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1.
Molecules ; 28(7)2023 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-37049868

RESUMEN

Human immunodeficiency virus type I (HIV-1) is a retrovirus that infects cells of the host's immune system leading to acquired immunodeficiency syndrome and potentially death. Although treatments are available to prevent its progression, HIV-1 remains a major burden on health resources worldwide. Continued emergence of drug-resistance mutations drives the need for novel drugs that can inhibit HIV-1 replication through new pathways. The viral protein reverse transcriptase (RT) plays a fundamental role in the HIV-1 replication cycle, and multiple approved medications target this enzyme. In this study, fragment-based drug discovery was used to optimize a previously identified hit fragment (compound B-1), which bound RT at a novel site. Three series of compounds were synthesized and evaluated for their HIV-1 RT binding and inhibition. These series were designed to investigate different vectors around the initial hit in an attempt to improve inhibitory activity against RT. Our results show that the 4-position of the core scaffold is important for binding of the fragment to RT, and a lead compound with a cyclopropyl substitution was selected and further investigated. Requirements for binding to the NNRTI-binding pocket (NNIBP) and a novel adjacent site were investigated, with lead compound 27-a minimal but efficient NNRTI-offering a starting site for the development of novel dual NNIBP-Adjacent site inhibitors.


Asunto(s)
Síndrome de Inmunodeficiencia Adquirida , Fármacos Anti-VIH , VIH-1 , Humanos , Inhibidores de la Transcriptasa Inversa/química , Transcriptasa Inversa del VIH , Síndrome de Inmunodeficiencia Adquirida/tratamiento farmacológico , Fármacos Anti-VIH/farmacología , Fármacos Anti-VIH/uso terapéutico
2.
J Chem Inf Model ; 62(19): 4605-4619, 2022 10 10.
Artículo en Inglés | MEDLINE | ID: mdl-36178379

RESUMEN

The ability to predict cell-permeable candidate molecules has great potential to assist drug discovery projects. Large molecules that lie beyond the Rule of Five (bRo5) are increasingly important as drug candidates and tool molecules for chemical biology. However, such large molecules usually do not cross cell membranes and cannot access intracellular targets or be developed as orally bioavailable drugs. Here, we describe a random forest (RF) machine learning model for the prediction of passive membrane permeation rates developed using a set of over 1000 bRo5 macrocyclic compounds. The model is based on easily calculated chemical features/descriptors as independent variables. Our random forest (RF) model substantially outperforms a multiple linear regression model based on the same features and achieves better performance metrics than previously reported models using the same underlying data. These features include: (1) polar surface area in water, (2) the octanol-water partitioning coefficient, (3) the number of hydrogen-bond donors, (4) the sum of the topological distances between nitrogen atoms, (5) the sum of the topological distances between nitrogen and oxygen atoms, and (6) the multiple molecular path count of order 2. The last three features represent molecular flexibility, the ability of the molecule to adopt different conformations in the aqueous and membrane interior phases, and the molecular "chameleonicity." Guided by the model, we propose design guidelines for membrane-permeating macrocycles. It is anticipated that this model will be useful in guiding the design of large, bioactive molecules for medicinal chemistry and chemical biology applications.


Asunto(s)
Compuestos Macrocíclicos , Hidrógeno , Aprendizaje Automático , Nitrógeno , Octanoles , Oxígeno , Agua
3.
Bioorg Chem ; 123: 105763, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35366581

RESUMEN

The SPRY domain-containing SOCS box protein-2 (SPSB2) plays a critical role in the degradation of inducible nitric oxide synthase (iNOS) in macrophages. In this study, we have conjugated a peptide inhibitor of the iNOS-SPSB2 interaction with a cell-penetrating peptide (CPP) for delivery into macrophages, and confirmed its binding to SPSB2. We have assessed the uptake of a fluorophore-tagged analogue by RAW 264.7 and immortalised bone marrow derived macrophage (iBMDM) cell lines, and shown that the CPP-peptide conjugate enhanced NO production. The findings of this study will be useful in further refinement of CPP-peptide conjugates as leads in the development of new antibiotics that target the host innate immune response.


Asunto(s)
Péptidos de Penetración Celular , Óxido Nítrico , Péptidos de Penetración Celular/farmacología , Macrófagos/metabolismo , Modelos Moleculares , Óxido Nítrico Sintasa de Tipo II/metabolismo
4.
Bioorg Med Chem ; 29: 115906, 2021 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-33310547

RESUMEN

Inhibitors of protein-protein interactions can be developed through a number of technologies to provide leads that include cell-impermeable molecules. Redesign of these impermeable leads to provide cell-permeable derivatives can be challenging and costly. We hypothesised that intracellular toxicity of leads could be assessed by microinjection prior to investing in the redesign process. We demonstrate this approach for our development of inhibitors of the protein-protein interaction between inducible nitric-oxide synthase (iNOS) and SPRY domain-containing SOCS box proteins (SPSBs). We microinjected a lead molecule into AD-293 cells and were able to perform an intracellular toxicity assessment. We also investigated the intracellular distribution and localisation of injected inhibitor using a fluorescently-labelled analogue. Our findings show that a lead peptide inhibitor, CP2, had no toxicity even at intracellular concentrations four orders of magnitude higher than its Kd for binding to SPSB2. This early toxicity assessment justifies further development of this cell-impermeable lead to confer cell permeability. Our investigation highlights the utility of microinjection as a tool for assessing toxicity during development of drugs targeting protein-protein interactions.


Asunto(s)
Citoplasma/metabolismo , Inhibidores Enzimáticos/química , Óxido Nítrico Sintasa de Tipo II/metabolismo , Péptidos/química , Proteínas Supresoras de la Señalización de Citocinas/metabolismo , Secuencia de Aminoácidos , Línea Celular , Permeabilidad de la Membrana Celular , Citoplasma/ultraestructura , Desarrollo de Medicamentos , Inhibidores Enzimáticos/administración & dosificación , Inhibidores Enzimáticos/efectos adversos , Humanos , Microinyecciones , Modelos Moleculares , Imagen Óptica , Péptidos/administración & dosificación , Péptidos/efectos adversos , Unión Proteica , Relación Estructura-Actividad
5.
BMC Anesthesiol ; 19(1): 214, 2019 11 20.
Artículo en Inglés | MEDLINE | ID: mdl-31747898

RESUMEN

BACKGROUND: In different models of hypoxia, blockade of opioid or N-methyl-D-aspartate (NMDA) receptors shows cardio- and neuroprotective effects with a consequent increase in animal survival. The aim of the study was to investigate effects of pre-treatment with Morphine or Ketamine on hemodynamic, acid-base status, early survival, and biochemical markers of brain damage in a rat model of asphyxial cardiac arrest (ACA). METHODS: Under anaesthesia with Thiopental Sodium 60 mg/kg, i.p., Wistar rats (n = 42) were tracheostomized and catheters were inserted in a femoral vein and artery. After randomization, the rats were pre-treated with: Morphine 5 mg/kg i.v. (n = 14); Ketamine 40 mg/kg i.v. (n = 14); or equal volume of i.v. NaCl 0.9% as a Control (n = 14). ACA was induced by corking of the tracheal tube for 8 min, and defined as a mean arterial pressure (MAP) < 20 mmHg. Resuscitation was started at 5 min after cardiac arrest (CA). Invasive MAP was recorded during experiments. Arterial pH and blood gases were sampled at baseline (BL) and 10 min after CA. At the end of experiments, all surviving rats were euthanised, brain and blood samples for measurement of Neuron Specific Enolase (NSE), s100 calcium binding protein B (s100B) and Caspase-3 (CS-3) were retrieved. RESULTS: At BL no differences between groups were found in hemodynamic or acid-base status. After 3 min of asphyxia, all animals had cardiac arrest (CA). Return of spontaneous circulation (MAP > 60 mmHg) was achieved in all animals within 3 min after CA. At the end of the experiment, the Ketamine pre-treated group had increased survival (13 of 14; 93%) compared to the Control (7 of 14; 50%) and Morphine (10 of 14; 72%) groups (p = 0.035). Biochemical analysis of plasma concentration of NSE and s100B as well as an analysis of CS-3 levels in the brain tissue did not reveal any differences between the study groups. CONCLUSION: In rats after ACA, pre-treatment with Morphine or Ketamine did not have any significant influence on hemodynamic and biochemical markers of brain damage. However, significantly better pH level and increased early survival were found in the Ketamine pre-treated group.


Asunto(s)
Lesiones Encefálicas/etiología , Paro Cardíaco/terapia , Ketamina/farmacología , Morfina/farmacología , Analgésicos Opioides/administración & dosificación , Analgésicos Opioides/farmacología , Animales , Asfixia/complicaciones , Análisis de los Gases de la Sangre , Lesiones Encefálicas/fisiopatología , Reanimación Cardiopulmonar , Modelos Animales de Enfermedad , Antagonistas de Aminoácidos Excitadores/administración & dosificación , Antagonistas de Aminoácidos Excitadores/farmacología , Paro Cardíaco/complicaciones , Paro Cardíaco/fisiopatología , Hemodinámica/efectos de los fármacos , Concentración de Iones de Hidrógeno , Ketamina/administración & dosificación , Masculino , Morfina/administración & dosificación , Ratas , Ratas Wistar , Sobrevida
6.
Chemistry ; 24(8): 1922-1930, 2018 Feb 06.
Artículo en Inglés | MEDLINE | ID: mdl-29171692

RESUMEN

Dihydropteroate synthase (DHPS) is an enzyme of the folate biosynthesis pathway, which catalyzes the formation of 7,8-dihydropteroate (DHPt) from 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) and para-aminobenzoic acid (pABA). DHPS is the long-standing target of the sulfonamide class of antibiotics that compete with pABA. In the wake of sulfa drug resistance, targeting the structurally rigid (and more conserved) pterin site has been proposed as an alternate strategy to inhibit DHPS in wild-type and sulfa drug resistant strains. Following the work on developing pterin-site inhibitors of the adjacent enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), we now present derivatives of 8-mercaptoguanine, a fragment that binds weakly within both enzymes, and quantify sub-µm binding using surface plasmon resonance (SPR) to Escherichia coli DHPS (EcDHPS). Eleven ligand-bound EcDHPS crystal structures delineate the structure-activity relationship observed providing a structural framework for the rational development of novel, substrate-envelope-compliant DHPS inhibitors.


Asunto(s)
Dihidropteroato Sintasa/antagonistas & inhibidores , Inhibidores Enzimáticos/química , Guanina/análogos & derivados , Antibacterianos/química , Antibacterianos/metabolismo , Sitios de Unión , Dominio Catalítico , Cristalografía por Rayos X , Dihidropteroato Sintasa/metabolismo , Inhibidores Enzimáticos/metabolismo , Escherichia coli/enzimología , Guanina/metabolismo , Enlace de Hidrógeno , Ligandos , Unión Proteica , Estructura Terciaria de Proteína , Relación Estructura-Actividad , Especificidad por Sustrato , Sulfonamidas/química , Resonancia por Plasmón de Superficie
7.
Bioorg Med Chem Lett ; 27(2): 254-260, 2017 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-27923620

RESUMEN

Activity-based probes are small molecules that covalently bind to the active site of a protease in an activity-dependent manner. We synthesized and characterized two fluorescent activity-based probes that target serine proteases with trypsin-like or elastase-like activity. We assessed the selectivity and potency of these probes against recombinant enzymes and demonstrated that while they are efficacious at labeling active proteases in complex protein mixtures in vitro, they are less valuable for in vivo studies. We used these probes to evaluate serine protease activity in two mouse models of acute inflammation, including pancreatitis and colitis. As anticipated, the activity of trypsin-like proteases was increased during pancreatitis. Levels of elastase-like proteases were low in pancreatic lysates and colonic luminal fluids, whether healthy or inflamed. Exogenously added recombinant neutrophil elastase was inhibited upon incubation with these samples, an effect that was augmented in inflamed samples compared to controls. These data suggest that endogenous inhibitors and elastase-degrading proteases are upregulated during inflammation.


Asunto(s)
Colorantes Fluorescentes/química , Inflamación/metabolismo , Organofosfonatos/química , Serina Proteasas/análisis , Animales , Colitis/metabolismo , Colorantes Fluorescentes/síntesis química , Ratones , Estructura Molecular , Organofosfonatos/síntesis química , Pancreatitis/metabolismo , Serina Proteasas/metabolismo
8.
J Biol Chem ; 290(22): 13875-87, 2015 May 29.
Artículo en Inglés | MEDLINE | ID: mdl-25878251

RESUMEN

Proteases that cleave protease-activated receptor-2 (PAR(2)) at Arg(36)↓Ser(37) reveal a tethered ligand that binds to the cleaved receptor. PAR(2) activates transient receptor potential (TRP) channels of nociceptive neurons to induce neurogenic inflammation and pain. Although proteases that cleave PAR(2) at non-canonical sites can trigger distinct signaling cascades, the functional importance of the PAR(2)-biased agonism is uncertain. We investigated whether neutrophil elastase, a biased agonist of PAR(2), causes inflammation and pain by activating PAR2 and TRP vanilloid 4 (TRPV4). Elastase cleaved human PAR(2) at Ala(66)↓Ser(67) and Ser(67)↓Val(68). Elastase stimulated PAR(2)-dependent cAMP accumulation and ERK1/2 activation, but not Ca(2+) mobilization, in KNRK cells. Elastase induced PAR(2) coupling to Gαs but not Gαq in HEK293 cells. Although elastase did not promote recruitment of G protein-coupled receptor kinase-2 (GRK(2)) or ß-arrestin to PAR(2), consistent with its inability to promote receptor endocytosis, elastase did stimulate GRK6 recruitment. Elastase caused PAR(2)-dependent sensitization of TRPV4 currents in Xenopus laevis oocytes by adenylyl cyclase- and protein kinase A (PKA)-dependent mechanisms. Elastase stimulated PAR(2)-dependent cAMP formation and ERK1/2 phosphorylation, and a PAR(2)- and TRPV4-mediated influx of extracellular Ca(2+) in mouse nociceptors. Adenylyl cyclase and PKA-mediated elastase-induced activation of TRPV4 and hyperexcitability of nociceptors. Intraplantar injection of elastase to mice caused edema and mechanical hyperalgesia by PAR(2)- and TRPV4-mediated mechanisms. Thus, the elastase-biased agonism of PAR(2) causes Gαs-dependent activation of adenylyl cyclase and PKA, which activates TRPV4 and sensitizes nociceptors to cause inflammation and pain. Our results identify a novel mechanism of elastase-induced activation of TRPV4 and expand the role of PAR(2) as a mediator of protease-driven inflammation and pain.


Asunto(s)
Inflamación/metabolismo , Elastasa de Leucocito/metabolismo , Dolor/metabolismo , Receptor PAR-2/metabolismo , Canales Catiónicos TRPV/metabolismo , Animales , Calcio/metabolismo , Membrana Celular/metabolismo , AMP Cíclico/metabolismo , Edema/metabolismo , Edema/patología , Proteínas de Unión al GTP/metabolismo , Ganglios Espinales/metabolismo , Células HEK293 , Humanos , Masculino , Ratones , Ratones Endogámicos C57BL , Neuronas/metabolismo , Nocicepción , Oocitos/citología , Oocitos/metabolismo , Técnicas de Placa-Clamp , Péptido Hidrolasas/metabolismo , Estructura Terciaria de Proteína , Transducción de Señal , Xenopus laevis/metabolismo
9.
J Biol Chem ; 289(39): 27215-27234, 2014 Sep 26.
Artículo en Inglés | MEDLINE | ID: mdl-25118282

RESUMEN

Serine proteases such as trypsin and mast cell tryptase cleave protease-activated receptor-2 (PAR2) at R(36)↓S(37) and reveal a tethered ligand that excites nociceptors, causing neurogenic inflammation and pain. Whether proteases that cleave PAR2 at distinct sites are biased agonists that also induce inflammation and pain is unexplored. Cathepsin S (Cat-S) is a lysosomal cysteine protease of antigen-presenting cells that is secreted during inflammation and which retains activity at extracellular pH. We observed that Cat-S cleaved PAR2 at E(56)↓T(57), which removed the canonical tethered ligand and prevented trypsin activation. In HEK and KNRK cell lines and in nociceptive neurons of mouse dorsal root ganglia, Cat-S and a decapeptide mimicking the Cat-S-revealed tethered ligand-stimulated PAR2 coupling to Gαs and formation of cAMP. In contrast to trypsin, Cat-S did not mobilize intracellular Ca(2+), activate ERK1/2, recruit ß-arrestins, or induce PAR2 endocytosis. Cat-S caused PAR2-dependent activation of transient receptor potential vanilloid 4 (TRPV4) in Xenopus laevis oocytes, HEK cells and nociceptive neurons, and stimulated neuronal hyperexcitability by adenylyl cyclase and protein kinase A-dependent mechanisms. Intraplantar injection of Cat-S caused inflammation and hyperalgesia in mice that was attenuated by PAR2 or TRPV4 deletion and adenylyl cyclase inhibition. Cat-S and PAR2 antagonists suppressed formalin-induced inflammation and pain, which implicates endogenous Cat-S and PAR2 in inflammatory pain. Our results identify Cat-S as a biased agonist of PAR2 that causes PAR2- and TRPV4-dependent inflammation and pain. They expand the role of PAR2 as a mediator of protease-driven inflammatory pain.


Asunto(s)
Catepsinas/metabolismo , Dolor , Receptor PAR-2 , Canales Catiónicos TRPV , Adenilil Ciclasas/genética , Adenilil Ciclasas/metabolismo , Animales , Catepsinas/genética , Células HEK293 , Humanos , Hiperalgesia/genética , Hiperalgesia/metabolismo , Hiperalgesia/patología , Inflamación/genética , Inflamación/metabolismo , Inflamación/patología , Ratones , Ratones Noqueados , Dolor/genética , Dolor/metabolismo , Dolor/patología , Receptor PAR-2/agonistas , Receptor PAR-2/genética , Receptor PAR-2/metabolismo , Canales Catiónicos TRPV/agonistas , Canales Catiónicos TRPV/genética , Canales Catiónicos TRPV/metabolismo , Xenopus laevis
10.
Bioconjug Chem ; 24(2): 260-8, 2013 Feb 20.
Artículo en Inglés | MEDLINE | ID: mdl-23294422

RESUMEN

Pseudocontact shifts (PCS) from paramagnetic lanthanide ions present powerful long-range structural restraints for structural biology by NMR spectroscopy, but site-specific tagging of proteins with lanthanides remains a challenge, as most of the available lanthanide tags require proteins with single cysteine residues. We show that cyclen-based paramagnetic lanthanide tags can be attached to proteins in a site-specific manner by Cu(I)-catalyzed azide-alkyne cycloaddition to a genetically encoded p-azido-l-phenylalanine residue with a tether that proved sufficiently short and rigid for the observation of PCSs in several proteins. Despite the sterically demanding conditions associated with bulky tags and reactions close to the protein surface, ligation yields consistently above 50% and approaching 100% were obtained with the help of the Cu(I)-stabilizing ligand BTTAA. The yields were high independent of the presence of cysteine residues, thereby avoiding the need for cysteine mutations associated with conventional lanthanide-tagging strategies.


Asunto(s)
Elementos de la Serie de los Lantanoides/química , Fenilalanina/análogos & derivados , Proteínas/química , Alquinos/química , Azidas/química , Catálisis , Química Clic , Cobre/química , Ciclamas , Reacción de Cicloadición , Escherichia coli/genética , Compuestos Heterocíclicos/química , Histidina/química , Histidina/genética , Humanos , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular , Oligopéptidos/química , Oligopéptidos/genética , Fenilalanina/genética , Proteínas/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Ubiquitina/química , Ubiquitina/genética
11.
Radiography (Lond) ; 29(1): 119-123, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-36347134

RESUMEN

INTRODUCTION: Patient positioning may impact diagnostic quality when obtaining radiographs of the musculoskeletal (MSK) system. Hence, knowledge on patient positioning, as seen in the radiograph, followed by informed adjusted retake if appropriate, is key when undertaking MSK radiographs. Forearm positioning is particularly important in lateral wrist radiographs where rotation impacts anatomic measurements. The purpose was to evaluate the accuracy of MSK and non-MSK radiographers' immediate assessments of wrist positioning including need for retake. METHODS: A questionnaire including images of 18 lateral wrist radiographs and questions regarding positioning, i.e. forearm rotation and flexion of the wrist, were developed and distributed to radiographers worldwide via the European Federation of Radiographer Societies (EFRS) and the Research Hub at the European Congress of Radiology (ECR) 2021. Demographic data such as area of expertise, years of experience etc. were collected. RESULTS: In total, 156 replies were included in the analyses. The inter-observer agreement of radiographers' assessment of the need for a retake was 47% (kappa = .25) and the intra-observer agreement was 81% (kappa = .62). Radiographers working with MSK radiography had more correct positioning assessments than radiographers who did not routinely obtain radiographs of the MSK system (p = 0.0003). CONCLUSION: Results indicated that MSK radiographers are more consistent in assessment of the need for a retake in lateral wrist radiographs and more able to correctly judge positioning compared to non-MSK radiographers. IMPLICATIONS FOR PRACTICE: Constant focus on image quality may lead to increased awareness and adherence to image criteria. Improved image quality will in turn improve the diagnostic value for the benefit of the patients potentially leading to better outcomes.


Asunto(s)
Radiología , Muñeca , Humanos , Muñeca/diagnóstico por imagen , Competencia Clínica , Radiografía , Radiología/educación , Técnicos Medios en Salud
12.
J Med Chem ; 66(5): 3273-3283, 2023 03 09.
Artículo en Inglés | MEDLINE | ID: mdl-36808973

RESUMEN

While a range of strategies exist to accomplish peptide macrocyclization, they are frequently limited by the need for orthogonal protection or provide little opportunity for structural diversification. We have evaluated an efficient macrocyclization method that employs nucleophilic aromatic substitution (SNAr) to create thioether macrocycles. This versatile macrocyclization, orthogonal to conventional peptide synthesis, can be performed in solution on unprotected peptidomimetics or on resin-bound peptides with side-chain protection in place. We show that the electron-withdrawing groups present in the products can be further utilized in subsequent orthogonal reactions to alter the peptide properties or to add prosthetic groups. The macrocyclization strategy was applied to the design of melanocortin ligands, generating a library of potent melanocortin agonists that exhibit distinct subtype selectivity.


Asunto(s)
Péptidos Cíclicos , Péptidos , Péptidos Cíclicos/farmacología , Péptidos Cíclicos/química , Ciclización , Péptidos/química , Receptores de Melanocortina , Biblioteca de Genes
13.
PLoS One ; 17(7): e0270584, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35881628

RESUMEN

Granzyme K (GzmK) is a tryptic member of the granzyme family of chymotrypsin-like serine proteases produced by cells of the immune system. Previous studies have indicated that GzmK activates protease-activated receptor 1 (PAR1) enhancing activation of monocytes and wound healing in endothelial cells. Here, we show using peptides and full length proteins that GzmK and, to a lesser extent the related protease GzmA, are capable of activating PAR1 and PAR2. These cleavage events occur at the canonical arginine P1 residue and involve exosite interactions between protease and receptor. Despite cleaving PAR2 at the same point as trypsin, GzmK does not induce a classical Ca2+ flux but instead activates a distinct signalling cascade, involving recruitment of ß-arrestin and phosphorylation of ERK. In epithelial A549 cells, PAR2 activation by GzmK results in the release of inflammatory cytokines IL-6 and IL-8. These data suggest that during an immune response GzmK acts as a pro-inflammatory regulator, rather than as a cytotoxin.


Asunto(s)
Receptor PAR-1 , Receptor PAR-2 , Endopeptidasas/metabolismo , Células Endoteliales/metabolismo , Células Epiteliales/metabolismo , Granzimas/metabolismo , Interleucina-6/metabolismo , Interleucina-8/metabolismo , Receptor PAR-1/metabolismo , Receptor PAR-2/metabolismo
14.
Bioconjug Chem ; 22(10): 2118-25, 2011 Oct 19.
Artículo en Inglés | MEDLINE | ID: mdl-21877751

RESUMEN

Structural studies of proteins and protein-ligand complexes by nuclear magnetic resonance (NMR) spectroscopy can be greatly enhanced by site-specific attachment of lanthanide ions to create paramagnetic centers. In particular, pseudocontact shifts (PCS) generated by paramagnetic lanthanides contain important and unique long-range structure information. Here, we present a high-affinity lanthanide binding tag that can be attached to single cysteine residues of proteins. The new tag has many advantageous features that are not available in this combination from previously published tags: (i) it binds lanthanide ions very tightly, minimizing the generation of nonspecific effects, (ii) it produces PCSs with high reliability as its bulkiness prevents complete motional averaging of PCSs, (iii) it can be attached to single cysteine residues, alleviating the need of detailed prior knowledge of the 3D structure of the target protein, and (iv) it does not display conformational exchange phenomena that would increase the number of signals in the NMR spectrum. The performance of the tag is demonstrated with the N-terminal domain of the E. coli arginine repressor and the A28C mutant of human ubiquitin.


Asunto(s)
Compuestos Heterocíclicos con 1 Anillo/química , Elementos de la Serie de los Lantanoides/química , Resonancia Magnética Nuclear Biomolecular/métodos , Proteínas/química , Cisteína/química , Escherichia coli/química , Proteínas de Escherichia coli/química , Humanos , Modelos Moleculares , Mutación , Conformación Proteica , Proteínas Represoras/química , Ubiquitina/química , Ubiquitina/genética
15.
Front Pharmacol ; 11: 585930, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33101040

RESUMEN

The insulin regulated aminopeptidase (IRAP) has been proposed as an important therapeutic target for indications including Alzheimer's disease and immune disorders. To date, a number of IRAP inhibitor designs have been investigated but the total number of molecules investigated remains quite small. As a member the M1 aminopeptidase family, IRAP shares numerous structural features with the other M1 aminopeptidases. The study of those enzymes and the development of inhibitors provide key learnings and new approaches and are potential sources of inspiration for future IRAP inhibitors.

16.
ACS Chem Biol ; 15(8): 2070-2078, 2020 08 21.
Artículo en Inglés | MEDLINE | ID: mdl-32628005

RESUMEN

A wide range of drug targets can be effectively modulated by peptides and macrocycles. Unfortunately, the size and polarity of these compounds prevents them from crossing the cell membrane to reach target sites in the cell cytosol. As such, these compounds do not conform to standard measures of drug-likeness and exist in beyond the rule-of-five space. In this work, we investigate whether prodrug moieties that mask hydrogen bond donors can be applied in the beyond rule-of-five domain to improve the permeation of macrocyclic compounds. Using a cyclic peptide model, we show that masking hydrogen bond donors in the natural polar amino acid residues (His, Ser, Gln, Asn, Glu, Asp, Lys, and Arg) imparts membrane permeability to the otherwise impermeable parent molecules, even though the addition of the masking group increases the overall compound molecular weight and the number of hydrogen bond acceptors. We demonstrate this strategy in PAMPA and Caco2 membrane permeability assays and show that masking with groups that reduce the number of hydrogen-bond donors at the cost of additional mass and hydrogen bond acceptors, a donor-acceptor swap, is effective.


Asunto(s)
Permeabilidad de la Membrana Celular , Profármacos/química , Células CACO-2 , Humanos , Enlace de Hidrógeno
17.
RSC Med Chem ; 11(2): 234-244, 2020 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-33479630

RESUMEN

Macrocyclic analogues of the linear hexapeptide, angiotensin IV (AngIV) have proved to be potent inhibitors of insulin-regulated aminopeptidase (IRAP, oxytocinase, EC 3.4.11.3). Along with higher affinity, macrocycles may also offer better metabolic stability, membrane permeability and selectivity, however predicting the outcome of particular cycle modifications is challenging. Here we describe the development of a series of macrocyclic IRAP inhibitors with either disulphide, olefin metathesis or lactam bridges and variations of ring size and other functionality. The binding mode of these compounds is proposed based on molecular dynamics analysis. Estimation of binding affinities (ΔG) and relative binding free energies (ΔΔG) with the linear interaction energy (LIE) method and free energy perturbation (FEP) method showed good general agreement with the observed inhibitory potency. Experimental and calculated data highlight the cumulative importance of an intact N-terminal peptide, the specific nature of the macrocycle, the phenolic oxygen and the C-terminal functionality.

18.
ACS Chem Biol ; 13(10): 2930-2938, 2018 10 19.
Artículo en Inglés | MEDLINE | ID: mdl-30226743

RESUMEN

SPRY domain- and SOCS box-containing proteins SPSB1, SPSB2, and SPSB4 interact with inducible nitric oxide synthase (iNOS), causing the iNOS to be polyubiquitinated and targeted for degradation. Inhibition of this interaction increases iNOS levels, and consequently cellular nitric oxide (NO) concentrations, and has been proposed as a potential strategy for killing intracellular pathogens. We previously described two DINNN-containing cyclic peptides (CP1 and CP2) as potent inhibitors of the murine SPSB-iNOS interaction. In this study, we report the crystal structures of human SPSB4 bound to CP1 and CP2 and human SPSB2 bound to CP2. We then used these structures to design a new inhibitor in which an intramolecular hydrogen bond was replaced with a hydrocarbon linkage to form a smaller macrocycle while maintaining the bound geometry of CP2 observed in the crystal structures. This resulting pentapeptide SPSB-iNOS inhibitor (CP3) has a reduced macrocycle ring size, fewer nonbinding residues, and includes additional conformational constraints. CP3 has a greater affinity for SBSB2 ( KD = 7 nM as determined by surface plasmon resonance) and strongly inhibits the SPSB2-iNOS interaction in macrophage cell lysates. We have also determined the crystal structure of CP3 in complex with human SPSB2, which reveals the structural basis for the increased potency of CP3 and validates the original design.


Asunto(s)
Antiinfecciosos/química , Péptidos y Proteínas de Señalización Intracelular/química , Óxido Nítrico Sintasa de Tipo II/metabolismo , Oligopéptidos/química , Péptidos Cíclicos/química , Proteínas Supresoras de la Señalización de Citocinas/química , Animales , Antiinfecciosos/farmacología , Diseño de Fármacos , Humanos , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Ratones , Oligopéptidos/farmacología , Péptidos Cíclicos/farmacología , Unión Proteica , Células RAW 264.7 , Proteínas Supresoras de la Señalización de Citocinas/metabolismo
19.
Sci Transl Med ; 9(392)2017 05 31.
Artículo en Inglés | MEDLINE | ID: mdl-28566424

RESUMEN

Typically considered to be cell surface sensors of extracellular signals, heterotrimeric GTP-binding protein (G protein)-coupled receptors (GPCRs) control many pathophysiological processes and are the target of 30% of therapeutic drugs. Activated receptors redistribute to endosomes, but researchers have yet to explore whether endosomal receptors generate signals that control complex processes in vivo and are viable therapeutic targets. We report that the substance P (SP) neurokinin 1 receptor (NK1R) signals from endosomes to induce sustained excitation of spinal neurons and pain transmission and that specific antagonism of the NK1R in endosomes with membrane-anchored drug conjugates provides more effective and sustained pain relief than conventional plasma membrane-targeted antagonists. Pharmacological and genetic disruption of clathrin, dynamin, and ß-arrestin blocked SP-induced NK1R endocytosis and prevented SP-stimulated activation of cytosolic protein kinase C and nuclear extracellular signal-regulated kinase, as well as transcription. Endocytosis inhibitors prevented sustained SP-induced excitation of neurons in spinal cord slices in vitro and attenuated nociception in vivo. When conjugated to cholestanol to promote endosomal targeting, NK1R antagonists selectively inhibited endosomal signaling and sustained neuronal excitation. Cholestanol conjugation amplified and prolonged the antinociceptive actions of NK1R antagonists. These results reveal a critical role for endosomal signaling of the NK1R in the complex pathophysiology of pain and demonstrate the use of endosomally targeted GPCR antagonists.


Asunto(s)
Endosomas/metabolismo , Terapia Molecular Dirigida , Nocicepción , Dolor/tratamiento farmacológico , Receptores de Neuroquinina-1/metabolismo , Transducción de Señal , Animales , Compartimento Celular , Clatrina/metabolismo , Dinaminas/metabolismo , Endocitosis/efectos de los fármacos , Endosomas/efectos de los fármacos , Proteínas de Unión al GTP/metabolismo , Células HEK293 , Humanos , Lípidos/química , Modelos Biológicos , Antagonistas del Receptor de Neuroquinina-1/farmacología , Antagonistas del Receptor de Neuroquinina-1/uso terapéutico , Neuronas/efectos de los fármacos , Neuronas/metabolismo , Neuronas/patología , Nocicepción/efectos de los fármacos , Dolor/patología , Unión Proteica/efectos de los fármacos , Ratas , Transducción de Señal/efectos de los fármacos , Médula Espinal/patología , Fracciones Subcelulares/metabolismo , Sustancia P/metabolismo , beta-Arrestinas/metabolismo
20.
Nat Struct Mol Biol ; 22(7): 555-64, 2015 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-26030874

RESUMEN

Rapid neurotransmitter release depends on the Ca2+ sensor Synaptotagmin-1 (Syt1) and the SNARE complex formed by synaptobrevin, syntaxin-1 and SNAP-25. How Syt1 triggers release has been unclear, partly because elucidating high-resolution structures of Syt1-SNARE complexes has been challenging. An NMR approach based on lanthanide-induced pseudocontact shifts now reveals a dynamic binding mode in which basic residues in the concave side of the Syt1 C2B-domain ß-sandwich interact with a polyacidic region of the SNARE complex formed by syntaxin-1 and SNAP-25. The physiological relevance of this dynamic structural model is supported by mutations in basic residues of Syt1 that markedly impair SNARE-complex binding in vitro and Syt1 function in neurons. Mutations with milder effects on binding have correspondingly milder effects on Syt1 function. Our results support a model whereby dynamic interaction facilitates cooperation between Syt1 and the SNAREs in inducing membrane fusion.


Asunto(s)
Proteínas SNARE/metabolismo , Sinaptotagmina I/metabolismo , Animales , Células Cultivadas , Humanos , Ratones Endogámicos C57BL , Modelos Moleculares , Neuronas/metabolismo , Resonancia Magnética Nuclear Biomolecular , Unión Proteica , Estructura Terciaria de Proteína , Ratas , Proteínas SNARE/química , Sinaptotagmina I/química
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