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1.
Curr Opin Chem Biol ; 80: 102444, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38520774

RESUMEN

Fluorescence imaging plays a pivotal role in the study of biological processes, and cell-permeable fluorogenic dyes are crucial to visualize intracellular structures with high specificity. Polymethine dyes are vitally important fluorophores in single-molecule localization microscopy and in vivo imaging, but their use in live cells has been limited by high background fluorescence and low membrane permeability. In this review, we summarize recent advances in the development of fluorogenic polymethine dyes via intramolecular cyclization. Finally, we offer an outlook on the prospects of fluorogenic polymethine dyes for bioimaging.


Asunto(s)
Colorantes Fluorescentes , Colorantes Fluorescentes/química , Ciclización , Humanos , Imagen Óptica/métodos , Animales
2.
Bioorg Med Chem Lett ; 97: 129568, 2024 01 01.
Artículo en Inglés | MEDLINE | ID: mdl-38008337

RESUMEN

Transthyretin Amyloidosis arises from the misfolding of monomers or oligomers of the normal transthyretin protein. Our investigation revealed that certain guanine-rich regions within the 5' UTR sequence of the transthyretin gene possess the ability to form G2-quadruplex structures, as determined through analysis with QGRS mapper. We demonstrated that small molecule ligands, including TMPyP4, Braco-19, NMM, and TO, have a significant impact on the stabilization of transthyretin G-quadruplexes. The objective of this study was to confirm the effect of ligands on transthyretin gene transcription through the stabilization of G-quadruplexes. To comprehend the interaction between ligands and transthyretin G-quadruplexes, a range of analytical techniques were employed, includingUV titration, fluorescence titration assays, circular dichroism, quantitative RT-PCR and cytotoxicity tests. The results revealed the presence of four putative G2-quadruplex sequences, which formed stable anti-parallel, parallel, and hybrid G2-quadruplex structures. Notably, Ttrg 3 (5'-GGAAGGAAGGGAGGGAGGG-3') exhibited the highest stability to form G-quadruplex. Furthermore, TmPyP4, Braco-19, NMM and TO were found to stabilize the parallel topology of Ttrg 3. After 48 h of incubation, the RT-PCR experiments revealed a significant reduction in transthyretin mRNA transcription in HepG2 cells when treated with 20 µM TmPyP4 and Braco-19, without inducing apoptosis. Our findings suggested that ligand-mediated stabilization of G-quadruplexes within the 5'-UTR can effectively silence transthyretin expression, highlighting the potential of G-quadruplex as a novel therapeutic target for Transthyretin Amyloidosis. This study might shed valuable lights for the development of innovative therapeutic approach against Transthyretin Amyloidosis.


Asunto(s)
G-Cuádruplex , Prealbúmina , ARN Mensajero , Prealbúmina/química , Prealbúmina/genética , ARN Mensajero/genética , Transcripción Genética
3.
ChemMedChem ; 18(19): e202300271, 2023 10 04.
Artículo en Inglés | MEDLINE | ID: mdl-37649155

RESUMEN

RNA structures, including those formed from coding and noncoding RNAs, alternative to protein-based drug targets, could be a promising target of small molecules for drug discovery against various human diseases, particularly in anticancer, antibacterial and antivirus development. The normal cellular activity of cells is critically dependent on the function of various RNA molecules generated from DNA transcription. Moreover, many studies support that mRNA-targeting small molecules may regulate the synthesis of disease-related proteins via the non-covalent mRNA-ligand interactions that do not involve gene modification. RNA-ligand interaction is thus an attractive approach to address the challenge of "undruggable" proteins in drug discovery because the intracellular activity of these proteins is hard to be suppressed with small molecule ligands. We selectively surveyed a specific area of RNA structure-selective small molecule ligands in fluorescence live cell imaging and drug discovery because the area was currently underexplored. This state-of-the-art review thus mainly focuses on the research published within the past three years and aims to provide the most recent information on this research area; hopefully, it could be complementary to the previously reported reviews and give new insights into the future development on RNA-specific small molecule ligands for live cell imaging and drug discovery.


Asunto(s)
ARN , Bibliotecas de Moléculas Pequeñas , Humanos , ARN/metabolismo , Ligandos , Bibliotecas de Moléculas Pequeñas/química , Descubrimiento de Drogas , ARN Mensajero , Proteínas
4.
Int J Mol Sci ; 24(12)2023 Jun 14.
Artículo en Inglés | MEDLINE | ID: mdl-37373293

RESUMEN

The melanocortin receptors are involved in numerous physiological pathways, including appetite, skin and hair pigmentation, and steroidogenesis. In particular, the melanocortin-3 receptor (MC3R) is involved in fat storage, food intake, and energy homeostasis. Small-molecule ligands developed for the MC3R may serve as therapeutic lead compounds for treating disease states of energy disequilibrium. Herein, three previously reported pyrrolidine bis-cyclic guanidine compounds with five sites for molecular diversity (R1-R5) were subjected to parallel structure-activity relationship studies to identify the common pharmacophore of this scaffold series required for full agonism at the MC3R. The R2, R3, and R5 positions were required for full MC3R efficacy, while truncation of either the R1 or R4 positions in all three compounds resulted in full MC3R agonists. Two additional fragments, featuring molecular weights below 300 Da, were also identified that possessed full agonist efficacy and micromolar potencies at the mMC5R. These SAR experiments may be useful in generating new small-molecule ligands and chemical probes for the melanocortin receptors to help elucidate their roles in vivo and as therapeutic lead compounds.


Asunto(s)
Farmacóforo , Receptor de Melanocortina Tipo 3 , Receptor de Melanocortina Tipo 3/agonistas , Receptor de Melanocortina Tipo 3/metabolismo , Guanidina/farmacología , Ligandos , Receptores de Melanocortina/metabolismo , Guanidinas , Relación Estructura-Actividad
5.
Biochimie ; 204: 8-21, 2023 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-36063975

RESUMEN

G-quadruplexes (G4s) are gaining increasing attention as possible regulators of chromatin packaging, and robust approaches to their studies in pseudo-native context are much needed. Here, we designed a simple in vitro model of G4-prone genomic DNA and employed it to elucidate the impact of G4s and G4-stabilizing ligands on nucleosome occupancy. We obtained two 226-bp dsDNA constructs composed of the strong nucleosome positioning sequence and an internucleosomal DNA-imitating tail. The tail was G4-free in the control construct and harbored a "strong" (stable) G4 motif in the construct of interest. An additional "weak" (semi-stable) G4 motif was found within the canonical nucleosome positioning sequence. Both G4s were confirmed by optical methods and 1H NMR spectroscopy. Electrophoretic mobility assays showed that the weak G4 motif did not obstruct nucleosome assembly, while the strong G4 motif in the tail sequence diminished nucleosome yield. Atomic force microscopy data and molecular modeling confirmed that the strong G4 was maintained in the tail of the correctly assembled nucleosome structure. Using both in vitro and in silico models, we probed three known G4 ligands and detected nucleosome-disrupting effects of the least selective ligand. Our results are in line with the negative correlation between stable G4s and nucleosome density, support G4 tolerance between regularly positioned nucleosomes, and highlight the importance of considering chromatin context when targeting genomic G4s.


Asunto(s)
Cromatina , G-Cuádruplex , Cromatina/genética , Nucleosomas , Ligandos , ADN/química
6.
Biomolecules ; 12(10)2022 10 04.
Artículo en Inglés | MEDLINE | ID: mdl-36291635

RESUMEN

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.


Asunto(s)
Biología Computacional , Proteínas , Humanos , Conformación Proteica , Bases de Datos de Proteínas , Biología Computacional/métodos , Proteínas/química , Estudiantes
7.
J Neurochem ; 163(6): 478-499, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36153691

RESUMEN

The developmental process of central nervous system (CNS) myelin sheath formation is characterized by well-coordinated cellular activities ultimately ensuring rapid and synchronized neural communication. During this process, myelinating CNS cells, namely oligodendrocytes (OLGs), undergo distinct steps of differentiation, whereby the progression of earlier maturation stages of OLGs represents a critical step toward the timely establishment of myelinated axonal circuits. Given the complexity of functional integration, it is not surprising that OLG maturation is controlled by a yet fully to be defined set of both negative and positive modulators. In this context, we provide here first evidence for a role of lysophosphatidic acid (LPA) signaling via the G protein-coupled receptor LPA6 as a negative modulatory regulator of myelination-associated gene expression in OLGs. More specifically, the cell surface accessibility of LPA6 was found to be restricted to the earlier maturation stages of differentiating OLGs, and OLG maturation was found to occur precociously in Lpar6 knockout mice. To further substantiate these findings, a novel small molecule ligand with selectivity for preferentially LPA6 and LPA6 agonist characteristics was functionally characterized in vitro in primary cultures of rat OLGs and in vivo in the developing zebrafish. Utilizing this approach, a negative modulatory role of LPA6 signaling in OLG maturation could be corroborated. During development, such a functional role of LPA6 signaling likely serves to ensure timely coordination of circuit formation and myelination. Under pathological conditions as seen in the major human demyelinating disease multiple sclerosis (MS), however, persistent LPA6 expression and signaling in OLGs can be seen as an inhibitor of myelin repair. Thus, it is of interest that LPA6 protein levels appear elevated in MS brain samples, thereby suggesting that LPA6 signaling may represent a potential new druggable pathway suitable to promote myelin repair in MS.


Asunto(s)
Oligodendroglía , Pez Cebra , Ratones , Animales , Ratas , Humanos , Oligodendroglía/metabolismo , Vaina de Mielina/metabolismo , Neurogénesis/fisiología , Diferenciación Celular/fisiología , Receptores del Ácido Lisofosfatídico
8.
Chemistry ; 28(54): e202201749, 2022 Sep 27.
Artículo en Inglés | MEDLINE | ID: mdl-35727679

RESUMEN

Expansions of short tandem repeats (STRs) in the human genome cause nearly 50 neurodegenerative diseases, which are mostly inheritable, nonpreventable and incurable, posing as a huge threat to human health. Non-B DNAs formed by STRs are thought to be structural intermediates that can cause repeat expansions. The subsequent transcripts harboring expanded RNA repeats can further induce cellular toxicity through forming specific structures. Direct targeting of these pathogenic DNA and RNA repeats has emerged as a new potential therapeutic strategy to cure repeat expansion diseases. In this conceptual review, we first introduce the roles of DNA and RNA structures in the genetic instabilities and pathomechanisms of repeat expansion diseases, then describe structural features of DNA and RNA repeats with a focus on the tertiary structures determined by X-ray crystallography and solution nuclear magnetic resonance spectroscopy, and finally discuss recent progress and perspectives of developing chemical tools that target pathogenic DNA and RNA repeats for curing repeat expansion diseases.


Asunto(s)
ADN , ARN , Humanos
9.
Angew Chem Int Ed Engl ; 61(17): e202115472, 2022 04 19.
Artículo en Inglés | MEDLINE | ID: mdl-35199422

RESUMEN

The control of endogenous protein activity with light inside live cells is helpful for the high spatiotemporal probing of their dynamic roles. Herein, we report the first small-molecule-ligand-directed caging approach to control the endogenous human O6 -alkylguanine-DNA alkyltransferase (AGT) activity with light, and the caged AGT is constructed from the native intracellular AGT. The photo-responsive O6 -benzylguanine derivative O6 -NBG3 is developed to site-specifically cage the AGT's catalytic cysteine residue, and the light irradiation on-demand restores AGT's activity in vitro, in bacteria, and in mammalian cells. With O6 -NBG3, the alkylated AGT is dealkylated for the first time to recover the DNA repair activity in breast cancer MCF-7 cells by the dose-dependent light irradiation. This decaging strategy enables the localized modulation of endogenous AGT activity with high temporal precision without genetic engineering, which holds great potential for therapeutic applications.


Asunto(s)
Transferasas Alquil y Aril , Guanina , Animales , Guanina/química , Humanos , Ligandos , Mamíferos/metabolismo , O(6)-Metilguanina-ADN Metiltransferasa/química
10.
Structure ; 29(4): 393-400.e1, 2021 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-33657417

RESUMEN

The Worldwide Protein Data Bank (wwPDB) has provided validation reports based on recommendations from community Validation Task Forces for structures in the PDB since 2013. To further enhance validation of small molecules as recommended from the 2016 Ligand Validation Workshop, wwPDB, Global Phasing Ltd., and the Noguchi Institute, recently formed a public/private partnership to incorporate some of their software tools into the wwPDB validation package. Augmented wwPDB validation report features include: two-dimensional (2D) diagrams of small-molecule ligands and carbohydrates, highlighting geometric validation outcomes; 2D topological diagrams of oligosaccharides present in branched entities generated using 2D Symbol Nomenclature for Glycan representation; and views of 3D electron density maps for ligands and carbohydrates, illustrating the goodness-of-fit between the atomic structure and experimental data (X-ray crystallographic structures only). These improvements will impact confidence in ligand conformation and ligand-macromolecular interactions that will aid in understanding biochemical function and contribute to small-molecule drug discovery.


Asunto(s)
Carbohidratos/química , Bases de Datos de Proteínas/normas , Simulación del Acoplamiento Molecular/métodos , Proteómica/métodos , Bibliotecas de Moléculas Pequeñas/química , Quimioinformática/métodos , Bases de Datos de Compuestos Químicos/normas , Humanos , Ligandos , Unión Proteica , Proteoma/química , Proteoma/metabolismo
11.
Molecules ; 26(4)2021 Feb 05.
Artículo en Inglés | MEDLINE | ID: mdl-33562720

RESUMEN

G-quadruplexes, a family of tetraplex helical nucleic acid topologies, have emerged in recent years as novel targets, with untapped potential for anticancer research. Their potential stems from the fact that G-quadruplexes occur in functionally-important regions of the human genome, such as the telomere tandem sequences, several proto-oncogene promoters, other regulatory regions and sequences of DNA (e.g. rDNA), as well as in mRNAs encoding for proteins with roles in tumorigenesis. Modulation of G-quadruplexes, via interaction with high-affinity ligands, leads to their stabilization, with numerous observed anticancer effects. Despite the fact that only a few lead compounds for G-quadruplex modulation have progressed to clinical trials so far, recent advancements in the field now create conditions that foster further development of drug candidates. This review highlights biological processes through which G-quadruplexes can exert their anticancer effects and describes, via selected case studies, progress of the last few years on the development of efficient and drug-like G-quadruplex-targeted ligands, intended to harness the anticancer potential offered by G-quadruplexes. The review finally provides a critical discussion of perceived challenges and limitations that have previously hampered the progression of G-quadruplex-targeted lead compounds to clinical trials, concluding with an optimistic future outlook.


Asunto(s)
Antineoplásicos/farmacología , G-Cuádruplex/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/farmacología , Animales , Antineoplásicos/metabolismo , Humanos , Ligandos , Proto-Oncogenes Mas , Bibliotecas de Moléculas Pequeñas/metabolismo
12.
Eur J Med Chem ; 193: 112228, 2020 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-32199134

RESUMEN

Glucose Regulated Protein 78 kDa (GRP78) is an attractive antiangiogenic and anticancer target for its selective accumulation on the surface of cancer cells and cancer endothelial cells rather than normal cells. In this study, we identified a novel series of small molecules that binds to GRP78, exhibiting potent antiangiogenic and anticancer activities without affecting normal cells. Among these, FL5,2-(4-((4-acetamidophenoxy)methyl)phenyl)-N-isobutylbenzofuran-3-carboxamide, was superior to others due to its strong binding affinity to GRP78 (an increase in the Tm > 2 °C stabilising the GRP78 protein) and potent antiangiogenic and anticancer activities against human umbilical vein endothelial cells (HUVEC) (EC50 = 1.514 µM) and human renal cancer cells (786-O) (50% cell death at 10 µM). Furthermore, FL5 displayed no cytotoxic activity towards mouse fibroblast cells (Swiss-3T3), which do not harbour cell surface GRP78 under normal condition. FL5 was less detrimental to ATPase activity, which is essential for normal cells, as seen in the virtual docking studies. This study reports the discovery of novel small molecules targeting GRP78 with potent antiangiogenic and anticancer activities and less toxicity to normal cells, which provides prototype candidates for novel paths for cancer therapy.


Asunto(s)
Inhibidores de la Angiogénesis/farmacología , Antineoplásicos/farmacología , Descubrimiento de Drogas , Proteínas de Choque Térmico/antagonistas & inhibidores , Bibliotecas de Moléculas Pequeñas/farmacología , Células 3T3 , Inhibidores de la Angiogénesis/química , Animales , Antineoplásicos/química , Apoptosis/efectos de los fármacos , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Supervivencia Celular/efectos de los fármacos , Relación Dosis-Respuesta a Droga , Ensayos de Selección de Medicamentos Antitumorales , Chaperón BiP del Retículo Endoplásmico , Células Endoteliales de la Vena Umbilical Humana/efectos de los fármacos , Humanos , Ratones , Simulación del Acoplamiento Molecular , Estructura Molecular , Bibliotecas de Moléculas Pequeñas/química , Relación Estructura-Actividad
13.
Biochim Biophys Acta Mol Cell Res ; 1866(12): 118539, 2019 12.
Artículo en Inglés | MEDLINE | ID: mdl-31491448

RESUMEN

Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.


Asunto(s)
ADN de Neoplasias/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/farmacología , ADN de Neoplasias/genética , ADN de Neoplasias/metabolismo , Humanos , Ligandos , Mutación , Conformación de Ácido Nucleico , Bibliotecas de Moléculas Pequeñas/química
15.
Cell Chem Biol ; 26(5): 662-673.e7, 2019 05 16.
Artículo en Inglés | MEDLINE | ID: mdl-30827936

RESUMEN

The G protein-coupled receptor (GPCR) CXCR4 is a co-receptor for HIV and is involved in cancers and autoimmune diseases. We characterized five purine or quinazoline core polyamine pharmacophores used for targeting CXCR4 dysregulation in diseases. All were neutral antagonists for wild-type CXCR4 and two were biased antagonists with effects on ß-arrestin-2 only at high concentrations. These compounds displayed various activities for a constitutively active mutant (CAM). We use the IT1t-CXCR4 crystal structure and molecular dynamics (MD) simulations to develop two hypotheses for the activation of the N1193.35A CAM. The N1193.35A mutation facilitates increased coupling of TM helices III and VI. IT1t deactivates the CAM by disrupting the coupling between TM helices III and VI, mediated primarily by residue F872.53. Mutants of F872.53 in N1193.35A CXCR4 precluded constitutive signaling and prevented inverse agonism. This work characterizes CXCR4 ligands and provides a mechanism for N1193.35A constitutive activation.


Asunto(s)
Simulación de Dinámica Molecular , Receptores CXCR4/antagonistas & inhibidores , Bibliotecas de Moléculas Pequeñas/metabolismo , Bencilaminas , Quimiocina CXCL12/farmacología , Ciclamas , Células HEK293 , Infecciones por VIH/metabolismo , Infecciones por VIH/patología , Infecciones por VIH/virología , VIH-1/efectos de los fármacos , Compuestos Heterocíclicos/farmacología , Humanos , Interacciones Hidrofóbicas e Hidrofílicas , Ligandos , Mutagénesis Sitio-Dirigida , Conformación Proteica en Hélice alfa , Estructura Terciaria de Proteína , Receptores CXCR4/genética , Receptores CXCR4/metabolismo , Transducción de Señal/efectos de los fármacos , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/farmacología , Arrestina beta 2/metabolismo
16.
Angew Chem Int Ed Engl ; 57(40): 13242-13247, 2018 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-30134013

RESUMEN

Structural studies of the 3'-end of the oncogenic long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) confirmed a unique triple-helix structure. This structure enables accumulation of the transcript, and high levels of MALAT1 are found in several cancers. Here, we synthesize a small molecule library based on an RNA-binding scaffold, diphenylfuran (DPF), screen it against a variety of nucleic acid constructs, and demonstrate for the first time that the MALAT1 triple helix can be selectively targeted with small molecules. Computational analysis revealed a trend between subunit positioning and composition on DPF shape and intramolecular interactions, which in turn generally correlated with selectivity and binding strengths. This work thus provides design strategies toward chemical probe development for the MALAT1 triple helix and suggests that comprehensive analyses of RNA-focused libraries can generate insights into selective RNA recognition.


Asunto(s)
ARN Largo no Codificante/metabolismo , ARN/química , Bibliotecas de Moléculas Pequeñas/química , Teoría Funcional de la Densidad , Furanos/química , Furanos/metabolismo , Humanos , Ligandos , Conformación de Ácido Nucleico , ARN/metabolismo , ARN Largo no Codificante/química , Bibliotecas de Moléculas Pequeñas/metabolismo
17.
Mol Biol (Mosk) ; 52(3): 555-564, 2018.
Artículo en Ruso | MEDLINE | ID: mdl-29989588

RESUMEN

Identifying amino acid positions that determine the specific interaction of proteins with small molecule ligands, is required for search of pharmaceutical targets, drug design, and solution of other biotechnology problems. We studied applicability of an original method SPrOS (specificity projection on sequence) developed to recognize functionally significant positions in amino acid sequences. The method allows residues specific to functional subgroups to be determined within the protein family based on their local surroundings in amino acid sequences. The efficiency of the method has been estimated on the protein kinase family. The residues associated with the protein specificity to inhibitors have been predicted. The results have been verified using 3D structures of protein-ligand complexes. Three small molecule inhibitors have been tested. Residues predicted with SPrOS either in contacted the inhibitor or influenced the conformation of the ligand-binding area. Excluding close homologues from the studied set makes it possible to decrease the number of difficult to interpret positions. The expediency of this procedure was determined by the relationship between an inhibitory spectrum and phylogenic partition. Thus, the method efficiency has been confirmed by matching the prediction results with the protein 3D structures.


Asunto(s)
Inhibidores de Proteínas Quinasas/química , Proteínas Quinasas/química , Análisis de Secuencia de Proteína/métodos , Animales , Sitios de Unión , Humanos
18.
Cell Chem Biol ; 25(2): 143-153.e4, 2018 02 15.
Artículo en Inglés | MEDLINE | ID: mdl-29198568

RESUMEN

Nosiheptide, an archetypal member of thiopeptide antibiotics, arises from post-translational modifications of a ribosomally synthesized precursor peptide that contains an N-terminal leader peptide (LP) sequence and a C-terminal core peptide (CP) sequence. Despite extensive efforts concerning the biosynthesis of thiopeptide antibiotics, the regulatory mechanisms in this process remain poorly understood. Using the nosiheptide-producing Streptomyces actuosus strain as a model system, we report here that NosP, a Streptomyces antibiotic regulatory protein, serves as the only cluster-situated regulator and activates the transcription of all structural genes, which are organized into two divergently transcribed operons in the nos cluster, by binding to their intergenic region. NocP, the counterpart of NosP in Nocardia sp., regulates the production of structurally related nocathiacin I in a similar manner. NosP activity senses the nosiheptide biosynthetic process by interactions with both peptidyl and small-molecule ligands that result from the LP and CP parts of the precursor peptide, respectively.


Asunto(s)
Proteínas Bacterianas/metabolismo , Péptidos/metabolismo , Bibliotecas de Moléculas Pequeñas/metabolismo , Ligandos , Conformación Molecular , Péptidos/química , Bibliotecas de Moléculas Pequeñas/química , Streptomyces/química , Streptomyces/metabolismo , Tiazoles/metabolismo
19.
Methods Mol Biol ; 1607: 611-625, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28573591

RESUMEN

Models of target proteins in complex with small molecule ligands or peptide ligands are of significant interest to the biomedical research community. Structure-guided lead discovery and structure-based drug design make extensive use of such models. The bound ligands comprise only a small fraction of the total X-ray scattering mass, and therefore particular care must be taken to properly validate the atomic model of the ligand as experimental data can often be scarce. The ligand model must be validated against both the primary experimental data and the local environment, specifically: (1) the primary evidence in the form of the electron density, (2) examined for reasonable stereochemistry, and (3) the chemical plausibility of the binding interactions must be inspected. Tools that assist the researcher in the validation process are presented.


Asunto(s)
Cristalografía por Rayos X/métodos , Electrones , Péptidos/química , Proteínas/ultraestructura , Bibliotecas de Moléculas Pequeñas/química , Programas Informáticos , Sitios de Unión , Cristalografía por Rayos X/estadística & datos numéricos , Diseño de Fármacos , Ligandos , Modelos Moleculares , Unión Proteica , Conformación Proteica , Proteínas/química , Estereoisomerismo , Estudios de Validación como Asunto
20.
Med Res Rev ; 36(3): 494-575, 2016 May.
Artículo en Inglés | MEDLINE | ID: mdl-26992114

RESUMEN

For the purpose of this review, active targeting in cancer research encompasses strategies wherein a ligand for a cell surface receptor expressed on tumor cells is used to deliver a cytotoxic or imaging cargo. This area of research is more than two decades old, but in those 20 and more years, how many receptors have been studied extensively? What kinds of the ligands are used for active targeting? Are they mostly naturally occurring molecules such as folic acid, or synthetic substances developed in campaigns for medicinal chemistry efforts? This review outlines the most important receptor or ligand combinations that have been used in active targeting to answer these questions, and therefore to address the most important one of all: is research in active targeting affording diminishing returns, or is this an area for which the potential far exceeds progress made so far?


Asunto(s)
Antineoplásicos/uso terapéutico , Sistemas de Liberación de Medicamentos/métodos , Neoplasias/tratamiento farmacológico , Antineoplásicos/farmacocinética , Antineoplásicos/farmacología , Humanos , Ligandos
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