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1.
PLoS Pathog ; 20(5): e1012176, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38709846

RESUMEN

Magnaporthe AVRs and ToxB-like (MAX) effectors constitute a family of secreted virulence proteins in the fungus Pyricularia oryzae (syn. Magnaporthe oryzae), which causes blast disease on numerous cereals and grasses. In spite of high sequence divergence, MAX effectors share a common fold characterized by a ß-sandwich core stabilized by a conserved disulfide bond. In this study, we investigated the structural landscape and diversity within the MAX effector repertoire of P. oryzae. Combining experimental protein structure determination and in silico structure modeling we validated the presence of the conserved MAX effector core domain in 77 out of 94 groups of orthologs (OG) identified in a previous population genomic study. Four novel MAX effector structures determined by NMR were in remarkably good agreement with AlphaFold2 (AF2) predictions. Based on the comparison of the AF2-generated 3D models we propose a classification of the MAX effectors superfamily in 20 structural groups that vary in the canonical MAX fold, disulfide bond patterns, and additional secondary structures in N- and C-terminal extensions. About one-third of the MAX family members remain singletons, without strong structural relationship to other MAX effectors. Analysis of the surface properties of the AF2 MAX models also highlights the high variability within the MAX family at the structural level, potentially reflecting the wide diversity of their virulence functions and host targets.


Asunto(s)
Ascomicetos , Proteínas Fúngicas , Enfermedades de las Plantas , Proteínas Fúngicas/química , Proteínas Fúngicas/metabolismo , Proteínas Fúngicas/genética , Ascomicetos/genética , Ascomicetos/patogenicidad , Ascomicetos/metabolismo , Enfermedades de las Plantas/microbiología , Modelos Moleculares , Conformación Proteica , Virulencia , Factores de Virulencia/genética , Factores de Virulencia/química , Factores de Virulencia/metabolismo , Secuencia de Aminoácidos
2.
Commun Biol ; 7(1): 607, 2024 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-38769168

RESUMEN

A critical step to maximize the usefulness of genome-wide association studies (GWAS) in plant breeding is the identification and validation of candidate genes underlying genetic associations. This is of particular importance in disease resistance breeding where allelic variants of resistance genes often confer resistance to distinct populations, or races, of a pathogen. Here, we perform a genome-wide association analysis of rice blast resistance in 500 genetically diverse rice accessions. To facilitate candidate gene identification, we produce de-novo genome assemblies of ten rice accessions with various rice blast resistance associations. These genome assemblies facilitate the identification and functional validation of novel alleles of the rice blast resistance genes Ptr and Pia. We uncover an allelic series for the unusual Ptr rice blast resistance gene, and additional alleles of the Pia resistance genes RGA4 and RGA5. By linking these associations to three thousand rice genomes we provide a useful tool to inform future rice blast breeding efforts. Our work shows that GWAS in combination with whole-genome sequencing is a powerful tool for gene cloning and to facilitate selection of specific resistance alleles for plant breeding.


Asunto(s)
Alelos , Resistencia a la Enfermedad , Estudio de Asociación del Genoma Completo , Oryza , Enfermedades de las Plantas , Oryza/genética , Oryza/inmunología , Oryza/microbiología , Resistencia a la Enfermedad/genética , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/inmunología , Proteínas de Plantas/genética , Genoma de Planta , Genes de Plantas , Fitomejoramiento/métodos
3.
PLoS Pathog ; 19(9): e1011294, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37695773

RESUMEN

Plant pathogens secrete proteins called effectors that target host cellular processes to promote disease. Recently, structural genomics has identified several families of fungal effectors that share a similar three-dimensional structure despite remarkably variable amino-acid sequences and surface properties. To explore the selective forces that underlie the sequence variability of structurally-analogous effectors, we focused on MAX effectors, a structural family of effectors that are major determinants of virulence in the rice blast fungus Pyricularia oryzae. Using structure-informed gene annotation, we identified 58 to 78 MAX effector genes per genome in a set of 120 isolates representing seven host-associated lineages. The expression of MAX effector genes was primarily restricted to the early biotrophic phase of infection and strongly influenced by the host plant. Pangenome analyses of MAX effectors demonstrated extensive presence/absence polymorphism and identified gene loss events possibly involved in host range adaptation. However, gene knock-in experiments did not reveal a strong effect on virulence phenotypes suggesting that other evolutionary mechanisms are the main drivers of MAX effector losses. MAX effectors displayed high levels of standing variation and high rates of non-synonymous substitutions, pointing to widespread positive selection shaping the molecular diversity of MAX effectors. The combination of these analyses with structural data revealed that positive selection acts mostly on residues located in particular structural elements and at specific positions. By providing a comprehensive catalog of amino acid polymorphism, and by identifying the structural determinants of the sequence diversity, our work will inform future studies aimed at elucidating the function and mode of action of MAX effectors.


Asunto(s)
Aminoácidos , Ascomicetos , Virulencia/genética , Secuencia de Aminoácidos , Ascomicetos/genética
4.
Molecules ; 28(16)2023 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-37630320

RESUMEN

Does a similar 3D structure mean a similar folding pathway? This question is particularly meaningful when it concerns proteins sharing a similar 3D structure, but low sequence identity or homology. MAX effectors secreted by the phytopathogenic fungus Magnaporthe oryzae present such characteristics. They share a common 3D structure, a ß-sandwich with the same topology for all the family members, but an extremely low sequence identity/homology. In a previous study, we have investigated the folding of two MAX effectors, AVR-Pia and AVR-Pib, using High-Hydrostatic-Pressure NMR and found that they display a similar folding pathway, with a common folding intermediate. In the present work, we used a similar strategy to investigate the folding conformational landscape of another MAX effector, MAX60, and found a very different folding intermediate. Our analysis strongly supports that the presence of a C-terminal α-helical extension in the 3D structure of MAX60 could be responsible for its different folding pathway.


Asunto(s)
Ascomicetos , Transporte Biológico , Presión Hidrostática , Pliegue de Proteína , Proteínas Fúngicas
5.
Biomol NMR Assign ; 16(2): 305-309, 2022 10.
Artículo en Inglés | MEDLINE | ID: mdl-35657473

RESUMEN

Effectors are small and very diverse proteins secreted by fungi and translocated in plant cells during infection. Among them, MAX effectors (for Magnaporthe Avrs and ToxB) were identified as a family of effectors that share an identical fold topology despite having highly divergent sequences. They are mostly secreted by ascomycetes from the Magnaporthe genus, a fungus that causes the rice blast, a plant disease leading to huge crop losses. As rice is the first source of calories in many countries, especially in Asia and Africa, this constitutes a threat for world food security. Hence, a better understanding of these effectors, including structural and functional characterization, constitutes a strategic milestone in the fight against phytopathogen fungi and may give clues for the development of resistant varieties of rice. We report here the near complete 1H, 15 N and 13C NMR resonance assignment of three new putative MAX effectors (MAX47, MAX60 and MAX67). Secondary structure determination using TALOS-N and CSI.3 demonstrates a high content of ß-strands in all the three proteins, in agreement with the canonic ß-sandwich structure of MAX effectors. This preliminary study provides foundations for further structural characterization, that will help in turn to improve sequence predictions of other MAX effectors through data mining.


Asunto(s)
Ascomicetos , Magnaporthe , Oryza , Ascomicetos/metabolismo , Proteínas Fúngicas/química , Magnaporthe/metabolismo , Resonancia Magnética Nuclear Biomolecular , Oryza/metabolismo , Oryza/microbiología
6.
Mol Plant Pathol ; 23(9): 1320-1330, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35766176

RESUMEN

The rice nucleotide-binding (NB) and leucine-rich repeat (LRR) domain immune receptors (NLRs) RGA4 and RGA5 form a helper NLR/sensor NLR (hNLR/sNLR) pair that specifically recognizes the effectors AVR-Pia and AVR1-CO39 from the blast fungus Magnaporthe oryzae. While RGA4 contains only canonical NLR domains, RGA5 has an additional unconventional heavy metal-associated (HMA) domain integrated after its LRR domain. This RGA5HMA domain binds the effectors and is crucial for their recognition. Investigation of the three-dimensional structure of the AVR1-CO39/RGA5HMA complex by X-ray crystallography identified a candidate surface for effector binding in the HMA domain and showed that the HMA domain self-interacts in the absence of effector through the same surface. Here, we investigated the relevance of this HMA homodimerization for RGA5 function and the role of the RGA5HMA effector-binding and self-interaction surface in effector recognition. By analysing structure-informed point mutations in the RGA5HMA -binding surface in protein interaction studies and in Nicotiana benthamiana cell death assays, we found that HMA self-interaction does not contribute to RGA5 function. However, the effector-binding surface of RGA5HMA identified by X-ray crystallography is crucial for both in vitro and in vivo effector binding as well as effector recognition. These results support the current hypothesis that noncanonical integrated domains of NLRs act primarily as effector traps and deepen our understanding of the sNLRs' function within NLR pairs.


Asunto(s)
Magnaporthe , Metales Pesados , Oryza , Magnaporthe/genética , Metales Pesados/metabolismo , Oryza/microbiología , Enfermedades de las Plantas/microbiología , Proteínas de Plantas/metabolismo , Nicotiana
7.
Int J Mol Sci ; 23(10)2022 May 13.
Artículo en Inglés | MEDLINE | ID: mdl-35628267

RESUMEN

Despite advances in experimental and computational methods, the mechanisms by which an unstructured polypeptide chain regains its unique three-dimensional structure remains one of the main puzzling questions in biology. Single-molecule techniques, ultra-fast perturbation and detection approaches and improvement in all-atom and coarse-grained simulation methods have greatly deepened our understanding of protein folding and the effects of environmental factors on folding landscape. However, a major challenge remains the detailed characterization of the protein folding landscape. Here, we used high hydrostatic pressure 2D NMR spectroscopy to obtain high-resolution experimental structural information in a site-specific manner across the polypeptide sequence and along the folding reaction coordinate. We used this residue-specific information to constrain Cyana3 calculations, in order to obtain a topological description of the entire folding landscape. This approach was used to describe the conformers populating the folding landscape of two small globular proteins, AVR-Pia and AVR-Pib, that belong to the structurally conserved but sequence-unrelated MAX effectors superfamily. Comparing the two folding landscapes, we found that, in spite of their divergent sequences, the folding pathway of these two proteins involves a similar, inescapable, folding intermediate, even if, statistically, the routes used are different.


Asunto(s)
Ascomicetos , Pliegue de Proteína , Espectroscopía de Resonancia Magnética , Proteínas/química
8.
Nat Commun ; 13(1): 1524, 2022 03 21.
Artículo en Inglés | MEDLINE | ID: mdl-35314704

RESUMEN

Plant nucleotide-binding and leucine-rich repeat domain proteins (NLRs) are immune sensors that recognize pathogen effectors. Here, we show that molecular engineering of the integrated decoy domain (ID) of an NLR can extend its recognition spectrum to a new effector. We relied for this on detailed knowledge on the recognition of the Magnaporthe oryzae effectors AVR-PikD, AVR-Pia, and AVR1-CO39 by, respectively, the rice NLRs Pikp-1 and RGA5. Both receptors detect their effectors through physical binding to their HMA (Heavy Metal-Associated) IDs. By introducing into RGA5_HMA the AVR-PikD binding residues of Pikp-1_HMA, we create a high-affinity binding surface for this effector. RGA5 variants carrying this engineered binding surface perceive the new ligand, AVR-PikD, and still recognize AVR-Pia and AVR1-CO39 in the model plant N. benthamiana. However, they do not confer extended disease resistance specificity against M. oryzae in transgenic rice plants. Altogether, our study provides a proof of concept for the design of new effector recognition specificities in NLRs through molecular engineering of IDs.


Asunto(s)
Magnaporthe , Oryza , Interacciones Huésped-Patógeno , Proteínas NLR/metabolismo , Oryza/metabolismo , Enfermedades de las Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Modificadas Genéticamente/metabolismo , Receptores Inmunológicos/metabolismo
9.
Structure ; 28(2): 244-251.e3, 2020 02 04.
Artículo en Inglés | MEDLINE | ID: mdl-31753618

RESUMEN

LicT belongs to an essential family of bacterial transcriptional antitermination proteins controlling the expression of sugar-metabolizing operons. When activated, they bind to nascent mRNAs, preventing premature arrest of transcription. The RNA binding capacity of the N-terminal domain CAT is controlled by phosphorylations of two homologous regulation modules by the phosphotransferase system (PTS). Previous studies on truncated and mutant proteins provided partial insight into the mechanism of signal transduction between the effector and regulatory modules. We report here the conformational and functional investigation on the allosteric activation of full-length LicT. Combining fluorescence anisotropy and NMR, we find a tight correlation between LicT RNA binding capacity and CAT closure upon PTS-mediated phosphorylation and phosphomimetic mutations. Our study highlights fine structural differences between activation processes. Furthermore, the NMR study of full-length proteins points to the back and forth propagation of structural restraints from the RNA binding to the distal regulatory module.


Asunto(s)
Bacterias/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Fosfotransferasas/metabolismo , ARN Bacteriano/metabolismo , Factores de Transcripción/química , Factores de Transcripción/metabolismo , Regulación Alostérica , Bacterias/química , Bacterias/genética , Proteínas Bacterianas/genética , Sitios de Unión , Regulación Bacteriana de la Expresión Génica , Modelos Moleculares , Mutación , Resonancia Magnética Nuclear Biomolecular , Fosforilación , Unión Proteica , Conformación Proteica , Factores de Transcripción/genética
10.
Sci Rep ; 9(1): 18084, 2019 12 02.
Artículo en Inglés | MEDLINE | ID: mdl-31792250

RESUMEN

Rust fungi are plant pathogens that secrete an arsenal of effector proteins interfering with plant functions and promoting parasitic infection. Effectors are often species-specific, evolve rapidly, and display low sequence similarities with known proteins. How rust fungal effectors function in host cells remains elusive, and biochemical and structural approaches have been scarcely used to tackle this question. In this study, we produced recombinant proteins of eleven candidate effectors of the leaf rust fungus Melampsora larici-populina in Escherichia coli. We successfully purified and solved the three-dimensional structure of two proteins, MLP124266 and MLP124017, using NMR spectroscopy. Although both MLP124266 and MLP124017 show no sequence similarity with known proteins, they exhibit structural similarities to knottins, which are disulfide-rich small proteins characterized by intricate disulfide bridges, and to nuclear transport factor 2-like proteins, which are molecular containers involved in a wide range of functions, respectively. Interestingly, such structural folds have not been reported so far in pathogen effectors, indicating that MLP124266 and MLP124017 may bear novel functions related to pathogenicity. Our findings show that sequence-unrelated effectors can adopt folds similar to known proteins, and encourage the use of biochemical and structural approaches to functionally characterize effector candidates.


Asunto(s)
Basidiomycota/química , Cistina/química , Proteínas Fúngicas/química , Proteínas de Transporte Nucleocitoplasmático/química , Basidiomycota/genética , Cistina/genética , Proteínas Fúngicas/genética , Genoma Fúngico , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular , Proteínas de Transporte Nucleocitoplasmático/genética , Enfermedades de las Plantas/microbiología , Conformación Proteica , Estabilidad Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética
11.
Proc Natl Acad Sci U S A ; 115(45): 11637-11642, 2018 11 06.
Artículo en Inglés | MEDLINE | ID: mdl-30355769

RESUMEN

The structurally conserved but sequence-unrelated MAX (Magnaporthe oryzae avirulence and ToxB-like) effectors AVR1-CO39 and AVR-PikD from the blast fungus M. oryzae are recognized by the rice nucleotide-binding domain and leucine-rich repeat proteins (NLRs) RGA5 and Pikp-1, respectively. This involves, in both cases, direct interaction of the effector with a heavy metal-associated (HMA) integrated domain (ID) in the NLR. Here, we solved the crystal structures of a C-terminal fragment of RGA5 carrying the HMA ID (RGA5_S), alone, and in complex with AVR1-CO39 and compared it to the structure of the Pikp1HMA/AVR-PikD complex. In both complexes, HMA ID/MAX effector interactions involve antiparallel alignment of ß-sheets from each partner. However, effector-binding occurs at different surfaces in Pikp1HMA and RGA5HMA, indicating that these interactions evolved independently by convergence of these two MAX effectors to the same type of plant target proteins. Interestingly, the effector-binding surface in RGA5HMA overlaps with the surface that mediates RGA5HMA self-interaction. Mutations in the HMA-binding interface of AVR1-CO39 perturb RGA5HMA-binding, in vitro and in vivo, and affect the recognition of M. oryzae in a rice cultivar containing Pi-CO39 Our study provides detailed insight into the mechanisms of effector recognition by NLRs, which has substantial implications for future engineering of NLRs to expand their recognition specificities. In addition, we propose, as a hypothesis for the understanding of effector diversity, that in the structurally conserved MAX effectors the molecular mechanism of host target protein-binding is conserved rather than the host target proteins themselves.


Asunto(s)
Proteínas Fúngicas/química , Magnaporthe/genética , Proteínas NLR/química , Oryza/inmunología , Proteínas de Plantas/química , Factores de Virulencia/química , Sitios de Unión , Clonación Molecular , Cristalografía por Rayos X , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Interacciones Huésped-Patógeno/genética , Interacciones Huésped-Patógeno/inmunología , Magnaporthe/patogenicidad , Modelos Moleculares , Proteínas NLR/genética , Proteínas NLR/inmunología , Oryza/genética , Oryza/microbiología , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/inmunología , Enfermedades de las Plantas/microbiología , Inmunidad de la Planta/genética , Proteínas de Plantas/genética , Proteínas de Plantas/inmunología , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Factores de Virulencia/genética , Factores de Virulencia/metabolismo
12.
Plant Cell ; 29(1): 156-168, 2017 01.
Artículo en Inglés | MEDLINE | ID: mdl-28087830

RESUMEN

Nucleotide binding domain and leucine-rich repeat proteins (NLRs) are important receptors in plant immunity that allow recognition of pathogen effectors. The rice (Oryza sativa) NLR RGA5 recognizes the Magnaporthe oryzae effector AVR-Pia through direct interaction. Here, we gained detailed insights into the molecular and structural bases of AVR-Pia-RGA5 interaction and the role of the RATX1 decoy domain of RGA5. NMR titration combined with in vitro and in vivo protein-protein interaction analyses identified the AVR-Pia interaction surface that binds to the RATX1 domain. Structure-informed AVR-Pia mutants showed that, although AVR-Pia associates with additional sites in RGA5, binding to the RATX1 domain is necessary for pathogen recognition but can be of moderate affinity. Therefore, RGA5-mediated resistance is highly resilient to mutations in the effector. We propose a model that explains such robust effector recognition as a consequence, and an advantage, of the combination of integrated decoy domains with additional independent effector-NLR interactions.


Asunto(s)
Proteínas Fúngicas/metabolismo , Magnaporthe/metabolismo , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Receptores Inmunológicos/metabolismo , Sitios de Unión/genética , Resistencia a la Enfermedad/genética , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Interacciones Huésped-Patógeno , Magnaporthe/genética , Magnaporthe/fisiología , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Mutación , Oryza/genética , Oryza/microbiología , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología , Inmunidad de la Planta/genética , Hojas de la Planta/genética , Hojas de la Planta/metabolismo , Hojas de la Planta/microbiología , Proteínas de Plantas/química , Proteínas de Plantas/genética , Unión Proteica , Dominios Proteicos , Receptores Inmunológicos/química , Receptores Inmunológicos/genética
13.
PLoS Pathog ; 11(10): e1005228, 2015 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-26506000

RESUMEN

Phytopathogenic ascomycete fungi possess huge effector repertoires that are dominated by hundreds of sequence-unrelated small secreted proteins. The molecular function of these effectors and the evolutionary mechanisms that generate this tremendous number of singleton genes are largely unknown. To get a deeper understanding of fungal effectors, we determined by NMR spectroscopy the 3-dimensional structures of the Magnaporthe oryzae effectors AVR1-CO39 and AVR-Pia. Despite a lack of sequence similarity, both proteins have very similar 6 ß-sandwich structures that are stabilized in both cases by a disulfide bridge between 2 conserved cysteins located in similar positions of the proteins. Structural similarity searches revealed that AvrPiz-t, another effector from M. oryzae, and ToxB, an effector of the wheat tan spot pathogen Pyrenophora tritici-repentis have the same structures suggesting the existence of a family of sequence-unrelated but structurally conserved fungal effectors that we named MAX-effectors (Magnaporthe Avrs and ToxB like). Structure-informed pattern searches strengthened this hypothesis by identifying MAX-effector candidates in a broad range of ascomycete phytopathogens. Strong expansion of the MAX-effector family was detected in M. oryzae and M. grisea where they seem to be particularly important since they account for 5-10% of the effector repertoire and 50% of the cloned avirulence effectors. Expression analysis indicated that the majority of M. oryzae MAX-effectors are expressed specifically during early infection suggesting important functions during biotrophic host colonization. We hypothesize that the scenario observed for MAX-effectors can serve as a paradigm for ascomycete effector diversity and that the enormous number of sequence-unrelated ascomycete effectors may in fact belong to a restricted set of structurally conserved effector families.


Asunto(s)
Ascomicetos/química , Secuencia de Aminoácidos , Ascomicetos/patogenicidad , Proteínas Fúngicas/química , Espectroscopía de Resonancia Magnética , Datos de Secuencia Molecular , Estructura Secundaria de Proteína
14.
PLoS One ; 9(8): e105688, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25144743

RESUMEN

The Cop9 signalosome complex (CSN) regulates the functional cycle of the major E3 ubiquitin ligase family, the cullin RING E3 ubiquitin ligases (CRLs). Activated CRLs are covalently modified by the ubiquitin-like protein Nedd8 (neural precursor cell expressed developmentally down-regulated protein 8). CSN serves an essential role in myriad cellular processes by reversing this modification through the isopeptidase activity of its CSN5 subunit. CSN5 alone is inactive due to an auto-inhibited conformation of its catalytic domain. Here we report the molecular basis of CSN5 catalytic domain activation and unravel a molecular hierarchy in CSN deneddylation activity. The association of CSN5 and CSN6 MPN (for Mpr1/Pad1 N-terminal) domains activates its isopeptidase activity. The CSN5/CSN6 module, however, is inefficient in CRL deneddylation, indicating a requirement of further elements in this reaction such as other CSN subunits. A hybrid molecular model of CSN5/CSN6 provides a structural framework to explain these functional observations. Docking this model into a published CSN electron density map and using distance constraints obtained from cross-linking coupled to mass-spectrometry, we find that the C-termini of the CSN subunits could form a helical bundle in the centre of the structure. They likely play a key scaffolding role in the spatial organization of CSN and precise positioning of the dimeric MPN catalytic core.


Asunto(s)
Proteínas Adaptadoras Transductoras de Señales/química , Péptidos y Proteínas de Señalización Intracelular/química , Complejos Multiproteicos/química , Péptido Hidrolasas/química , Multimerización de Proteína , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Complejo del Señalosoma COP9 , Humanos , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Modelos Moleculares , Complejos Multiproteicos/metabolismo , Proteína NEDD8 , Péptido Hidrolasas/metabolismo , Unión Proteica , Conformación Proteica , Dominios y Motivos de Interacción de Proteínas , Subunidades de Proteína , Ubiquitinas/metabolismo
15.
Eur J Med Chem ; 85: 418-37, 2014 Oct 06.
Artículo en Inglés | MEDLINE | ID: mdl-25108359

RESUMEN

The 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (DNPH1) has been proposed as a new molecular target for cancer treatment. Here, we describe the synthesis of a series of novel 6-aryl- and 6-heteroarylpurine riboside 5'-monophosphates via Suzuki-Miyaura cross-coupling reactions, and their ability to inhibit recombinant rat and human DNPH1. Enzymatic inhibition studies revealed competitive inhibitors in the low micromolar range. Crystal structures of human and rat DNPH1 in complex with one nucleotide from this series, the 6-naphthylpurine derivative, provided detailed structural information, in particular regarding the possible conformations of a long and flexible loop wrapping around the large hydrophobic substituent. Taking advantage of these high-resolution structures, we performed virtual docking studies in order to evaluate enzyme-inhibitor interactions for the whole compound series. Among the synthesized compounds, several molecules exhibited significant in vitro cytotoxicity against human colon cancer (HCT15, HCT116) and human promyelocytic leukemia (HL60) cell lines with IC50 values in the low micromolar range, which correlated with in vitro DNPH1 inhibitory potency.


Asunto(s)
Diseño de Fármacos , Terapia Molecular Dirigida , N-Glicosil Hidrolasas/antagonistas & inhibidores , Proteínas Nucleares/antagonistas & inhibidores , Proteínas Proto-Oncogénicas/antagonistas & inhibidores , Nucleótidos de Purina/síntesis química , Nucleótidos de Purina/farmacología , Animales , Antineoplásicos/síntesis química , Antineoplásicos/química , Antineoplásicos/metabolismo , Antineoplásicos/farmacología , Línea Celular Tumoral , Técnicas de Química Sintética , Ensayos de Selección de Medicamentos Antitumorales , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/metabolismo , Inhibidores Enzimáticos/farmacología , Humanos , Simulación del Acoplamiento Molecular , N-Glicosil Hidrolasas/química , N-Glicosil Hidrolasas/metabolismo , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Conformación Proteica , Proteínas Proto-Oncogénicas/química , Proteínas Proto-Oncogénicas/metabolismo , Nucleótidos de Purina/química , Nucleótidos de Purina/metabolismo , Ratas , Relación Estructura-Actividad
16.
PLoS One ; 9(8): e105441, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25162372

RESUMEN

Multidrug resistance, which is acquired by both Gram-positive and Gram-negative bacteria, causes infections that are associated with significant morbidity and mortality in many clinical settings around the world. Because of the rapidly increasing incidence of pathogens that have become resistant to all or nearly all available antibiotics, there is a need for a new generation of antimicrobials with a broad therapeutic range for specific applications against infections. Aedesin is a cecropin-like anti-microbial peptide that was recently isolated from dengue virus-infected salivary glands of the Aedes aegypti mosquito. In the present study, we have refined the analysis of its structural characteristics and have determined its antimicrobial effects against a large panel of multidrug resistant bacterial strains, directly isolated from infected patients. Based the results from nuclear magnetic resonance spectroscopy analysis, Aedesin has a helix-bend-helix structure typical for a member of the family of α-helix anti-microbial peptides. Aedesin efficiently killed Gram-negative bacterial strains that display the most worrisome resistance mechanisms encountered in the clinic, including resistance to carbapenems, aminoglycosides, cephalosporins, 4th generation fluoroquinolones, folate inhibitors and monobactams. In contrast, Gram-positive strains were insensitive to the lytic effects of the peptide. The anti-bacterial activity of Aedesin was found to be salt-resistant, indicating that it is active under physiological conditions encountered in body fluids characterized by ionic salt concentrations. In conclusion, because of its strong lytic activity against multidrug resistant Gram-negative bacterial strains displaying all types of clinically relevant resistance mechanisms known today, Aedesin might be an interesting candidate for the development of alternative treatment for infections caused by these types of bacteria.


Asunto(s)
Aedes/química , Antibacterianos/farmacología , Péptidos Catiónicos Antimicrobianos/farmacología , Farmacorresistencia Bacteriana Múltiple/efectos de los fármacos , Bacterias Gramnegativas/efectos de los fármacos , Proteínas de Insectos/farmacología , Aedes/inmunología , Secuencia de Aminoácidos , Animales , Antibacterianos/síntesis química , Antibacterianos/química , Antibacterianos/aislamiento & purificación , Péptidos Catiónicos Antimicrobianos/síntesis química , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/aislamiento & purificación , Bacterias Gramnegativas/crecimiento & desarrollo , Proteínas de Insectos/síntesis química , Proteínas de Insectos/química , Proteínas de Insectos/aislamiento & purificación , Pruebas de Sensibilidad Microbiana , Modelos Moleculares , Datos de Secuencia Molecular , Estructura Secundaria de Proteína , Glándulas Salivales/química , Glándulas Salivales/inmunología , Tolerancia a la Sal
17.
PLoS One ; 8(11): e80755, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-24260472

RESUMEN

The gene dnph1 (or rcl) encodes a hydrolase that cleaves the 2'-deoxyribonucleoside 5'-monophosphate (dNMP) N-glycosidic bond to yield a free nucleobase and 2-deoxyribose 5-phosphate. Recently, the crystal structure of rat DNPH1, a potential target for anti-cancer therapies, suggested that various analogs of AMP may inhibit this enzyme. From this result, we asked whether N (6)-substituted AMPs, and among them, cytotoxic cytokinin riboside 5'-monophosphates, may inhibit DNPH1. Here, we characterized the structural and thermodynamic aspects of the interactions of these various analogs with DNPH1. Our results indicate that DNPH1 is inhibited by cytotoxic cytokinins at concentrations that inhibit cell growth.


Asunto(s)
Adenosina Monofosfato/farmacología , N-Glicosil Hidrolasas/metabolismo , Proteínas Nucleares/metabolismo , Proteínas Proto-Oncogénicas/metabolismo , Adenosina Monofosfato/análogos & derivados , Adenosina Monofosfato/química , Adenosina Monofosfato/metabolismo , Secuencia de Aminoácidos , Animales , Dominio Catalítico , Activación Enzimática/efectos de los fármacos , Humanos , Cinética , Modelos Moleculares , Conformación Molecular , Datos de Secuencia Molecular , N-Glicosil Hidrolasas/química , N-Glicosil Hidrolasas/genética , Proteínas Nucleares/química , Proteínas Nucleares/genética , Unión Proteica , Proteínas Proto-Oncogénicas/química , Proteínas Proto-Oncogénicas/genética , Ratas , Alineación de Secuencia , Termodinámica
18.
J Med Chem ; 56(21): 8497-511, 2013 Nov 14.
Artículo en Inglés | MEDLINE | ID: mdl-24112024

RESUMEN

By virtual screening using a fragment-based drug design (FBDD) approach, 33 fragments were selected within small pockets around interaction hot spots on the Sec7 surface of the nucleotide exchange factor Arno, and then their ability to interfere with the Arno-catalyzed nucleotide exchange on the G-protein Arf1 was evaluated. By use of SPR, NMR, and fluorescence assays, the direct binding of three of the identified fragments to Arno Sec7 domain was demonstrated and the promiscuous aggregate behavior evaluated. Then the binding mode of one fragment and of a more active analogue was solved by X-ray crystallography. This highlighted the role of stable and transient pockets at the Sec7 domain surface in the discovery and binding of interfering compounds. These results provide structural information on how small organic compounds can interfere with the Arf1-Arno Sec7 domain interaction and may guide the rational drug design of competitive inhibitors of Arno enzymatic activity.


Asunto(s)
Factor 1 de Ribosilacion-ADP/antagonistas & inhibidores , Diseño de Fármacos , Factores de Intercambio de Guanina Nucleótido/antagonistas & inhibidores , Sulfonamidas/farmacología , Factor 1 de Ribosilacion-ADP/química , Cristalografía por Rayos X , Relación Dosis-Respuesta a Droga , Factores de Intercambio de Guanina Nucleótido/química , Ensayos Analíticos de Alto Rendimiento , Concentración de Iones de Hidrógeno , Modelos Moleculares , Estructura Molecular , Unión Proteica/efectos de los fármacos , Relación Estructura-Actividad , Sulfonamidas/química
19.
Acta Crystallogr D Biol Crystallogr ; 69(Pt 2): 247-55, 2013 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-23385460

RESUMEN

Rcl is a novel N-glycoside hydrolase found in mammals that shows specificity for the hydrolysis of 5'-monophosphate nucleotides. Its role in nucleotide catabolism and the resulting production of 2-deoxyribose 5-phosphate has suggested that it might fuel cancer growth. Its expression is regulated by c-Myc, but its role as an oncoprotein remains to be clarified. In parallel, various nucleosides have been shown to acquire pro-apoptotic properties upon 5'-monophosphorylation in cells. These include triciribine, a tricyclic nucleoside analogue that is currently in clinical trials in combination with a farnesyltransferase inhibitor. Similarly, an N(6)-alkyl-AMP has been shown to be cytotoxic. Interestingly, Rcl has been shown to be inhibited by such compounds in vitro. In order to gain better insight into the precise ligand-recognition determinants, the crystallization of Rcl with these nucleotide analogues was attempted. The first crystal structure of Rcl was solved by molecular replacement using its NMR structure in combination with distantly related crystal structures. The structures of Rcl bound to two other nucleotides were then solved by molecular replacement using the previous crystal structure as a template. The resulting structures, solved at high resolution, led to a clear characterization of the protein-ligand interactions that will guide further rational drug design.


Asunto(s)
N-Glicosil Hidrolasas/química , N-Glicosil Hidrolasas/metabolismo , Nucleótidos/química , Proteínas Oncogénicas/química , Proteínas Oncogénicas/metabolismo , Acenaftenos/química , Adenosina Monofosfato/análogos & derivados , Adenosina Monofosfato/química , Adenosina Monofosfato/genética , Secuencia de Aminoácidos , Sustitución de Aminoácidos/genética , Animales , Cristalización , Ligandos , Datos de Secuencia Molecular , N-Glicosil Hidrolasas/genética , Nucleótidos/genética , Proteínas Oncogénicas/genética , Organofosfonatos/química , Fosforilación , Unión Proteica/genética , Mapeo de Interacción de Proteínas/métodos , Ratas , Ribonucleótidos/química , Ribonucleótidos/genética , Tionucleótidos/química , Tionucleótidos/genética , Timidina/análogos & derivados , Timidina/química , Timidina/genética , Difracción de Rayos X
20.
J Biol Chem ; 288(7): 4659-72, 2013 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-23255605

RESUMEN

The GDP/GTP nucleotide exchange of Arf1 is catalyzed by nucleotide exchange factors (GEF), such as Arno, which act through their catalytic Sec7 domain. This exchange is a complex mechanism that undergoes conformational changes and intermediate complex species involving several allosteric partners such as nucleotides, Mg(2+), and Sec7 domains. Using a surface plasmon resonance approach, we characterized the kinetic binding parameters for various intermediate complexes. We first confirmed that both GDP and GTP counteract equivalently to the free-nucleotide binary Arf1-Arno complex stability and revealed that Mg(2+) potentiates by a factor of 2 the allosteric effect of GDP. Then we explored the uncompetitive inhibitory mechanism of brefeldin A (BFA) that conducts to an abortive pentameric Arf1-Mg(2+)-GDP-BFA-Sec7 complex. With BFA, the association rate of the abortive complex is drastically reduced by a factor of 42, and by contrast, the 15-fold decrease of the dissociation rate concurs to stabilize the pentameric complex. These specific kinetic signatures have allowed distinguishing the level and nature as well as the fate in real time of formed complexes according to experimental conditions. Thus, we showed that in the presence of GDP, the BFA-resistant Sec7 domain of Arno can also associate to form a pentameric complex, which suggests that the uncompetitive inhibition by BFA and the nucleotide allosteric effect combine to stabilize such abortive complex.


Asunto(s)
Factor 1 de Ribosilacion-ADP/química , Brefeldino A/química , Proteínas Activadoras de GTPasa/química , Factores de Intercambio de Guanina Nucleótido/metabolismo , Factor 1 de Ribosilacion-ADP/metabolismo , Sitio Alostérico , Unión Competitiva , Biotinilación , Catálisis , Escherichia coli/metabolismo , Factores de Intercambio de Guanina Nucleótido/química , Guanosina Difosfato/química , Guanosina Trifosfato/química , Humanos , Cinética , Plásmidos/metabolismo , Unión Proteica , Resonancia por Plasmón de Superficie
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