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1.
J Comput Aided Mol Des ; 38(1): 22, 2024 May 16.
Artículo en Inglés | MEDLINE | ID: mdl-38753096

RESUMEN

Although the size of virtual libraries of synthesizable compounds is growing rapidly, we are still enumerating only tiny fractions of the drug-like chemical universe. Our capability to mine these newly generated libraries also lags their growth. That is why fragment-based approaches that utilize on-demand virtual combinatorial libraries are gaining popularity in drug discovery. These à la carte libraries utilize synthetic blocks found to be effective binders in parts of target protein pockets and a variety of reliable chemistries to connect them. There is, however, no data on the potential impact of the chemistries used for making on-demand libraries on the hit rates during virtual screening. There are also no rules to guide in the selection of these synthetic methods for production of custom libraries. We have used the SAVI (Synthetically Accessible Virtual Inventory) library, constructed using 53 reliable reaction types (transforms), to evaluate the impact of these chemistries on docking hit rates for 40 well-characterized protein pockets. The data shows that the virtual hit rates differ significantly for different chemistries with cross coupling reactions such as Sonogashira, Suzuki-Miyaura, Hiyama and Liebeskind-Srogl coupling producing the highest hit rates. Virtual hit rates appear to depend not only on the property of the formed chemical bond but also on the diversity of available building blocks and the scope of the reaction. The data identifies reactions that deserve wider use through increasing the number of corresponding building blocks and suggests the reactions that are more effective for pockets with certain physical and hydrogen bond-forming properties.


Asunto(s)
Simulación del Acoplamiento Molecular , Unión Proteica , Proteínas , Bibliotecas de Moléculas Pequeñas , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/farmacología , Proteínas/química , Proteínas/metabolismo , Sitios de Unión , Descubrimiento de Drogas/métodos , Ligandos , Diseño de Fármacos , Humanos
2.
Nat Commun ; 15(1): 1703, 2024 Feb 24.
Artículo en Inglés | MEDLINE | ID: mdl-38402212

RESUMEN

Fusion-positive rhabdomyosarcoma (FP-RMS) is an aggressive pediatric sarcoma driven primarily by the PAX3-FOXO1 fusion oncogene, for which therapies targeting PAX3-FOXO1 are lacking. Here, we screen 62,643 compounds using an engineered cell line that monitors PAX3-FOXO1 transcriptional activity identifying a hitherto uncharacterized compound, P3FI-63. RNA-seq, ATAC-seq, and docking analyses implicate histone lysine demethylases (KDMs) as its targets. Enzymatic assays confirm the inhibition of multiple KDMs with the highest selectivity for KDM3B. Structural similarity search of P3FI-63 identifies P3FI-90 with improved solubility and potency. Biophysical binding of P3FI-90 to KDM3B is demonstrated using NMR and SPR. P3FI-90 suppresses the growth of FP-RMS in vitro and in vivo through downregulating PAX3-FOXO1 activity, and combined knockdown of KDM3B and KDM1A phenocopies P3FI-90 effects. Thus, we report KDM inhibitors P3FI-63 and P3FI-90 with the highest specificity for KDM3B. Their potent suppression of PAX3-FOXO1 activity indicates a possible therapeutic approach for FP-RMS and other transcriptionally addicted cancers.


Asunto(s)
Rabdomiosarcoma Alveolar , Rabdomiosarcoma , Niño , Humanos , Factores de Transcripción Paired Box/genética , Factores de Transcripción Paired Box/metabolismo , Rabdomiosarcoma Alveolar/genética , Línea Celular Tumoral , Rabdomiosarcoma/tratamiento farmacológico , Rabdomiosarcoma/genética , Proteína Forkhead Box O1/genética , Proteína Forkhead Box O1/metabolismo , Proteínas de Fusión Oncogénica/genética , Proteínas de Fusión Oncogénica/metabolismo , Regulación Neoplásica de la Expresión Génica , Factor de Transcripción PAX3/genética , Factor de Transcripción PAX3/metabolismo , Histona Demetilasas con Dominio de Jumonji/genética , Histona Demetilasas con Dominio de Jumonji/metabolismo , Histona Demetilasas/metabolismo
3.
Front Oncol ; 13: 1144153, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37182134

RESUMEN

STAT3 N-terminal domain is a promising molecular target for cancer treatment and modulation of immune responses. However, STAT3 is localized in the cytoplasm, mitochondria, and nuclei, and thus, is inaccessible to therapeutic antibodies. Its N-terminal domain lacks deep pockets on the surface and represents a typical "non-druggable" protein. In order to successfully identify potent and selective inhibitors of the domain, we have used virtual screening of billion structure-sized virtual libraries of make-on-demand screening samples. The results suggest that the expansion of accessible chemical space by cutting-edge ultra-large virtual compound databases can lead to successful development of small molecule drugs for hard-to-target intracellular proteins.

4.
Int J Mol Sci ; 24(2)2023 Jan 13.
Artículo en Inglés | MEDLINE | ID: mdl-36675167

RESUMEN

Four Ras guanine nucleotide-releasing proteins (RasGRP1 through 4) belong to the family of guanine nucleotide exchange factors (GEFs). RasGRPs catalyze the release of GDP from small GTPases Ras and Rap and facilitate their transition from an inactive GDP-bound to an active GTP-bound state. Thus, they regulate critical cellular responses via many downstream GTPase effectors. Similar to other RasGRPs, the catalytic module of RasGRP1 is composed of the Ras exchange motif (REM) and Cdc25 domain, and the EF hands and C1 domain contribute to its cellular localization and regulation. RasGRP1 can be activated by a diacylglycerol (DAG)-mediated membrane recruitment and protein kinase C (PKC)-mediated phosphorylation. RasGRP1 acts downstream of the T cell receptor (TCR), B cell receptors (BCR), and pre-TCR, and plays an important role in the thymocyte maturation and function of peripheral T cells, B cells, NK cells, mast cells, and neutrophils. The dysregulation of RasGRP1 is known to contribute to numerous disorders that range from autoimmune and inflammatory diseases and schizophrenia to neoplasia. Given its position at the crossroad of cell development, inflammation, and cancer, RASGRP1 has garnered interest from numerous disciplines. In this review, we outline the structure, function, and regulation of RasGRP1 and focus on the existing knowledge of the role of RasGRP1 in leukemia and other cancers.


Asunto(s)
Factores de Intercambio de Guanina Nucleótido , Sistema Inmunológico , Neoplasias , Humanos , Factores de Intercambio de Guanina Nucleótido/genética , Factores de Intercambio de Guanina Nucleótido/inmunología , Factores de Intercambio de Guanina Nucleótido/metabolismo , Nucleótidos de Guanina , Neoplasias/genética , Neoplasias/inmunología , Neoplasias/metabolismo , Receptores de Antígenos de Linfocitos T , Linfocitos T/inmunología , Sistema Inmunológico/citología , Sistema Inmunológico/inmunología
5.
Nat Commun ; 12(1): 7318, 2021 12 16.
Artículo en Inglés | MEDLINE | ID: mdl-34916494

RESUMEN

Proteasome substrate receptor hRpn13 is a promising anti-cancer target. By integrated in silico and biophysical screening, we identified a chemical scaffold that binds hRpn13 with non-covalent interactions that mimic the proteasome and a weak electrophile for Michael addition. hRpn13 Pru domain binds proteasomes and ubiquitin whereas its DEUBAD domain binds deubiquitinating enzyme UCHL5. NMR revealed lead compound XL5 to interdigitate into a hydrophobic pocket created by lateral movement of a Pru ß-hairpin with an exposed end for Proteolysis Targeting Chimeras (PROTACs). Implementing XL5-PROTACs as chemical probes identified a DEUBAD-lacking hRpn13 species (hRpn13Pru) present naturally with cell type-dependent abundance. XL5-PROTACs preferentially target hRpn13Pru, causing its ubiquitination. Gene-editing and rescue experiments established hRpn13 requirement for XL5-PROTAC-triggered apoptosis. These data establish hRpn13 as an anti-cancer target for multiple myeloma and introduce an hRpn13-targeting scaffold that can be optimized for preclinical trials against hRpn13Pru-producing cancer types.


Asunto(s)
Péptidos y Proteínas de Señalización Intracelular/química , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Mieloma Múltiple/metabolismo , Ubiquitinación , Apoptosis , Línea Celular Tumoral , Regulación Neoplásica de la Expresión Génica , Humanos , Péptidos y Proteínas de Señalización Intracelular/genética , Mieloma Múltiple/genética , Complejo de la Endopetidasa Proteasomal/metabolismo , Factores de Transcripción/metabolismo , Activación Transcripcional , Ubiquitina/metabolismo
6.
Sci Data ; 7(1): 384, 2020 11 11.
Artículo en Inglés | MEDLINE | ID: mdl-33177514

RESUMEN

We have made available a database of over 1 billion compounds predicted to be easily synthesizable, called Synthetically Accessible Virtual Inventory (SAVI). They have been created by a set of transforms based on an adaptation and extension of the CHMTRN/PATRAN programming languages describing chemical synthesis expert knowledge, which originally stem from the LHASA project. The chemoinformatics toolkit CACTVS was used to apply a total of 53 transforms to about 150,000 readily available building blocks (enamine.net). Only single-step, two-reactant syntheses were calculated for this database even though the technology can execute multi-step reactions. The possibility to incorporate scoring systems in CHMTRN allowed us to subdivide the database of 1.75 billion compounds in sets according to their predicted synthesizability, with the most-synthesizable class comprising 1.09 billion synthetic products. Properties calculated for all SAVI products show that the database should be well-suited for drug discovery. It is being made publicly available for free download from https://doi.org/10.35115/37n9-5738.

7.
Cancers (Basel) ; 12(8)2020 Aug 08.
Artículo en Inglés | MEDLINE | ID: mdl-32784501

RESUMEN

(1) Background: The hedgehog (HH) signaling pathway is a key regulator of embryonic patterning, tissue regeneration, stem cell renewal, and cancer growth. The smoothened (SMO) protein regulates the HH signaling pathway and has demonstrated oncogenic activity. (2) Methods: To clarify the role of the HH signaling pathway in tumorigenesis, the expression profile of key HH signaling molecules, including SMO, PTCH1, GLI1, GLI2, and GLI3, were determined in 33 cancer cell lines and normal prostate cells and tissues. We performed a computational analysis of the upstream region of the SMO gene to identify the regulatory elements. (3) Results: Three potential CpG islands and several putative SMO promoter elements were identified. Luciferase reporter assays mapped key SMO promoter elements, and functional binding sites for SP1, AP1, CREB, and AP-2α transcription factors in the core SMO promoter region were confirmed. A hypermethylated SMO promoter was identified in several cancer cell lines suggesting an important role for epigenetic silencing of SMO expression in certain cancer cells. (4) Discussion: These results have important implications for our understanding of regulatory mechanisms controlling HH pathway activity and the molecular basis of SMO gene function. Moreover, this study may prove valuable for future research aimed at producing therapeutic downregulation of SMO expression in cancer cells.

8.
Nat Commun ; 11(1): 1291, 2020 03 10.
Artículo en Inglés | MEDLINE | ID: mdl-32157086

RESUMEN

Regulated proteolysis by proteasomes involves ~800 enzymes for substrate modification with ubiquitin, including ~600 E3 ligases. We report here that E6AP/UBE3A is distinguished from other E3 ligases by having a 12 nM binding site at the proteasome contributed by substrate receptor hRpn10/PSMD4/S5a. Intrinsically disordered by itself, and previously uncharacterized, the E6AP-binding domain in hRpn10 locks into a well-defined helical structure to form an intermolecular 4-helix bundle with the E6AP AZUL, which is unique to this E3. We thus name the hRpn10 AZUL-binding domain RAZUL. We further find in human cells that loss of RAZUL by CRISPR-based gene editing leads to loss of E6AP at proteasomes. Moreover, proteasome-associated ubiquitin is reduced following E6AP knockdown or displacement from proteasomes, suggesting that E6AP ubiquitinates substrates at or for the proteasome. Altogether, our findings indicate E6AP to be a privileged E3 for the proteasome, with a dedicated, high affinity binding site contributed by hRpn10.


Asunto(s)
Complejo de la Endopetidasa Proteasomal/metabolismo , Proteínas de Unión al ARN/metabolismo , Ubiquitina-Proteína Ligasas/metabolismo , Sitios de Unión , Células HCT116 , Humanos , Modelos Biológicos , Modelos Moleculares , Unión Proteica , Dominios Proteicos , Estructura Secundaria de Proteína , Proteínas de Unión al ARN/química , Especificidad por Sustrato , Ubiquitina-Proteína Ligasas/química
9.
J Allergy Clin Immunol ; 143(2): 669-680.e12, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-29778505

RESUMEN

BACKGROUND: Chemokine signaling through CCR3 is a key regulatory pathway for eosinophil recruitment into tissues associated with allergic inflammation and asthma. To date, none of the CCR3 antagonists have shown efficacy in clinical trials. One reason might be their unbiased mode of inhibition that prevents receptor internalization, leading to drug tolerance. OBJECTIVE: We sought to develop a novel peptide nanoparticle CCR3 inhibitor (R321) with a biased mode of inhibition that would block G protein signaling but enable or promote receptor internalization. METHODS: Self-assembly of R321 peptide into nanoparticles and peptide binding to CCR3 were analyzed by means of dynamic light scattering and nuclear magnetic resonance. Inhibitory activity on CCR3 signaling was assessed in vitro by using flow cytometry, confocal microscopy, and Western blot analysis in a CCR3+ eosinophil cell line and blood eosinophils. In vivo effects of R321 were assessed by using a triple-allergen mouse asthma model. RESULTS: R321 self-assembles into nanoparticles and binds directly to CCR3, altering receptor function. Half-maximal inhibitory concentration values for eotaxin-induced chemotaxis of blood eosinophils are in the low nanomolar range. R321 inhibits only the early phase of extracellular signal-regulated kinase 1/2 activation and not the late phase generally associated with ß-arrestin recruitment and receptor endocytosis, promoting CCR3 internalization and degradation. In vivo R321 effectively blocks eosinophil recruitment into the blood, lungs, and airways and prevents airway hyperresponsiveness in a mouse eosinophilic asthma model. CONCLUSIONS: R321 is a potent and selective antagonist of the CCR3 signaling cascade. Inhibition through a biased mode of antagonism might hold significant therapeutic promise by eluding the formation of drug tolerance.


Asunto(s)
Eosinófilos/inmunología , Hipersensibilidad/tratamiento farmacológico , Pulmón/inmunología , Nanopartículas/uso terapéutico , Péptidos/uso terapéutico , Receptores CCR3/antagonistas & inhibidores , Hipersensibilidad Respiratoria/tratamiento farmacológico , Alérgenos/inmunología , Línea Celular , Movimiento Celular , Proteínas de Unión al GTP/antagonistas & inhibidores , Humanos , Espectroscopía de Resonancia Magnética , Unión Proteica , Transducción de Señal
10.
Sci Rep ; 8(1): 16610, 2018 11 09.
Artículo en Inglés | MEDLINE | ID: mdl-30413750

RESUMEN

Here we demonstrate that aerosols of host directed therapies [HDT] administered during a chronic Mycobacterium tuberculosis (Mtb) infection have bactericidal effect. The pulmonary bacterial load of C57BL/6 mice chronically infected with Mtb was reduced by 1.7 and 0.6 log10CFU after two weeks of treatment via aerosol delivery with ST3-H2A2, [a selective peptide inhibitor of the STAT3 N-terminal domain] or IL10R1-7 [selective peptide inhibitor for the IL-10Ra] respectively and when compared to control mice treated with IL10R1-14 [peptide inhibitor used as negative control] or untreated mice infected with Mtb. Accordingly, when compared to control mice, the bactericidal capacity in mice was enhanced upon treatment with peptide inhibitors ST3-H2A2 and IL10R1-7 as evidenced by higher pulmonary activities of nitric oxide synthase, NADPH oxidase and lysozyme enzymes and decreased arginase enzyme activity. This therapy also modulated important checkpoints [Bcl2, Beclin-1, Atg 5, bax] in the apoptosis-autophagy pathways. Thus, even in the absence of antibiotics, targeting of the host pulmonary IL-10-STAT3 pathway can significantly reduce the Mtb bacilli load in the lungs, modulate the host own bactericidal capacity and apoptosis and autophagy pathways. Our approach here also allows targeting checkpoints of the lungs to determine their specific contribution in pulmonary immunity or pathogenesis.


Asunto(s)
Sistemas de Liberación de Medicamentos , Interleucina-10/antagonistas & inhibidores , Mycobacterium tuberculosis/efectos de los fármacos , Fragmentos de Péptidos/administración & dosificación , Factor de Transcripción STAT3/antagonistas & inhibidores , Tuberculosis Pulmonar/tratamiento farmacológico , Tuberculosis/tratamiento farmacológico , Administración por Inhalación , Animales , Femenino , Ratones , Ratones Endogámicos C57BL , Fragmentos de Péptidos/farmacología , Tuberculosis/microbiología , Tuberculosis Pulmonar/microbiología
11.
Sci Signal ; 11(552)2018 10 16.
Artículo en Inglés | MEDLINE | ID: mdl-30327409

RESUMEN

Repeated dosing of drugs targeting G protein-coupled receptors can stimulate antagonist tolerance, which reduces their efficacy; thus, strategies to avoid tolerance are needed. The efficacy of AMD3100, a competitive antagonist of the chemokine receptor CXCR4 that mobilizes leukemic blasts from the bone marrow into the blood to sensitize them to chemotherapy, is reduced after prolonged treatment. Tolerance to AMD3100 increases the abundance of CXCR4 on the surface of leukemic blasts, which promotes their rehoming to the bone marrow. AMD3100 inhibits both G protein signaling by CXCR4 and ß-arrestin1/2-dependent receptor endocytosis. We demonstrated that biased antagonists of G protein-dependent chemotaxis but not ß-arrestin1/2 recruitment and subsequent receptor endocytosis avoided tolerance. The peptide antagonist X4-2-6, which is derived from transmembrane helix 2 and extracellular loop 1 of CXCR4, limited chemotaxis and signaling but did not promote CXCR4 accumulation on the cell surface or cause tolerance. The activity of X4-2-6 was due to its distinct mechanism of inhibition of CXCR4. The peptide formed a ternary complex with the receptor and its ligand, the chemokine CXCL12. Within this complex, X4-2-6 released the portion of CXCL12 critical for receptor-mediated activation of G proteins but enabled the rest of the chemokine to recruit ß-arrestins to the receptor. In contrast, AMD3100 displaced all components of the chemokine responsible for CXCR4 activation. We further identified a small molecule with similar biased antagonist properties to those of X4-2-6, which may provide a viable alternative to patients when antagonist tolerance prevents drugs from reaching efficacy.


Asunto(s)
Tolerancia a Medicamentos , Proteínas de Unión al GTP/antagonistas & inhibidores , Receptores CXCR4/antagonistas & inhibidores , Receptores CXCR4/química , Transducción de Señal , Animales , Bencilaminas , Células CHO , Quimiocina CXCL12/metabolismo , Quimiotaxis , Cricetinae , Cricetulus , Ciclamas , Endocitosis , Fibroblastos/efectos de los fármacos , Compuestos Heterocíclicos/farmacología , Humanos , Células Jurkat , Ligandos , Ratones , Fosforilación , Dominios Proteicos , Células THP-1 , beta-Arrestina 1/metabolismo , Arrestina beta 2/metabolismo
12.
Nat Commun ; 8: 15540, 2017 06 09.
Artículo en Inglés | MEDLINE | ID: mdl-28598414

RESUMEN

Proteasome-ubiquitin receptor hRpn13/Adrm1 binds and activates deubiquitinating enzyme Uch37/UCHL5 and is targeted by bis-benzylidine piperidone RA190, which restricts cancer growth in mice xenografts. Here, we solve the structure of hRpn13 with a segment of hRpn2 that serves as its proteasome docking site; a proline-rich C-terminal hRpn2 extension stretches across a narrow canyon of the ubiquitin-binding hRpn13 Pru domain blocking an RA190-binding surface. Biophysical analyses in combination with cell-based assays indicate that hRpn13 binds preferentially to hRpn2 and proteasomes over RA190. hRpn13 also exists outside of proteasomes where it may be RA190 sensitive. RA190 does not affect hRpn13 interaction with Uch37, but rather directly binds and inactivates Uch37. hRpn13 deletion from HCT116 cells abrogates RA190-induced accumulation of substrates at proteasomes. We propose that RA190 targets hRpn13 and Uch37 through parallel mechanisms and at proteasomes, RA190-inactivated Uch37 cannot disassemble hRpn13-bound ubiquitin chains.


Asunto(s)
Antineoplásicos/química , Compuestos de Bencilideno/química , Hexosiltransferasas/metabolismo , Glicoproteínas de Membrana/metabolismo , Neoplasias/metabolismo , Complejo de la Endopetidasa Proteasomal/metabolismo , Ubiquitina Tiolesterasa/metabolismo , Antineoplásicos/farmacología , Compuestos de Bencilideno/farmacología , Biofisica , Ensayos de Selección de Medicamentos Antitumorales , Regulación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Células HCT116 , Humanos , Péptidos y Proteínas de Señalización Intracelular , Neoplasias/tratamiento farmacológico , Prolina/química , Unión Proteica , Dominios Proteicos
13.
Int J Mol Sci ; 17(5)2016 Jun 20.
Artículo en Inglés | MEDLINE | ID: mdl-27331810

RESUMEN

Recent evidence suggests that C-X-C chemokine receptor type 4 (CXCR4) heteromerizes with α1A/B-adrenoceptors (AR) and atypical chemokine receptor 3 (ACKR3) and that CXCR4:α1A/B-AR heteromers are important for α1-AR function in vascular smooth muscle cells (VSMC). Structural determinants for CXCR4 heteromerization and functional consequences of CXCR4:α1A/B-AR heteromerization in intact arteries, however, remain unknown. Utilizing proximity ligation assays (PLA) to visualize receptor interactions in VSMC, we show that peptide analogs of transmembrane-domain (TM) 2 and TM4 of CXCR4 selectively reduce PLA signals for CXCR4:α1A-AR and CXCR4:ACKR3 interactions, respectively. While both peptides inhibit CXCL12-induced chemotaxis, only the TM2 peptide inhibits phenylephrine-induced Ca(2+)-fluxes, contraction of VSMC and reduces efficacy of phenylephrine to constrict isolated arteries. In a Cre-loxP mouse model to delete CXCR4 in VSMC, we observed 60% knockdown of CXCR4. PLA signals for CXCR4:α1A/B-AR and CXCR4:ACKR3 interactions in VSMC, however, remained constant. Our observations point towards TM2/4 of CXCR4 as possible contact sites for heteromerization and suggest that TM-derived peptide analogs permit selective targeting of CXCR4 heteromers. A molecular dynamics simulation of a receptor complex in which the CXCR4 homodimer interacts with α1A-AR via TM2 and with ACKR3 via TM4 is presented. Our findings further imply that CXCR4:α1A-AR heteromers are important for intrinsic α1-AR function in intact arteries and provide initial and unexpected insights into the regulation of CXCR4 heteromerization in VSMC.


Asunto(s)
Músculo Liso Vascular/metabolismo , Multimerización de Proteína , Receptores Adrenérgicos alfa 1/metabolismo , Receptores CXCR4/metabolismo , Animales , Sitios de Unión , Calcio/metabolismo , Línea Celular , Células Cultivadas , Femenino , Humanos , Masculino , Ratones , Simulación de Dinámica Molecular , Unión Proteica , Ratas , Ratas Sprague-Dawley , Receptores CXCR/genética , Receptores CXCR/metabolismo , Receptores CXCR4/química , Receptores CXCR4/genética
14.
Proteins ; 84(2): 193-200, 2016 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-26650755

RESUMEN

Multiple genes in Mycobacterium tuberculosis (Mtb) are regulated by copper including socAB (small orf induced by copper A and B), which is induced by copper and repressed by RicR (regulated in copper repressor). socA and socB encode hypothetical proteins of 61 and 54 amino acids, respectively. Here, we use biophysical and computational methods to evaluate the SocB structure. We find that SocB lacks evidence for secondary structure, with no thermal cooperative unfolding event, according to circular dichroism measurements. 2D NMR spectra similarly exhibit hallmarks of a disordered structural state, which is also supported by analyzing SocB diffusion. Altogether, these findings suggest that by itself SocB is intrinsically disordered. Interestingly, SocB interacts with a synthetic phospholipid bilayer and becomes helical, which suggests that it may be membrane-associated.


Asunto(s)
Proteínas Bacterianas/química , Cobre/química , Proteínas Intrínsecamente Desordenadas/química , Proteínas de la Membrana/química , Mycobacterium tuberculosis/enzimología , Secuencia de Aminoácidos , Proteínas Bacterianas/metabolismo , Cobre/metabolismo , Proteínas Intrínsecamente Desordenadas/metabolismo , Membrana Dobles de Lípidos/química , Membrana Dobles de Lípidos/metabolismo , Proteínas de la Membrana/metabolismo , Datos de Secuencia Molecular
15.
Biophys J ; 109(12): 2602-2613, 2015 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-26682817

RESUMEN

Ras proteins are small GTPases that act as signal transducers between cell surface receptors and several intracellular signaling cascades. They contain highly homologous catalytic domains and flexible C-terminal hypervariable regions (HVRs) that differ across Ras isoforms. KRAS is among the most frequently mutated oncogenes in human tumors. Surprisingly, we found that the C-terminal HVR of K-Ras4B, thought to minimally impact the catalytic domain, directly interacts with the active site of the protein. The interaction is almost 100-fold tighter with the GDP-bound than the GTP-bound protein. HVR binding interferes with Ras-Raf interaction, modulates binding to phospholipids, and slightly slows down nucleotide exchange. The data indicate that contrary to previously suggested models of K-Ras4B signaling, HVR plays essential roles in regulation of signaling. High affinity binding of short peptide analogs of HVR to K-Ras active site suggests that targeting this surface with inhibitory synthetic molecules for the therapy of KRAS-dependent tumors is feasible.


Asunto(s)
Dominio Catalítico , Proteínas Proto-Oncogénicas p21(ras)/química , Proteínas Proto-Oncogénicas p21(ras)/metabolismo , Proteínas ras/química , Proteínas ras/metabolismo , Secuencia de Aminoácidos , Biocatálisis , Guanosina Difosfato/metabolismo , Guanosina Trifosfato/metabolismo , Simulación de Dinámica Molecular , Datos de Secuencia Molecular , Fragmentos de Péptidos/química , Fragmentos de Péptidos/metabolismo , Unión Proteica
16.
Structure ; 23(7): 1325-35, 2015 Jul 07.
Artículo en Inglés | MEDLINE | ID: mdl-26051715

RESUMEN

Ras proteins recruit and activate effectors, including Raf, that transmit receptor-initiated signals. Monomeric Ras can bind Raf; however, activation of Raf requires its dimerization. It has been suspected that dimeric Ras may promote dimerization and activation of Raf. Here, we show that the GTP-bound catalytic domain of K-Ras4B, a highly oncogenic splice variant of the K-Ras isoform, forms stable homodimers. We observe two major dimer interfaces. The first, highly populated ß-sheet dimer interface is at the Switch I and effector binding regions, overlapping the binding surfaces of Raf, PI3K, RalGDS, and additional effectors. This interface has to be inhibitory to such effectors. The second, helical interface also overlaps the binding sites of some effectors. This interface may promote activation of Raf. Our data reveal how Ras self-association can regulate effector binding and activity, and suggest that disruption of the helical dimer interface by drugs may abate Raf signaling in cancer.


Asunto(s)
Guanosina Trifosfato/química , Proteínas Proto-Oncogénicas p21(ras)/química , Dominio Catalítico , Humanos , Cinética , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Multimerización de Proteína
17.
Proc Natl Acad Sci U S A ; 112(13): E1659-68, 2015 Mar 31.
Artículo en Inglés | MEDLINE | ID: mdl-25775528

RESUMEN

Recent evidence suggests that chemokine (C-X-C motif) receptor 4 (CXCR4) contributes to the regulation of blood pressure through interactions with α1-adrenergic receptors (ARs) in vascular smooth muscle. The underlying molecular mechanisms, however, are unknown. Using proximity ligation assays to visualize single-molecule interactions, we detected that α1A/B-ARs associate with CXCR4 on the cell surface of rat and human vascular smooth muscle cells (VSMC). Furthermore, α1A/B-AR could be coimmunoprecipitated with CXCR4 in a HeLa expression system and in human VSMC. A peptide derived from the second transmembrane helix of CXCR4 induced chemical shift changes in the NMR spectrum of CXCR4 in membranes, disturbed the association between α1A/B-AR and CXCR4, and inhibited Ca(2+) mobilization, myosin light chain (MLC) 2 phosphorylation, and contraction of VSMC upon α1-AR activation. CXCR4 silencing reduced α1A/B-AR:CXCR4 heteromeric complexes in VSMC and abolished phenylephrine-induced Ca(2+) fluxes and MLC2 phosphorylation. Treatment of rats with CXCR4 agonists (CXCL12, ubiquitin) reduced the EC50 of the phenylephrine-induced blood pressure response three- to fourfold. These observations suggest that disruption of the quaternary structure of α1A/B-AR:CXCR4 heteromeric complexes by targeting transmembrane helix 2 of CXCR4 and depletion of the heteromeric receptor complexes by CXCR4 knockdown inhibit α1-AR-mediated function in VSMC and that activation of CXCR4 enhances the potency of α1-AR agonists. Our findings extend the current understanding of the molecular mechanisms regulating α1-AR and provide an example of the importance of G protein-coupled receptor (GPCR) heteromerization for GPCR function. Compounds targeting the α1A/B-AR:CXCR4 interaction could provide an alternative pharmacological approach to modulate blood pressure.


Asunto(s)
Receptores Adrenérgicos alfa 1/metabolismo , Receptores CXCR4/metabolismo , Secuencias de Aminoácidos , Animales , Bencilaminas , Presión Sanguínea/efectos de los fármacos , Membrana Celular , Quimiocina CXCL12/metabolismo , Ciclamas , Dimerización , Células HeLa , Compuestos Heterocíclicos/química , Humanos , Masculino , Músculo Liso Vascular/citología , Miocitos del Músculo Liso/metabolismo , Fenilefrina/química , Ratas , Ratas Endogámicas Lew , Ratas Sprague-Dawley , Receptores Acoplados a Proteínas G/metabolismo
18.
J Biol Chem ; 290(15): 9465-77, 2015 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-25713064

RESUMEN

K-Ras4B belongs to a family of small GTPases that regulates cell growth, differentiation and survival. K-ras is frequently mutated in cancer. K-Ras4B association with the plasma membrane through its farnesylated and positively charged C-terminal hypervariable region (HVR) is critical to its oncogenic function. However, the structural mechanisms of membrane association are not fully understood. Here, using confocal microscopy, surface plasmon resonance, and molecular dynamics simulations, we observed that K-Ras4B can be distributed in rigid and loosely packed membrane domains. Its membrane binding domain interaction with phospholipids is driven by membrane fluidity. The farnesyl group spontaneously inserts into the disordered lipid microdomains, whereas the rigid microdomains restrict the farnesyl group penetration. We speculate that the resulting farnesyl protrusion toward the cell interior allows oligomerization of the K-Ras4B membrane binding domain in rigid microdomains. Unlike other Ras isoforms, K-Ras4B HVR contains a single farnesyl modification and positively charged polylysine sequence. The high positive charge not only modulates specific HVR binding to anionic phospholipids but farnesyl membrane orientation. Phosphorylation of Ser-181 prohibits spontaneous farnesyl membrane insertion. The mechanism illuminates the roles of HVR modifications in K-Ras4B targeting microdomains of the plasma membrane and suggests an additional function for HVR in regulation of Ras signaling.


Asunto(s)
Membrana Celular/metabolismo , GTP Fosfohidrolasas/metabolismo , Péptidos/metabolismo , Proteínas Proto-Oncogénicas p21(ras)/metabolismo , Secuencia de Aminoácidos , Animales , Línea Celular , Membrana Celular/química , GTP Fosfohidrolasas/química , GTP Fosfohidrolasas/genética , Humanos , Membrana Dobles de Lípidos/química , Membrana Dobles de Lípidos/metabolismo , Fluidez de la Membrana , Microdominios de Membrana/química , Microdominios de Membrana/metabolismo , Microscopía Confocal , Modelos Químicos , Simulación de Dinámica Molecular , Datos de Secuencia Molecular , Péptidos/química , Péptidos/genética , Fosfolípidos/química , Fosfolípidos/metabolismo , Fosforilación , Unión Proteica , Multimerización de Proteína , Prenilación de Proteína , Proteínas Proto-Oncogénicas p21(ras)/química , Proteínas Proto-Oncogénicas p21(ras)/genética , Serina/química , Serina/genética , Serina/metabolismo , Resonancia por Plasmón de Superficie
19.
Proc Natl Acad Sci U S A ; 110(4): 1267-72, 2013 Jan 22.
Artículo en Inglés | MEDLINE | ID: mdl-23288901

RESUMEN

Activation of STAT3 in cancers leads to gene expression promoting cell proliferation and resistance to apoptosis, as well as tumor angiogenesis, invasion, and migration. In the characterization of effects of ST3-H2A2, a selective inhibitor of the STAT3 N-terminal domain (ND), we observed that the compound induced apoptotic death in cancer cells associated with robust activation of proapoptotic genes. Using ChIP and tiling human promoter arrays, we found that activation of gene expression in response to ST3-H2A2 is accompanied by altered STAT3 chromatin binding. Using inhibitors of STAT3 phosphorylation and a dominant-negative STAT3 mutant, we found that the unphosphorylated form of STAT3 binds to regulatory regions of proapoptotic genes and prevents their expression in tumor cells but not normal cells. siRNA knockdown confirmed the effects of ST3-HA2A on gene expression and chromatin binding to be STAT3 dependent. The STAT3-binding region of the C/EBP-homologous protein (CHOP) promoter was found to be localized in DNaseI hypersensitive site of chromatin in cancer cells but not in nontransformed cells, suggesting that STAT3 binding and suppressive action can be chromatin structure dependent. These data demonstrate a suppressive role for the STAT3 ND in the regulation of proapoptotic gene expression in cancer cells, providing further support for targeting STAT3 ND for cancer therapy.


Asunto(s)
Apoptosis/genética , Neoplasias de la Próstata/genética , Neoplasias de la Próstata/metabolismo , Factor de Transcripción STAT3/química , Factor de Transcripción STAT3/metabolismo , Apoptosis/efectos de los fármacos , Línea Celular Tumoral , Cromatina/metabolismo , Expresión Génica/efectos de los fármacos , Técnicas de Silenciamiento del Gen , Humanos , Masculino , Fosforilación , Regiones Promotoras Genéticas , Neoplasias de la Próstata/patología , Estructura Terciaria de Proteína , ARN Interferente Pequeño/genética , Factor de Transcripción STAT3/antagonistas & inhibidores , Factor de Transcripción STAT3/genética
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