RESUMEN
The introduction of AlphaFold 21 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design2-6. Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein-ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein-nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody-antigen prediction accuracy compared with AlphaFold-Multimer v.2.37,8. Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.
Asunto(s)
Aprendizaje Profundo , Ligandos , Modelos Moleculares , Proteínas , Programas Informáticos , Humanos , Anticuerpos/química , Anticuerpos/metabolismo , Antígenos/metabolismo , Antígenos/química , Aprendizaje Profundo/normas , Iones/química , Iones/metabolismo , Simulación del Acoplamiento Molecular , Ácidos Nucleicos/química , Ácidos Nucleicos/metabolismo , Unión Proteica , Conformación Proteica , Proteínas/química , Proteínas/metabolismo , Reproducibilidad de los Resultados , Programas Informáticos/normasRESUMEN
PURPOSE: Sphingosine kinase 1 (SK1) is a protooncogenic enzyme expressed in many human tumours and is associated with chemoresistance and poor prognosis. It is a potent therapy target and its inhibition chemosensitises solid tumours. Despite recent advances in SK1 inhibitors synthesis and validation, their clinical safety and chemosensitising options are not well described. In this study, we have designed, synthesised and tested a new specific SK1 inhibitor with a low toxicity profile. METHODS: Field template molecular modelling was used for compound design. Lead compounds were tested in cell and mouse cancer models. RESULTS: Field template analysis of three known SK1 inhibitors, SKI-178, 12aa and SK1-I, was performed and compound screening identified six potential new SK1 inhibitors. SK1 activity assays in both cell-free and in vitro settings showed that two compounds were effective SK1 inhibitors. Compound SK-F has potently decreased cancer cell viability in vitro and sensitised mouse breast tumours to docetaxel (DTX) in vivo, without significant whole-body toxicity. CONCLUSION: Through field template screening, we have identified a new SK1 inhibitor, SK-F, which demonstrated antitumour activity in vitro and in vivo without overt toxicity when combined with DTX.
Asunto(s)
Neoplasias de la Mama/tratamiento farmacológico , Docetaxel/farmacología , Inhibidores Enzimáticos/química , Fosfotransferasas (Aceptor de Grupo Alcohol)/antagonistas & inhibidores , Amino Alcoholes/química , Animales , Protocolos de Quimioterapia Combinada Antineoplásica/farmacología , Neoplasias de la Mama/genética , Neoplasias de la Mama/patología , Línea Celular Tumoral , Supervivencia Celular/efectos de los fármacos , Sistema Libre de Células/efectos de los fármacos , Resistencia a Antineoplásicos/efectos de los fármacos , Resistencia a Antineoplásicos/genética , Inhibidores Enzimáticos/administración & dosificación , Inhibidores Enzimáticos/síntesis química , Femenino , Humanos , Hidrazinas/química , Ligandos , Ratones , Modelos Moleculares , Fosfotransferasas (Aceptor de Grupo Alcohol)/química , Fosfotransferasas (Aceptor de Grupo Alcohol)/genética , Pirazoles/química , Ensayos Antitumor por Modelo de XenoinjertoRESUMEN
The association constants for formation a 1:1 complex between 4-phenyl azophenol and tri-n-butylphosphine oxide were measured in mixtures of n-octane and n-decanol, n-octane and n-hexanoic acid, and n-octane and 2-ethylhexyl acetamide. The experiments provide insight into the competition between solvent self-association and solvent-solute interactions in these systems. The solvation properties of the three polar solvents are quite different from one another and from polar solvents that do not self-associate. Carboxylic acids form dimers in concentrated solution (>1 mM in alkanes). Carboxylic acid dimers have exposed H-bond acceptor sites that solvate H-bond donor solutes with a similar binding affinity to carboxylic acid monomers. The carboxylic acid H-bond donor site is inaccessible in the dimer and is not available to solvate H-bond acceptor solutes. The result is that solvation of H-bond acceptor solutes is in competition with solvent dimerization, whereas solvation of H-bond donor solutes is not. Secondary amides form linear polymers in concentrated solution (>10 mM in alkanes). The solvation properties of the secondary amide aggregates are similar to those of carboxylic acid dimers. Solvation of H-bond acceptor solutes must compete with solvent self-association, because the amide H-bond donor site is not accessible in the middle of a polymeric aggregate. However, the amide aggregates have exposed H-bond acceptor sites, which solvate H-bond donor solutes with similar binding affinity to amide monomers. Alcohols form cyclic tetramers at concentrations of 100 mM in alkanes, and these cyclic aggregates are in equilibrium with linear polymeric aggregates at concentrations above 1 M. The alcohol aggregates have exposed H-bond acceptor sites that solvate H-bond donor solutes with similar binding affinity to alcohol monomers. Although the alcohol H-bond donor sites are involved in H-bond interactions with other alcohols in the aggregates, these sites are sufficiently exposed to form a second bifurcated H-bond with H-bond acceptor solutes, and these interactions have a similar binding affinity to alcohol monomers. The result is that self-association of alcohols does not compete with solvation of solutes, and alcohols are significantly more polar solvents than expected based on the properties of alcohol monomers.
Asunto(s)
Compuestos Azo/química , Óxidos/química , Fenol/química , Fosfinas/química , Alcoholes/química , Alcanos/química , Dimerización , Enlace de Hidrógeno , Modelos Moleculares , Solubilidad , Solventes/químicaRESUMEN
High-throughput UV-Vis experiments using four molecular recognition-based probes, made by the combination of two hydrogen bond acceptors, tri-n-butylphosphine oxide and N,N'-bis(2-ethylhexyl)acetamide, and two hydrogen bond donors, 4-phenylazophenol and 4-nitrophenol, were performed. The association constants for the 1 : 1 H-bond interaction involved in each probe system were measured in mixtures of a polar and non-polar solvent, di-n-hexyl ether and n-octane, respectively. Similar behaviour was observed for all four systems. When the concentration of the polar solvent was low, the association constant was identical to that observed in pure n-octane. However, once the concentration of the polar solvent exceeded a threshold, the association constant decreased linearly with the concentration of di-n-hexyl ether. Selective solvation in mixtures can be understood based on the competition between the multiple competing equilibria in the system. In this case, solvation thermodynamics are dominated by competition of the ether for solvation of H-bond donors. For the more polar solute, 4-nitrophenol, the selective solvation starts at lower concentrations of the polar solvent compared with the less polar solute, 4-phenylazophenol. Thus the speciation and hence the properties of systems containing multiple solutes and multiple solvents can be estimated from the H-bond properties and the concentrations of the individual functional groups.
Asunto(s)
Éteres/química , Sondas Moleculares/química , Octanos/química , Termodinámica , Enlace de Hidrógeno , Solubilidad , Solventes/química , Espectrofotometría UltravioletaRESUMEN
Antidepressants are increasingly recognized to have anti-inflammatory properties in addition to their ability to treat major depressive disorders. To explore if engagement of 5-hydroxytryptamine (5-HT) receptors was required for the anti-inflammatory effect of the tetracyclic antidepressant mianserin, a series of structural derivatives were generated with the aim of reducing 5-HT receptor binding. Primary human peripheral blood mononuclear cells were used to screen for anti-inflammatory activity. The lead compound demonstrated a significant loss in 5-HT receptor binding, as assessed by non-selective 5-HT binding of radiolabelled serotonin in rat cerebral cortex. However, it retained the ability to inhibit endosomal toll-like receptor 8 signaling in primary human macrophages and spontaneous cytokine production from human rheumatoid synovial tissue equivalent to that previously observed for mianserin. These data demonstrate that the anti-inflammatory mechanism of mianserin may be independent of 5-HT receptor activity. This research offers new insights into the mechanism and structural requirements for the anti-inflammatory action of mianserin.
Asunto(s)
Antiinflamatorios/farmacología , Antidepresivos/farmacología , Leucocitos Mononucleares/efectos de los fármacos , Mianserina/análogos & derivados , Mianserina/farmacología , Antiinflamatorios/química , Antidepresivos/química , Células Cultivadas , Humanos , Interleucina-1/metabolismo , Leucocitos Mononucleares/metabolismo , Macrófagos/efectos de los fármacos , Macrófagos/metabolismo , Mianserina/química , Estructura Molecular , Receptores de Serotonina/metabolismo , Membrana Sinovial/efectos de los fármacos , Membrana Sinovial/metabolismo , Receptor Toll-Like 8/metabolismo , Factor de Necrosis Tumoral alfa/metabolismoRESUMEN
Heart disease is a paramount cause of global death and disability. Although cardiomyocyte death plays a causal role and its suppression would be logical, no clinical counter-measures target the responsible intracellular pathways. Therapeutic progress has been hampered by lack of preclinical human validation. Mitogen-activated protein kinase kinase kinase kinase-4 (MAP4K4) is activated in failing human hearts and relevant rodent models. Using human induced-pluripotent-stem-cell-derived cardiomyocytes (hiPSC-CMs) and MAP4K4 gene silencing, we demonstrate that death induced by oxidative stress requires MAP4K4. Consequently, we devised a small-molecule inhibitor, DMX-5804, that rescues cell survival, mitochondrial function, and calcium cycling in hiPSC-CMs. As proof of principle that drug discovery in hiPSC-CMs may predict efficacy in vivo, DMX-5804 reduces ischemia-reperfusion injury in mice by more than 50%. We implicate MAP4K4 as a well-posed target toward suppressing human cardiac cell death and highlight the utility of hiPSC-CMs in drug discovery to enhance cardiomyocyte survival.
Asunto(s)
Doxorrubicina/farmacología , Infarto/tratamiento farmacológico , Infarto/patología , Péptidos y Proteínas de Señalización Intracelular/antagonistas & inhibidores , Miocitos Cardíacos/citología , Miocitos Cardíacos/efectos de los fármacos , Proteínas Serina-Treonina Quinasas/antagonistas & inhibidores , Animales , Supervivencia Celular/efectos de los fármacos , Células Cultivadas , Relación Dosis-Respuesta a Droga , Femenino , Humanos , Peróxido de Hidrógeno/farmacología , Células Madre Pluripotentes Inducidas/citología , Infarto/metabolismo , Péptidos y Proteínas de Señalización Intracelular/genética , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Transgénicos , Miocitos Cardíacos/metabolismo , Proteínas Serina-Treonina Quinasas/genética , Proteínas Serina-Treonina Quinasas/metabolismo , Relación Estructura-ActividadRESUMEN
Cholecystokinin 2 receptor antagonists encompass a wide range of structures. This makes them unsuitable candidates for existing 3D-QSAR methods and has led us to develop an alternative approach to account for their observed biological activities. A diverse set of 21 antagonists was subjected to a novel molecular field-based similarity analysis. The hypothesis is that compounds with similar field patterns will bind at the same target site regardless of their underlying structure. This initial report demonstrates a linear correlation between ligand similarity and biological activity for this challenging data set. A model generated with three molecules was used to predict the activity of 18 test compounds, with different chemotypes, with a root-mean-square error of 0.68 pKB units. The ability to automatically derive a molecular alignment without knowledge of the protein structure represents an improvement over existing pharmacophore methods and makes the method particularly suitable for scaffold-hopping.
Asunto(s)
Relación Estructura-Actividad Cuantitativa , Receptor de Colecistoquinina B/antagonistas & inhibidores , Receptor de Colecistoquinina B/química , Animales , Benzoatos/química , Benzoatos/farmacología , Sitios de Unión , Unión Competitiva , Hidrocarburos Aromáticos con Puentes/química , Hidrocarburos Aromáticos con Puentes/farmacología , Ciclohexanos/química , Ciclohexanos/farmacología , Mucosa Gástrica/metabolismo , Cobayas , Compuestos Heterocíclicos con 2 Anillos/química , Compuestos Heterocíclicos con 2 Anillos/farmacología , Interacciones Hidrofóbicas e Hidrofílicas , Técnicas In Vitro , Análisis de los Mínimos Cuadrados , Ligandos , Modelos Lineales , Modelos Moleculares , Páncreas/citología , Ácidos Ftálicos/química , Ácidos Ftálicos/farmacología , Ensayo de Unión Radioligante , Ratas , Receptor de Colecistoquinina A/antagonistas & inhibidoresRESUMEN
A 1,3,4-benzotriazepine was identified as a suitable lead in our effort toward obtaining a non-peptide parathyroid hormone-1 receptor (PTH1R) antagonist. A process of optimization afforded derivatives displaying nanomolar PTH1R affinity, a representative example of which behaved as a PTH1R antagonist in cell-based cyclic adenosine monophosphate (cAMP) assays, with selectivity over PTH2 receptors.
Asunto(s)
Benzazepinas/síntesis química , Receptor de Hormona Paratiroídea Tipo 1/antagonistas & inhibidores , Animales , Benzazepinas/química , Benzazepinas/farmacología , Unión Competitiva , Línea Celular , Línea Celular Tumoral , Cricetinae , Cricetulus , AMP Cíclico/biosíntesis , Humanos , Ratones , Ensayo de Unión Radioligante , Proteínas Recombinantes/antagonistas & inhibidores , Relación Estructura-ActividadRESUMEN
A series of 1,3,4-benzotriazepine-based CCK(2) antagonists have been devised by consideration of the structural features that govern CCK receptor affinity and the receptor subtype selectivity of 1,4-benzodiazepine-based CCK(2) antagonists. In contrast to the latter compounds, these novel 1,3,4-benzotriazepines are achiral, yet they display similar affinity for CCK(2) receptors to the earlier molecules and are highly selective over CCK(1) receptors.
Asunto(s)
Benzazepinas/síntesis química , Receptor de Colecistoquinina A/antagonistas & inhibidores , Receptor de Colecistoquinina B/antagonistas & inhibidores , Animales , Benzazepinas/química , Benzazepinas/farmacología , Benzodiazepinas/química , Línea Celular , Cricetinae , Cricetulus , Cristalografía por Rayos X , Humanos , Ratones , Estructura Molecular , Ensayo de Unión Radioligante , Ratas , Receptor de Colecistoquinina A/química , Receptor de Colecistoquinina B/química , Estereoisomerismo , Relación Estructura-ActividadRESUMEN
A new molecular modeling approach has been used to derive a pharmacophore of the potent and selective cholecystokinin-2 (CCK(2)) receptor antagonist 5 (JB93182), based on features shared with two related series. The technique uses "field points" as simple and effective descriptions of the electrostatic and van der Waals maxima and minima surrounding a molecule equipped with XED (extended electron distribution) charges. Problems associated with the high levels of biliary elimination of 5 in vivo required us to design a compound with significantly lower molecular weight without sacrificing its nanomolar levels of in vitro activity. Two new series of compounds were designed to mimic the arrangement of field points present in the pharmacophore rather than its structural elements. In a formal sense, two of the three amides in 5 were replaced with either a simple pyrrole or imidazole, while some features thought to be essential for the high levels of in vitro activity of the parent compounds were retained and others deleted. These compounds maintained activity and selectivity for this receptor over CCK(1). In addition, the reduction in molecular weight coupled with lower polarities greatly reduced levels of biliary elimination associated with 5. This makes them good lead compounds for development of drug candidates whose structures are not obviously related to those of the parents and represents the first example of scaffold hopping using molecular field points.
Asunto(s)
Imidazoles/química , Modelos Moleculares , Pirroles/química , Receptor de Colecistoquinina B/agonistas , Receptor de Colecistoquinina B/antagonistas & inhibidores , Animales , Unión Competitiva , Corteza Cerebral/metabolismo , Diseño de Fármacos , Imidazoles/síntesis química , Imidazoles/farmacología , Técnicas In Vitro , Ratones , Conformación Molecular , Pirroles/síntesis química , Pirroles/farmacología , Relación Estructura-Actividad Cuantitativa , Ensayo de Unión Radioligante , Receptor de Colecistoquinina B/metabolismoRESUMEN
The systematic optimization of the structure of a novel 2,4,5-trisubstituted imidazole-based cholecystokinin-2 (CCK(2)) receptor antagonist afforded analogues with nanomolar receptor affinity. These compounds were now comparable in their potency to the bicyclic heteroaromatic-based compounds 5 (JB93182) and 6 (JB95008), from which the initial examples were designed using a field-point based molecular modeling approach. They were also orally active as judged by their inhibition of pentagastrin stimulated acid secretion in conscious dogs, in contrast to the bicyclic heteroaromatic-based compounds, which were ineffective because of biliary elimination. Increasing the hydrophilicity through replacement of a particular methylene group with an ether oxygen, as in 3-{[5-(adamantan-1-yloxymethyl)-2-cyclohexyl-1H-imidazole-4-carbonyl]amino}benzoic acid (53), had little effect on the receptor affinity but significantly increased the oral potency. Comparison of the plasma pharmacokinetics and the inhibition of pentagastrin-stimulated acid output following bolus intraduodenal administration of both 53 and 6 indicated that 53 was well absorbed, had a longer half-life, and was not subject to the elimination pathways of the earlier series.
Asunto(s)
Imidazoles/síntesis química , Pirroles/síntesis química , Receptor de Colecistoquinina B/antagonistas & inhibidores , Administración Oral , Animales , Disponibilidad Biológica , Corteza Cerebral/metabolismo , Perros , Femenino , Ácido Gástrico/metabolismo , Imidazoles/química , Imidazoles/farmacología , Técnicas In Vitro , Infusiones Intravenosas , Ratones , Modelos Moleculares , Pentagastrina/administración & dosificación , Pentagastrina/farmacología , Pirroles/química , Pirroles/farmacología , Relación Estructura-Actividad Cuantitativa , Ensayo de Unión RadioliganteRESUMEN
Chemical double mutant cycles have been used to quantify cation-pi interactions in chloroform as a function of the nature of the counteranion. The cation-pi interaction is -2.5 +/- 0.4 kJ mol(-1) and independent of the anion, even though the overall stability of the complexes varies by an order of magnitude due to competition of the anion for alternative binding sites.
RESUMEN
Reversible zinc-pyridine coordination and hydrogen-bonding interactions have been used to assemble a [2]rotaxane from three components. Cooperativity in the macrocyclization process that results in the porphyrin dimer makes the system exceptionally stable. However, the kinetic lability of the zinc-porphyrin interaction means the dimer is in dynamic equilibrium with its monomer, and this has been exploited in the construction of a [2]rotaxane.
Asunto(s)
Tetracloruro de Carbono/química , Fluorocarburos/química , Solventes/química , Alcohol terc-Butílico/análogos & derivados , Enlace de Hidrógeno , Espectroscopía de Resonancia Magnética/métodos , Fosfinas/química , Isótopos de Fósforo , Sensibilidad y Especificidad , Solubilidad , Alcohol terc-Butílico/químicaRESUMEN
The association constants for formation of 1:1 complexes between a H-bond acceptor, tri-n-butylphosphine oxide, and a H-bond donor, 4-phenylazophenol, have been measured in a range of different solvent mixtures. Binary mixtures of n-octane and a more polar solvent (ether, ester, ketone, nitrile, sulfoxide, tertiary amide, and halogenated and aromatic solvents) have been investigated. Similar behavior was observed in all cases. When the concentration of the more polar solvent is low, the association constant is identical to that observed in pure n-octane. Once a threshold concentration of the more polar solvent in reached, the logarithm of the association constant decreases in direct proportion to the logarithm of the concentration of the more polar solvent. This indicates that one of the two solutes is preferentially solvated by the more polar solvent, and it is competition with this solvation equilibrium that determines the observed association constant. The concentration of the more polar solvent at which the onset of preferential solvation takes place depends on solvent polarity: 700 mM for toluene, 60 mM for 1,1,2,2-tetrachloroethane, 20 mM for the ether, ester, ketone, and nitrile, 0.2 mM for the tertiary amide, and 0.1 mM for the sulfoxide solvents. The results can be explained by a simple model that considers only pairwise interactions between specific sites on the surfaces of the solutes and solvents, which implies that the bulk properties of the solvent have little impact on solvation thermodynamics.
Asunto(s)
Sondas Moleculares/química , Solubilidad , Solventes/químicaRESUMEN
Synthetic supramolecular zipper complexes have been used to quantify substituent effects on the free energies of aromatic stacking interactions. The conformational properties of the complexes have been characterised using NMR spectroscopy in CDCl(3), and by comparison with the solid state structures of model compounds. The structural similarity of the complexes makes it possible to apply the double mutant cycle method to evaluate the magnitudes of 24 different aromatic stacking interactions. The major trends in the interaction energy can be rationalised using a simple model based on electrostatic interactions between the pi-faces of the two aromatic rings. However, electrostatic interactions between the substituents of one ring and the pi-face of the other make an additional contribution, due to the slight offset in the stacking geometry. This property makes aromatic stacking interactions particularly sensitive to changes in orientation as well as the nature and location of substituents.