophages. The aim of this study was to identify potent selective inhibitors of MptpB and to determine the efficacy of these compounds in mycobacterium-infected macrophages. METHODS: The inhibitory effect of a small library of compounds on MptpB was first examined in vitro. The efficacy of these compounds was further examined in mycobacterium-infected macrophages. RESULTS: We have identified a new family of double-site isoxazole-based compounds that are potent selective inhibitors of MptpB. Importantly, the inhibitors substantially reduce mycobacterial survival in infected macrophages. In contrast with current anti-tubercular drugs, these MptpB inhibitors do not have bactericidal action but rather, severely impair mycobacterial growth within macrophages. Docking analysis suggests a double-site binding mechanism of inhibition with the isoxazole head in the active site and a salicylate group in a secondary binding pocket that is a unique structural feature of MptpB. CONCLUSIONS: These results provide the first evidence that inhibition of phosphatases can be exploited against mycobacterial infections. The cell activity of the inhibitors together with the lack of MptpB human orthologues suggests a strong potential for these compounds to be developed as drug candidates against tuberculosis and promises a new therapeutic strategy to tackle clearance and reduce the persistence of M. tuberculosis infection.
Asunto(s)
Proteínas Bacterianas/antagonistas & inhibidores , Inhibidores Enzimáticos/farmacología , Macrófagos/microbiología , Viabilidad Microbiana , Mycobacterium tuberculosis/enzimología , Mycobacterium tuberculosis/inmunología , Proteínas Tirosina Fosfatasas/antagonistas & inhibidores , Animales , Línea Celular , Inhibidores Enzimáticos/química , Ratones , Modelos Moleculares , Estructura Molecular , Mycobacterium tuberculosis/efectos de los fármacos , Unión ProteicaRESUMEN
We report the discovery of the pyrimido-diazepine scaffolds as novel adenine mimics. Structure-based design led to the discovery of analogs with potent inhibitory activity against receptor tyrosine kinases, such as KDR, Flt3 and c-Kit. Compound 14 exhibited low nanomolar KDR enzymatic and cellular potencies (IC(50)=9 and 52 nM, respectively).
Asunto(s)
Azepinas/síntesis química , Azepinas/farmacología , Diseño de Fármacos , Inhibidores de Proteínas Quinasas/síntesis química , Inhibidores de Proteínas Quinasas/farmacología , Pirimidinas/química , Proteínas Tirosina Quinasas Receptoras/antagonistas & inhibidores , Células 3T3 , Animales , Azepinas/química , Enlace de Hidrógeno , Ratones , Modelos Moleculares , Estructura Molecular , Inhibidores de Proteínas Quinasas/química , Proteínas Tirosina Quinasas Receptoras/química , Proteínas Tirosina Quinasas Receptoras/metabolismo , Relación Estructura-ActividadAsunto(s)
Bases de Datos de Proteínas , Proteínas/química , Análisis de Varianza , Cristalografía por Rayos X , Bases de Datos de Proteínas/historia , Historia del Siglo XX , Historia del Siglo XXI , Análisis de los Mínimos Cuadrados , Resonancia Magnética Nuclear Biomolecular , Conformación ProteicaRESUMEN
On a glorious spring day in the American Midwest, friends, colleagues, collaborators, and alumni of Prof. M.G. Replacement gathered together at the campus of Purdue University, West Lafayette, Indiana to celebrate 40 years of structural biology and honor the man behind it all: M.G. Rossmann. The date also corresponded approximately to MGR's 75th birthday. It was a memorable occasion for several reasons. An earlier meeting 10 years ago did also render homage to Michael (New Directions in Protein-Structure Relationships: Symposium in Honor of Professor M.G. Rossmann's 65th Birthday, Purdue University, October 21, 1995), but on this occasion the symposium was much more encompassing of structural biology and had a more global character. A large number of featured speakers presented and discussed advances in vast areas of structural biology and came from the four corners of the world to share their work with the new generations of structural biologists currently being trained at Purdue University.
Asunto(s)
Biología Molecular/historia , Universidades , Historia del Siglo XX , IndianaRESUMEN
The c-Jun N-terminal kinases (JNK-1, -2, and -3) are members of the mitogen activated protein (MAP) kinase family of enzymes. They are activated in response to certain cytokines, as well as by cellular stresses including chemotoxins, peroxides, and irradiation. They have been implicated in the pathology of a variety of different diseases with an inflammatory component including asthma, stroke, Alzheimer's disease, and type 2 diabetes mellitus. In this work, high-throughput screening identified a JNK inhibitor with an excellent kinase selectivity profile. Using X-ray crystallography and biochemical screening to guide our lead optimization, we prepared compounds with inhibitory potencies in the low-double-digit nanomolar range, activity in whole cells, and pharmacokinetics suitable for in vivo use. The new compounds were over 1,000-fold selective for JNK-1 and -2 over other MAP kinases including ERK2, p38alpha, and p38delta and showed little inhibitory activity against a panel of 74 kinases.
Asunto(s)
Aminopiridinas/síntesis química , Proteína Quinasa 8 Activada por Mitógenos/antagonistas & inhibidores , Proteína Quinasa 9 Activada por Mitógenos/antagonistas & inhibidores , Aminopiridinas/química , Aminopiridinas/farmacología , Animales , Disponibilidad Biológica , Línea Celular Tumoral , Cristalografía por Rayos X , Semivida , Humanos , Proteína Quinasa 10 Activada por Mitógenos/metabolismo , Proteína Quinasa 8 Activada por Mitógenos/química , Proteína Quinasa 8 Activada por Mitógenos/metabolismo , Proteína Quinasa 9 Activada por Mitógenos/metabolismo , Modelos Moleculares , Fosforilación , Conformación Proteica , Ratas , Ratas Sprague-DawleyRESUMEN
C-Jun NH2 terminal kinases (JNKs) are important cell signaling enzymes. JNK1 plays a central role in linking obesity and insulin resistance. JNK2 and JNK3 may be involved in inflammatory and neurological disorders, respectively. Small-molecule JNK inhibitors could be valuable tools to study the therapeutic benefits of inhibiting these enzymes and as leads for potential drugs targeting JNKs. In this report, we disclose a series of potent and highly selective JNK inhibitors with good pharmacokinetic profiles.
Asunto(s)
Amidas/síntesis química , Proteínas Quinasas JNK Activadas por Mitógenos/antagonistas & inhibidores , Piridinas/síntesis química , Administración Oral , Amidas/farmacocinética , Amidas/farmacología , Animales , Disponibilidad Biológica , Cristalografía por Rayos X , Humanos , Técnicas In Vitro , Ratones , Microsomas/metabolismo , Modelos Moleculares , Piridinas/farmacocinética , Piridinas/farmacología , Ratas , Relación Estructura-Actividad , TermodinámicaRESUMEN
Dedicated to the people who designed, built, and currently work at synchrotron beamlines.
Asunto(s)
Investigadores/historia , Sincrotrones/historia , Difracción de Rayos X/historia , Historia del Siglo XX , Difracción de Rayos X/instrumentaciónAsunto(s)
Evolución Molecular , Proteínas/química , Proteínas/genética , Animales , Cristalografía por Rayos X , HumanosRESUMEN
Using an NMR-based fragment screening and X-ray crystal structure-based assembly, starting with millimolar ligands for both the catalytic site and the second phosphotyrosine binding site, we have identified a small-molecule inhibitor of protein tyrosine phosphatase 1B with low micromolar inhibition constant, high selectivity (30-fold) over the highly homologous T-cell protein tyrosine phosphatase, and good cellular activity in COS-7 cells.
Asunto(s)
Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Ácido Oxámico/análogos & derivados , Ácido Oxámico/farmacología , Proteínas Tirosina Fosfatasas/antagonistas & inhibidores , Animales , Sitios de Unión , Células COS , Dominio Catalítico , Cristalografía por Rayos X , Proteínas de Unión al ADN/antagonistas & inhibidores , Proteínas de Unión al ADN/metabolismo , Diseño de Fármacos , Modelos Moleculares , Imitación Molecular , Resonancia Magnética Nuclear Biomolecular/métodos , Ácido Oxámico/síntesis química , Fosforilación , Proteína Tirosina Fosfatasa no Receptora Tipo 1 , Proteína Tirosina Fosfatasa no Receptora Tipo 2 , Proteínas Tirosina Fosfatasas/metabolismo , Factor de Transcripción STAT3 , Relación Estructura-Actividad , Transactivadores/antagonistas & inhibidores , Transactivadores/metabolismoRESUMEN
Protein tyrosine phosphatase (PTPase) 1B (PTP1B) has been implicated as a key negative regulator of both insulin and leptin signaling cascades. We identified several salicylic acid-based ligands for the second phosphotyrosine binding site of PTP1B using a NMR-based screening. Structure-based linking with a catalytic site-directed oxalylarylaminobenzoic acid-based pharmacophore led to the identification of a novel series of potent PTP1B inhibitors exhibiting 6-fold selectivity over the highly homologous T-cell PTPase (TCPTP) and high selectivity over other phosphatases.
Asunto(s)
Inhibidores Enzimáticos/síntesis química , Fosfotirosina/química , Proteínas Tirosina Fosfatasas/antagonistas & inhibidores , Salicilatos/síntesis química , Dominio Catalítico , Técnicas Químicas Combinatorias , Cristalografía por Rayos X , Inhibidores Enzimáticos/química , Ligandos , Espectroscopía de Resonancia Magnética , Proteína Tirosina Fosfatasa no Receptora Tipo 1 , Proteínas Tirosina Fosfatasas/química , Salicilatos/química , Estereoisomerismo , Relación Estructura-Actividad , Linfocitos T/químicaRESUMEN
Protein Tyrosine phosphatase 1B (PTP1B) has been implicated as a key negative regulator of both insulin and leptin signaling pathways. Using an NMR-based screening approach with 15N- and 13C-labeled PTP1B, we have identified 2,3-dimethylphenyloxalylaminobenzoic acid (1) as a general, reversible, and competitive PTPase inhibitor. Structure-based approach guided by X-ray crystallography facilitated the development of 1 into a novel series of potent and selective PTP1B inhibitors occupying both the catalytic site and a portion of the noncatalytic, second phosphotyrosine binding site. Interestingly, oral biovailability has been observed in rats for some compounds. Furthermore, we demonstrated in vivo plasma glucose lowering effects with compound 12d in ob/ob mice.
Asunto(s)
Ácido 4-Aminobenzoico/síntesis química , Aminobenzoatos/síntesis química , Inhibidores Enzimáticos/síntesis química , Hipoglucemiantes/síntesis química , Fenilalanina/síntesis química , Proteínas Tirosina Fosfatasas/antagonistas & inhibidores , para-Aminobenzoatos , Ácido 4-Aminobenzoico/farmacocinética , Ácido 4-Aminobenzoico/farmacología , Administración Oral , Secuencia de Aminoácidos , Aminobenzoatos/farmacocinética , Aminobenzoatos/farmacología , Animales , Disponibilidad Biológica , Glucemia/análisis , Células CACO-2 , Dominio Catalítico , Cristalografía por Rayos X , Inhibidores Enzimáticos/farmacocinética , Inhibidores Enzimáticos/farmacología , Humanos , Hipoglucemiantes/farmacocinética , Hipoglucemiantes/farmacología , Espectroscopía de Resonancia Magnética , Masculino , Ratones , Modelos Moleculares , Datos de Secuencia Molecular , Permeabilidad , Fenilalanina/análogos & derivados , Fenilalanina/farmacocinética , Fenilalanina/farmacología , Proteína Tirosina Fosfatasa no Receptora Tipo 1 , Proteínas Tirosina Fosfatasas/química , Ratas , Estereoisomerismo , Relación Estructura-ActividadRESUMEN
A number of alternative variables have appeared in the medicinal chemistry literature trying to provide a more rigorous formulation of the guidelines proposed by Lipinski to exclude chemical entities with poor pharmacokinetic properties early in the discovery process. Typically, these variables combine the affinity towards the target with physicochemical properties of the ligand and are named efficiencies or ligand efficiencies. Several formulations have been defined and used by different laboratories with different degrees of success. A unified formulation, ligand efficiency indices, was proposed that included efficiency in two complementary variables (i.e., size and polarity) to map and monitor the drug-discovery process (AtlasCBS). The use of this formulation in combination with an extended multiparameter optimization is presented, with examples, as a promising methodology to optimize the drug-discovery process in the future. Future perspectives and challenges for this approach are also discussed.