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1.
J Phys Chem B ; 2024 Sep 25.
Artículo en Inglés | MEDLINE | ID: mdl-39322588

RESUMEN

Molecular dynamics (MD) simulations provide an invaluable platform for exploring the dynamics of complex biomolecular systems at atomic resolution. However, compatibility issues between force fields and MD software engines can limit the interoperability and transferability of simulations. This work demonstrates the successful use of the coarse-grained SIRAH force field on the widely used NAMD MD engine across a range of increasingly complex biomolecular systems. By leveraging NAMD's ability to read AMBER input files, SIRAH simulations can be run seamlessly on NAMD, including its recently released GPU-accelerated version, NAMD3. The benchmark systems demonstrate consistent results across AMBER, NAMD2, and NAMD3. Thus, these data highlight the enhanced simulation throughput achievable on GPU-accelerated desktop computers using all three engines along with SIRAH. Overall, this study expands the range of the SIRAH force field by utilizing advanced GPU computing resources and high-performance supercomputing facilities, which are particularly effective with NAMD.

2.
Bioorg Chem ; 151: 107681, 2024 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-39106711

RESUMEN

Aberrant activation of the Hedgehog (Hh) signalling pathway has been associated with the development and progression of pancreatic cancer. For this reason, blockade of Hh pathway by inhibitors targeting the G protein-coupled receptor Smoothened (SMO) has been considered as a therapeutic target for the treatment of this cancer. In our previous work, we obtained a new SMO ligand based on a purine scaffold (compound I), which showed interesting antitumor activity in several cancer cell lines. In this work, we report the design and synthesis of 17 new purine derivatives, some of which showed high cytotoxic effect on Mia-PaCa-2 (Hh-dependent pancreatic cancer cell lines) and low toxicity on non-neoplastic HEK-293 cells compared with gemcitabine, such as 8f, 8g and 8h (IC50 = 4.56, 4.11 and 3.08 µM, respectively). Two of these purines also showed their ability to bind to SMO through NanoBRET assays (pKi = 5.17 for 8f and 5.01 for 8h), with higher affinities to compound I (pKi = 1.51). In addition, docking studies provided insight the purine substitution pattern is related to the affinity on SMO. Finally, studies of Hh inhibition for selected purines, using a transcriptional functional assay based on luciferase activity in NIH3T3 Shh-Light II cells, demonstrated that 8g reduced GLI activity with a IC50 = 6.4 µM as well as diminished the expression of Hh target genes in two specific Hh-dependent cell models, Med1 cells and Ptch1-/- mouse embryonic fibroblasts. Therefore, our results provide a platform for the design of SMO ligands that could be potential selective cytotoxic agents for the treatment of pancreatic cancer.


Asunto(s)
Antineoplásicos , Neoplasias Pancreáticas , Purinas , Receptor Smoothened , Humanos , Receptor Smoothened/antagonistas & inhibidores , Receptor Smoothened/metabolismo , Purinas/química , Purinas/farmacología , Purinas/síntesis química , Neoplasias Pancreáticas/tratamiento farmacológico , Neoplasias Pancreáticas/patología , Neoplasias Pancreáticas/metabolismo , Ligandos , Antineoplásicos/farmacología , Antineoplásicos/química , Antineoplásicos/síntesis química , Animales , Ratones , Relación Estructura-Actividad , Ensayos de Selección de Medicamentos Antitumorales , Estructura Molecular , Proliferación Celular/efectos de los fármacos , Relación Dosis-Respuesta a Droga , Células HEK293 , Línea Celular Tumoral , Células 3T3 NIH , Simulación del Acoplamiento Molecular , Proteínas Hedgehog/metabolismo , Proteínas Hedgehog/antagonistas & inhibidores
3.
ACS Infect Dis ; 10(3): 938-950, 2024 03 08.
Artículo en Inglés | MEDLINE | ID: mdl-38329933

RESUMEN

The search for new anti-infectives based on metal complexes is gaining momentum. Among the different options taken by researchers, the one involving the use of organometallic complexes is probably the most successful one with a compound, namely, ferroquine, already in clinical trials against malaria. In this study, we describe the preparation and in-depth characterization of 10 new (organometallic) derivatives of the approved antifungal drug fluconazole. Our rationale is that the sterol 14α-demethylase is an enzyme part of the ergosterol biosynthesis route in Trypanosoma and is similar to the one in pathogenic fungi. To demonstrate our postulate, docking experiments to assess the binding of our compounds with the enzyme were also performed. Our compounds were then tested on a range of fungal strains and parasitic organisms, including the protozoan parasite Trypanosoma cruzi (T. cruzi) responsible for Chagas disease, an endemic disease in Latin America that ranks among some of the most prevalent parasitic diseases worldwide. Of high interest, the two most potent compounds of the study on T. cruzi that contain a ferrocene or cobaltocenium were found to be harmless for an invertebrate animal model, namely, Caenorhabditis elegans (C. elegans), without affecting motility, viability, or development.


Asunto(s)
Fluconazol , Trypanosoma cruzi , Animales , Antifúngicos/farmacología , Antifúngicos/uso terapéutico , Metalocenos , Antiparasitarios/farmacología , Caenorhabditis elegans , Inhibidores de 14 alfa Desmetilasa/química , Trypanosoma cruzi/química
4.
Chembiochem ; 24(19): e202300406, 2023 Oct 04.
Artículo en Inglés | MEDLINE | ID: mdl-37382991

RESUMEN

Current treatment for Chagas' disease is based on two drugs, Nifurtimox and Benznidazol, which have limitations that reduce the effectiveness and continuity of treatment. Thus, there is an urgent need to develop new, safe and effective drugs. In previous work, two new metal-based compounds with trypanocidal activity, Pd-dppf-mpo and Pt-dppf-mpo, were fully characterized. To unravel the mechanism of action of these two analogous metal-based drugs, high-throughput omics studies were performed. A multimodal mechanism of action was postulated with several candidates as molecular targets. In this work, we validated the ergosterol biosynthesis pathway as a target for these compounds through the determination of sterol levels by HPLC in treated parasites. To understand the molecular level at which these compounds participate, two enzymes that met eligibility criteria at different levels were selected for further studies: phosphomevalonate kinase (PMK) and lanosterol 14-α demethylase (CYP51). Molecular docking processes were carried out to search for potential sites of interaction for both enzymes. To validate these candidates, a gain-of-function strategy was used through the generation of overexpressing PMK and CYP51 parasites. Results here presented confirm that the mechanism of action of Pd-dppf-mpo and Pt-dppf-mpo compounds involves the inhibition of both enzymes.

5.
Molecules ; 28(9)2023 May 05.
Artículo en Inglés | MEDLINE | ID: mdl-37175319

RESUMEN

Grape pomaces have a wide and diverse antioxidant phenolics composition. Six Uruguayan red grape pomaces were evaluated in their phenolics composition, antioxidant capacity, and anti-inflammatory properties. Not only radical scavenging methods as DPPH· and ABTS·+ were employed but also ORAC and FRAP analyses were applied to assess the antioxidant potency of the extracts. The antioxidant reactivity of all extracts against hydroxyl radicals was assessed with ESR. The phenol profile of the most bioactive extract was analyzed by HPLC-MS, and a set of 57 structures were determined. To investigate the potential anti-inflammatory activity of the extracts, Nuclear Factor kappa-B (NF-κB) modulation was evaluated in the human colon cancer reporter cell line (HT-29-NF-κB-hrGFP). Our results suggest that Tannat grapes pomaces have higher phenolic content and antioxidant capacity compared to Cabernet Franc. These extracts inhibited TNF-alpha mediated NF-κB activation and IL-8 production when added to reporter cells. A molecular docking study was carried out to rationalize the experimental results allowing us to propose the proactive interaction between the NF-κB, the grape extracts phenols, and their putative anti-inflammatory bioactivity. The present findings show that red grape pomace constitutes a sustainable source of phenolic compounds, which may be valuable for pharmaceutical, cosmetic, and food industry applications.


Asunto(s)
Vitis , Humanos , Vitis/química , Antioxidantes/química , FN-kappa B , Simulación del Acoplamiento Molecular , Extractos Vegetales/farmacología , Extractos Vegetales/química , Fenoles/química , Antiinflamatorios/farmacología
6.
J Biomol Struct Dyn ; 41(23): 14510-14523, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36856082

RESUMEN

Sesquiterpene lactones are natural products of the Asteraceae family that have shown trypanocidal activity against Trypanosoma cruzi, even exceeding the effectiveness of drugs used in the treatment of American trypanosomiasis. However, there is no agreement on their mechanism of action and their specificity to interact with parasite proteins. For this reason, we aimed to find biological targets that can interact with these compounds by reverse virtual screening with ligand pharmacophores and putative binding sites and the use of bioinformatic databases. Therefore, 41 possible biological targets were found, and four of them (with crystallized proteins), interfering directly or indirectly in the trypanosomatid redox system, were studied in detail. As a first approach, we focused on the study of trypanothione reductase, and protein-ligand interaction fingerprint analyses were performed to find binding site determinants that promote a possible inhibition of the enzyme. This study contributes to the understanding of one of the putative mechanisms of action of sesquiterpene lactones on one of the numerous suggested targets.Communicated by Ramaswamy H. Sarma.


Asunto(s)
Enfermedad de Chagas , Sesquiterpenos , Tripanocidas , Trypanosoma cruzi , Humanos , Lactonas/química , Ligandos , Enfermedad de Chagas/tratamiento farmacológico , Enfermedad de Chagas/parasitología , Sesquiterpenos/farmacología , Sesquiterpenos/química , Sesquiterpenos/uso terapéutico , Tripanocidas/farmacología , Tripanocidas/química
7.
Eur J Med Chem ; 246: 114926, 2023 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-36508970

RESUMEN

Quinones are attractive pharmacological scaffolds for developing new agents for the treatment of different transmissible and non-transmissible human diseases due to their capacity to alter the cell redox homeostasis. The bioactivity and potential mode of action of 19 p-quinone derivatives fused to different aromatic rings (carbo or heterocycles) and harboring distinct substituents were investigated in infective Trypanosoma brucei brucei. All the compounds, except for a furanequinone (EC50=38 µM), proved to be similarly or even more potent (EC50 = 0.5-5.5 µM) than the clinical drug nifurtimox (EC50 = 5.3 µM). Three furanequinones and one thiazolequinone displayed a higher selectivity than nifurtimox. Two of these selective hits resulted potent inhibitors of T. cruzi proliferation (EC50=0.8-1.1 µM) but proved inactive against Leishmania infantum amastigotes. Most of the p-quinones induced a rapid and marked intracellular oxidation in T. b. brucei. DFT calculations on the oxidized quinone (Q), semiquinone (Q•-) and hydroquinone (QH2) suggest that all quinones have negative ΔG for the formation of Q•-. Qualitative and quantitative structure-activity relationship analyses in two or three dimensions of different electronic and biophysical descriptors of quinones and their corresponding bioactivities (killing potency and oxidative capacity) were performed. Charge distribution over the quinone ring carbons of Q and Q.- and the frontier orbitals energies of SUMO (Q.-) and LUMO (Q) correlate with their oxidative and trypanocidal activity. QSAR analysis also highlighted that both bromine substitution in the p-quinone ring and a bulky phenyl group attached to the furane and thiazole rings (which generates a negative charge due to the π electron system polarized by the nearby heteroatoms) are favorable for activity. By combining experimental and in silico procedures, this study disclosed important information about p-quinones that may help to rationally tune their electronic properties and biological activities.


Asunto(s)
Enfermedad de Chagas , Tripanocidas , Trypanosoma cruzi , Humanos , Nifurtimox/uso terapéutico , Quinonas/farmacología , Enfermedad de Chagas/tratamiento farmacológico , Oxidación-Reducción , Simulación por Computador , Tripanocidas/farmacología , Tripanocidas/uso terapéutico
8.
J Biomol Struct Dyn ; 41(4): 1414-1423, 2023 03.
Artículo en Inglés | MEDLINE | ID: mdl-34994278

RESUMEN

Nuclear receptors are ligand-activated transcription factors capable of regulating the expression of complex gene networks. The family includes seven subfamilies of protein with a wide phylogenetic distribution. A novel subfamily with two DNA-binding domains (2DBDs) has been first reported in Schistosoma mansoni (Platyhelminth, Trematoda). Employing an ab initio protocol and homology modeling methods, the full-length 3D structure of the Eg2DBDα.1 nuclear receptor from Echinococcus granulosus (Platyhelminth, Cestoda) was generated. The model analysis reveals the presence of the conserved three-layered alpha-helical sandwich structure in the ligand binding domain, and a particularly long and flexible hinge region. Molecular dynamics simulations were performed previous to dock a conformational library of fatty acids and retinoic acids. Our results indicate that oleic and linoleic acids are suitable ligands to this receptor. The ligand-protein complex is stabilized mainly by hydrogen bonds and hydrophobic interactions. The fact that 2DBD nuclear receptors have not been identified in vertebrates confers particular interest to these nuclear receptors, not only concerning their structure and function but as targets of new anthelmintic drugs.Communicated by Ramaswamy H. Sarma.


Asunto(s)
Echinococcus granulosus , Animales , Echinococcus granulosus/metabolismo , Simulación de Dinámica Molecular , Filogenia , Ligandos , Proteínas del Helminto/química , Receptores Citoplasmáticos y Nucleares , Simulación del Acoplamiento Molecular
9.
Molecules ; 27(22)2022 Nov 13.
Artículo en Inglés | MEDLINE | ID: mdl-36431912

RESUMEN

Carotenoids are isoprenoid pigments, and sources of vitamin A in humans. The first metabolic pathway for their synthesis is mediated by the enzymes ß,ß-carotene-15,15'-dioxygenase (BCO1) and ß,ß-carotene-9',10'-dioxygenase (BCO2), which cleave carotenoids into smaller compounds, called apocarotenoids. The objective of this study is to gain insight into the interaction of BCO1 and BCO2 with carotenoids, adding structural diversity and importance in the agro-food and/or health sectors. Homology modeling of BCO1 and BCO2, and the molecular dynamics of complexes with all carotenoids were performed. Interaction energy and structures were analyzed. For both enzymes, the general structure is conserved with a seven beta-sheet structure, and the ß-carotene is positioned at an optimal distance from the catalytic center. Fe2+ forms in an octahedral coordination sphere with four perfectly conserved histidine residues. BCO1 finds stability in a structure in which the ß-carotene is positioned ready for enzymatic catalysis at the 15-15' bond, and BCO2 in positioning the bond to be cleaved (C9-C10) close to the active site. In BCO1 the carotenoids interact with only seven residues with aromatic rings, while the interaction of BCO2 is much more varied in terms of the type of interaction, with more residues of different chemical natures.


Asunto(s)
Dioxigenasas , beta-Caroteno 15,15'-Monooxigenasa , Humanos , beta-Caroteno 15,15'-Monooxigenasa/metabolismo , beta Caroteno/metabolismo , Simulación por Computador , Dioxigenasas/metabolismo , Carotenoides/metabolismo
10.
Front Cell Infect Microbiol ; 12: 901994, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35770070

RESUMEN

Cystic echinococcosis (CE) is a zoonotic disease worldwide distributed, caused by the cestode Echinococcus granulosus sensu lato (E. granulosus), with an incidence rate of 50/100,000 person/year and a high prevalence in humans of 5-10%. Serology has variable sensitivity and specificity and low predictive values. Antigens used are from the hydatid fluid and recombinant antigens have not demonstrated superiority over hydatid fluid. A cell line called EGPE was obtained from E. granulosus sensu lato G1 strain from bovine liver. Serum from CE patients recognizes protein extracts from EGPE cells with higher sensitivity than protein extracts from hydatid fluid. In the present study, EGPE cell protein extracts and supernatants from cell colonies were eluted from a protein G affinity column performed with sera from 11 CE patients. LC-MS/MS proteomic analysis of the eluted proteins identified four E. granulosus histones: one histone H4 in the cell extract and supernatant, one histone H2A only in the cell extract, and two histones H2A only in the supernatant. This differential distribution of histones could reflect different parasite viability stages regarding their role in gene transcription and silencing and could interact with host cells. Bioinformatics tools characterized the linear and conformational epitopes involved in antibody recognition. The three-dimensional structure of each histone was obtained by molecular modeling and validated by molecular dynamics simulation and PCR confirmed the presence of the epitopes in the parasite genome. The three histones H2A were very different and had a less conserved sequence than the histone H4. Comparison of the histones of E. granulosus with those of other organisms showed exclusive regions for E. granulosus. Since histones play a role in the host-parasite relationship they could be good candidates to improve the predictive value of serology in CE.


Asunto(s)
Quistes , Equinococosis , Echinococcus granulosus , Animales , Bovinos , Extractos Celulares , Cromatografía Liquida , Equinococosis/epidemiología , Equinococosis/parasitología , Echinococcus granulosus/genética , Epítopos de Linfocito B , Genotipo , Histonas , Humanos , Hígado , Hepatopatías , Proteómica , Espectrometría de Masas en Tándem
11.
Molecules ; 27(9)2022 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-35566007

RESUMEN

A recent screen of 67,012 compounds identified a new family of compounds with excellent nematicidal activity: the ortho-substituted benzamide families Wact-11 and Wact-12. These compounds are active against Caenorhabditis elegans and parasitic nematodes by selectively inhibiting nematode complex II, and they display low toxicity in mammalian cells and vertebrate organisms. Although a big number of benzamides were tested against C. elegans in high-throughput screens, bioisosteres of the amide moiety were not represented in the chemical space examined. We thus identified an opportunity for the design, synthesis and evaluation of novel compounds, using bioisosteric replacements of the amide group present in benzamides. The compound Wact-11 was used as the reference scaffold to prepare a set of bioisosteres to be evaluated against C. elegans. Eight types of amide replacement were selected, including ester, thioamide, selenoamide, sulfonamide, alkyl thio- and oxo-amides, urea and triazole. The results allowed us to perform a structure-activity relationship, highlighting the relevance of the amide group for nematicide activity. Experimental evidence was complemented with in silico structural studies over a C. elegans complex II model as a molecular target of benzamides. Importantly, compound Wact-11 was active against the flatworm Echinococcus granulosus, suggesting a previously unreported pan-anthelmintic potential for benzamides.


Asunto(s)
Antihelmínticos , Caenorhabditis elegans , Amidas , Animales , Antihelmínticos/química , Antihelmínticos/farmacología , Antinematodos/farmacología , Benzamidas/farmacología , Mamíferos
12.
Int J Mol Sci ; 22(24)2021 Dec 19.
Artículo en Inglés | MEDLINE | ID: mdl-34948418

RESUMEN

Coloring is one of the most important characteristics in commercial flowers and fruits, generally due to the accumulation of carotenoid pigments. Enzymes of the CCD4 family in citrus intervene in the generation of ß-citraurin, an apocarotenoid responsible for the reddish-orange color of mandarins. Citrus CCD4s enzymes could be capable of interacting with the thylakoid membrane inside chloroplasts. However, to date, this interaction has not been studied in detail. In this work, we present three new complete models of the CCD4 family members (CCD4a, CCD4b, and CCD4c), modeled with a lipid membrane. To identify the preference for substrates, typical carotenoids were inserted in the active site of the receptors and the protein-ligand interaction energy was evaluated. The results show a clear preference of CCD4s for xanthophylls over aliphatic carotenes. Our findings indicate the ability to penetrate the membrane and maintain a stable interaction through the N-terminal α-helical domain, spanning a contact surface of 2250 to 3250 Å2. The orientation and depth of penetration at the membrane surface suggest that CCD4s have the ability to extract carotenoids directly from the membrane through a tunnel consisting mainly of hydrophobic residues that extends up to the catalytic center of the enzyme.


Asunto(s)
Carotenoides/metabolismo , Citrus/metabolismo , Dioxigenasas/metabolismo , Proteínas de Plantas/metabolismo , Carotenoides/química , Citrus/química , Dioxigenasas/química , Modelos Moleculares , Proteínas de Plantas/química , Unión Proteica , Dominios Proteicos , Especificidad por Sustrato , Xantófilas/química , Xantófilas/metabolismo
13.
Food Chem (Oxf) ; 3: 100053, 2021 Dec 30.
Artículo en Inglés | MEDLINE | ID: mdl-35415655

RESUMEN

The relationship between structural and physicochemical properties and antioxidant activity of peptides from amaranth 11S-globulin was studied. Peptides AWEEREQGSR, TEVWDSNEQ, IYIEQGNGITGM and YLAGKPQQEH had the greatest in vitro activity (ORAC, HORAC). GDRFQDQHQ, HVIKPPSRA and KFNRPETT were the most active ones against Cu+2/H2O2-induced-LDL oxidation. In a cellular system (H2O2-induced-Caco2-TC7), TEVWDSNEQ, IYIEQGNGITGM, GDRFQDQHQ, LAGKPQQEHSGEHQ and KFNRPETT were the most effective in decreasing ROS, while the effects on SOD, GPx, and GSH were variable. To understand the structure-antioxidant activity relationships, the content of aromatic and acidic amino acids, the degree of hydrophobicity and the charge distribution on the accessible surface of peptides structures obtained by molecular dynamics were analysed. The low correlation between in vitro, ex vivo and cellular activities could be explained by the influence of physicochemical and structural properties on the interaction with complex systems (LDL/cells), peptide modifications and/or mechanisms other than direct ROS inhibition in the cells.

14.
Arch Pharm (Weinheim) ; 353(1): e1900213, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31709599

RESUMEN

Continuing with a program to develop new quinone derivatives as biologically active compounds, we designed and synthesized a new series of aryloxy-quinones, which were evaluated in vitro against Trypanosoma cruzi in epimastigote form. Chemical modifications in three specific moieties on the aryloxy-quinone core were considered for developing new anti-T. cruzi agents. The majority of our new quinones showed higher potency (IC50 values of <0.70 µM) than nifurtimox, a known pharmaceutical used as a baseline drug (IC50 values of 7.00 µM); however, only two of them elicited higher selectivity than nifurtimox against Vero cells. A structure-activity relationship analysis provided information about the stereoelectronic features of these compounds, which are responsible for an increase in trypanosomicidal activity. Using a pharmacophore model, we mapped the substitution patterns of the five pharmacophoric features of trypanosomicidal activity. We chose the Epc1 compounds and found no relationship with the trypanosomicidal effects. These results provided useful information about the structural characteristics for developing new aryloxy-quinones with higher potency against the protozoan parasite T. cruzi.


Asunto(s)
Benzoquinonas/farmacología , Tripanocidas/farmacología , Trypanosoma cruzi/efectos de los fármacos , Benzoquinonas/química , Relación Dosis-Respuesta a Droga , Técnicas Electroquímicas , Estructura Molecular , Pruebas de Sensibilidad Parasitaria , Relación Estructura-Actividad , Tripanocidas/síntesis química , Tripanocidas/química
15.
PLoS One ; 14(11): e0224703, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31710619

RESUMEN

Nuclear receptors are ligand-activated transcription factors capable of regulating the expression of complex gene networks. The family includes seven subfamilies of proteins with a wide phylogenetic distribution. A novel subfamily with two DNA-binding domains (2DBDs) has been reported in Schistosoma mansoni (Platyhelminth, Trematoda). This work describes the cDNA cloning and bioinformatics analysis of Eg2DBDα, a 2DBD nuclear receptor isoform from the parasite Echinococcus granulosus (Platyhelminth, Cestoda). The Eg2DBDα gene coding domain structure was analysed. Although two additional 2DBD nuclear receptors are reported in the parasite database GeneDB, they are unlikely to be expressed in the larval stage. Phylogenetic relationships between these atypical proteins from different cestodes are also analysed including S. mansoni 2DBD nuclear receptors. The presence of two DNA binding domains confers particular interest to these nuclear receptors, not only concerning their function but to the development of new antihelminthic drugs.


Asunto(s)
Echinococcus granulosus/metabolismo , Proteínas del Helminto/metabolismo , Receptores Citoplasmáticos y Nucleares/metabolismo , Animales , Biología Computacional , Echinococcus granulosus/genética , Proteínas del Helminto/genética , Filogenia , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Receptores Citoplasmáticos y Nucleares/genética
16.
Chem Biol Drug Des ; 91(1): 29-38, 2018 01.
Artículo en Inglés | MEDLINE | ID: mdl-28643389

RESUMEN

A combination of three-dimensional quantitative structure-activity relationship (3D-QSAR), and molecular modelling methods were used to understand the potent inhibitory NAD(P)H:quinone oxidoreductase 1 (NQO1) activity of a set of 52 heterocyclic quinones. Molecular docking results indicated that some favourable interactions of key amino acid residues at the binding site of NQO1 with these quinones would be responsible for an improvement of the NQO1 activity of these compounds. The main interactions involved are hydrogen bond of the amino group of residue Tyr128, π-stacking interactions with Phe106 and Phe178, and electrostatic interactions with flavin adenine dinucleotide (FADH) cofactor. Three models were prepared by 3D-QSAR analysis. The models derived from Model I and Model III, shown leave-one-out cross-validation correlation coefficients (q2LOO ) of .75 and .73 as well as conventional correlation coefficients (R2 ) of .93 and .95, respectively. In addition, the external predictive abilities of these models were evaluated using a test set, producing the predicted correlation coefficients (r2pred ) of .76 and .74, respectively. The good concordance between the docking results and 3D-QSAR contour maps provides helpful information about a rational modification of new molecules based in quinone scaffold, in order to design more potent NQO1 inhibitors, which would exhibit highly potent antitumor activity.


Asunto(s)
Simulación del Acoplamiento Molecular , NAD(P)H Deshidrogenasa (Quinona)/metabolismo , Relación Estructura-Actividad Cuantitativa , Quinonas/metabolismo , Sitios de Unión , Diseño Asistido por Computadora , Flavina-Adenina Dinucleótido/química , Flavina-Adenina Dinucleótido/metabolismo , Humanos , Análisis de los Mínimos Cuadrados , NAD(P)H Deshidrogenasa (Quinona)/antagonistas & inhibidores , Estructura Terciaria de Proteína , Quinonas/química , Electricidad Estática
17.
Eur J Pharm Sci ; 106: 393-403, 2017 Aug 30.
Artículo en Inglés | MEDLINE | ID: mdl-28636950

RESUMEN

The ubiquitous flavonoid quercetin is broadly recognized for showing diverse biological and health-promoting effects, such as anti-cancer, anti-inflammatory and cytoprotective activities. The therapeutic potential of quercetin and similar compounds for preventing such diverse oxidative stress-related pathologies has been generally attributed to their direct antioxidant properties. Nevertheless, accumulated evidence indicates that quercetin is also able to interact with multiple cellular targets influencing the activity of diverse signaling pathways. Even though there are a number of well-established protein targets such as phosphatidylinositol 3 kinase and xanthine oxidase, there remains a lack of a comprehensive knowledge of the potential mechanisms of action of quercetin and its target space. In the present work we adopted a reverse screening strategy based on ligand similarity (SHAFTS) and target structure (idTarget, LIBRA) resulting in a set of predicted protein target candidates. Furthermore, using this method we corroborated a broad array of previously experimentally tested candidates among the predicted targets, supporting the suitability of this screening approach. Notably, all of the predicted target candidates belonged to two main protein families, protein kinases and poly [ADP-ribose] polymerases. They also included key proteins involved at different points within the same signaling pathways or within interconnected signaling pathways, supporting a pleiotropic, multilevel and potentially synergistic mechanism of action of quercetin. In this context we highlight the value of quercetin's broad target profile for its therapeutic potential in diseases like inflammation, neurodegeneration and cancer.


Asunto(s)
Quercetina/química , Adenosina Difosfato/química , Adenosina Trifosfato/química , Sitios de Unión , Simulación por Computador , Ligandos , Simulación del Acoplamiento Molecular , Estructura Molecular , Unión Proteica
18.
Mini Rev Med Chem ; 17(11): 939-946, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28302040

RESUMEN

BACKGROUND & OBJECTIVE: Chagas disease or American trypanosomiasis is a major parasitic disease in Latin America with restricted available treatment: nifurtimox and benznidazole. These two drugs are ineffective in the chronic phase of the disease; therefore, there is a need for the development of new, efficient and safe drugs for the treatment of this pathology. With this goal, one of the promising targets is trypanothione reductase (TR), a key enzyme in the metabolism of Trypanosoma cruzi. CONCLUSION: In this review, we analyse the importance of TR as a drug target, as well as the well-known and new inhibitors reported in the last decade as potential therapeutic agents for Chagas disease.


Asunto(s)
Enfermedad de Chagas/tratamiento farmacológico , Sistemas de Liberación de Medicamentos , NADH NADPH Oxidorreductasas/metabolismo , Tripanocidas/química , Tripanocidas/uso terapéutico , Trypanosoma cruzi/enzimología , Animales , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/farmacología , Humanos , Estructura Molecular , Nifurtimox/química , Nifurtimox/farmacología , Tripanocidas/farmacología , Trypanosoma cruzi/efectos de los fármacos
19.
J Biomol Struct Dyn ; 35(8): 1785-1803, 2017 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-27232454

RESUMEN

A set of aryloxy-quinones, previously synthesized and evaluated against Trypanosoma cruzi epimastigotes cultures, were found more potent and selective than nifurtimox. One of the possible mechanisms of the trypanocidal activity of these quinones could be inhibition of trypanothione reductase (TR). Considering that glutathione reductase (GR) is the equivalent of TR in humans, biochemical, kinetic, and molecular docking studies in TR and GR were envisaged and compared with the trypanocidal and cytotoxic data of a set of aryloxy-quinones. Biochemical assays indicated that three naphthoquinones (Nq-h, Nq-g, and Nq-d) selectively inhibit TR and the TR kinetic analyses indicated that Nq-h inhibit TR in a noncompetitive mechanism. Molecular dockings were performed in TR and GR in the following three putative binding sites: the catalytic site, the dimer interface, and the nicotinamide adenine dinucleotide phosphate-binding site. In TR and GR, the aryloxy-quinones were found to exhibit high affinity for a site near it cognate-binding site in a place in which the noncompetitive kinetics could be justified. Taking as examples the three compounds with TR specificity (TRS) (Nq-h, Nq-g, and Nq-d), the presence of a network of contacts with the quinonic ring sustained by the triad of Lys62, Met400', Ser464' residues, seems to contribute hardly to the TRS. Compound Nq-b, a naphthoquinone with nitrophenoxy substituent, proved to be the best scaffold for the design of trypanocidal compounds with low toxicity. However, the compound displayed only a poor and non-selective effect toward TR indicating that TR inhibition is not the main reason for the antiparasitic activity of the aryloxy-quinones.


Asunto(s)
Inhibidores Enzimáticos/química , NADH NADPH Oxidorreductasas/química , Naftoquinonas/química , Proteínas Protozoarias/química , Tripanocidas/química , Trypanosoma cruzi/efectos de los fármacos , Secuencias de Aminoácidos , Sitios de Unión , Cristalografía por Rayos X , Inhibidores Enzimáticos/farmacología , Glutatión Reductasa/antagonistas & inhibidores , Glutatión Reductasa/química , Glutatión Reductasa/metabolismo , Humanos , Cinética , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , NADH NADPH Oxidorreductasas/antagonistas & inhibidores , NADH NADPH Oxidorreductasas/metabolismo , NADP/química , NADP/metabolismo , Naftoquinonas/farmacología , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Multimerización de Proteína , Proteínas Protozoarias/antagonistas & inhibidores , Proteínas Protozoarias/metabolismo , Especificidad por Sustrato , Termodinámica , Tripanocidas/farmacología , Trypanosoma cruzi/enzimología , Trypanosoma cruzi/crecimiento & desarrollo
20.
Acta Trop ; 158: 59-67, 2016 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-26899679

RESUMEN

Echinoccocus granulosus is the causative agent of Cyst Echinococcosis, a zoonotic infection affecting humans and livestock representing a public health and an economic burden for several countries. Despite decades of investigation an effective vaccine still remains to be found. Parasitic cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 proteins (CAPs) have been proposed as vaccine candidates against helmith's infection. In this work we have identified two novel proteins of this superfamily expressed at the protoescoleces larval stage named EgVAL1 and EgVAL2. The open reading frame sequences were deduced. The aminoacidic sequence was analyzed and confronted against already known vertebrate' and helminth's proteins sequences in order to infer putative functions. Immunolocalization studies were also performed. The obtained data supported by immunolocalization studies and homology models suggest that these proteins could be involved in protease activity inhibition.


Asunto(s)
Echinococcus granulosus/química , Proteínas del Helminto/química , Proteínas del Helminto/genética , Larva/química , Secuencia de Aminoácidos , Animales , Humanos , Filogenia
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